| 1 |
commit: 70386b8c804f2bf2fb7aca4be74d511d765ad1e4 |
| 2 |
Author: David Seifert <soap <AT> gentoo <DOT> org> |
| 3 |
AuthorDate: Sat Sep 2 11:07:41 2017 +0000 |
| 4 |
Commit: David Seifert <soap <AT> gentoo <DOT> org> |
| 5 |
CommitDate: Sat Sep 2 12:37:02 2017 +0000 |
| 6 |
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=70386b8c |
| 7 |
|
| 8 |
sci-biology/samtools: Remove old |
| 9 |
|
| 10 |
Bug: https://bugs.gentoo.org/show_bug.cgi?id=548170 |
| 11 |
Bug: https://bugs.gentoo.org/show_bug.cgi?id=620618 |
| 12 |
Bug: https://bugs.gentoo.org/show_bug.cgi?id=625504 |
| 13 |
Package-Manager: Portage-2.3.8, Repoman-2.3.3 |
| 14 |
Closes: https://github.com/gentoo/gentoo/pull/5593 |
| 15 |
|
| 16 |
sci-biology/samtools/Manifest | 6 - |
| 17 |
.../files/samtools-0.1.19-buildsystem.patch | 183 ----- |
| 18 |
.../samtools/files/samtools-1.0-buildsystem.patch | 59 -- |
| 19 |
.../samtools/files/samtools-1.1-buildsystem.patch | 153 ----- |
| 20 |
.../samtools/files/samtools-1.2-buildsystem.patch | 193 ------ |
| 21 |
.../samtools/files/samtools-1.3-buildsystem.patch | 174 ----- |
| 22 |
.../samtools/files/samtools-1.3-ncurses.patch | 737 --------------------- |
| 23 |
sci-biology/samtools/samtools-0.1.12.ebuild | 30 - |
| 24 |
sci-biology/samtools/samtools-0.1.19-r2.ebuild | 60 -- |
| 25 |
sci-biology/samtools/samtools-1.0-r1.ebuild | 72 -- |
| 26 |
sci-biology/samtools/samtools-1.0.ebuild | 68 -- |
| 27 |
sci-biology/samtools/samtools-1.1.ebuild | 82 --- |
| 28 |
sci-biology/samtools/samtools-1.2.ebuild | 82 --- |
| 29 |
sci-biology/samtools/samtools-1.3-r1.ebuild | 96 --- |
| 30 |
14 files changed, 1995 deletions(-) |
| 31 |
|
| 32 |
diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest |
| 33 |
index 791e2050ee7..a1c0aa6b427 100644 |
| 34 |
--- a/sci-biology/samtools/Manifest |
| 35 |
+++ b/sci-biology/samtools/Manifest |
| 36 |
@@ -1,8 +1,2 @@ |
| 37 |
-DIST samtools-0.1.12a.tar.bz2 355633 SHA256 377ed5cd2a4bb2b1ad572ca6fcafdd8ed644b67f01ab00fa020618fac11e59ac SHA512 8a3273c174fb478772f31a9c73183b5f7c6841ba4e20586aafc2cd3e966830d3a4ca8c7485ce5981fe85d7cd820170e2ac2e124d8cf077e35218a7381f305012 WHIRLPOOL da61692666dffbb32e172f87e77287e145a0c0f6d62d47e5d04d153ce478db5df1d4694bd93d654af11643f9b656551232b5cc085b619bb8d8536720de36984c |
| 38 |
-DIST samtools-0.1.19.tar.bz2 514507 SHA256 d080c9d356e5f0ad334007e4461cbcee3c4ca97b8a7a5a48c44883cf9dee63d4 SHA512 d145f1d65eefefbdfb781945684b8b591419fb109ac7401a62cae65b9ca1e1271f001496e1038334ff9ab1c0e5bf9bcc059f70aaa273551193fbd68101fd188d WHIRLPOOL 7811388ae8b24c5d7a328d2da252b8d3afaefdab508bd97684d556d2d4ee60d9c8846ffa562beaa9d0c6a5e6bfac24fcd9d211dfee20383cf452609badc8ecd5 |
| 39 |
DIST samtools-0.1.20.tar.gz 566387 SHA256 500019b4d1886ad995513d5ce8b413b14b51f16f251ce76bc0b35a446b182a47 SHA512 15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5 WHIRLPOOL 3ea05df172ea6afe31bd3880f918e0b286f65839f78ed846a0d3aef84ec70df1e3741ff6dcad5f70d62a06687f07b35609829aabd33c6688fac0d59effd979e0 |
| 40 |
-DIST samtools-1.0.tar.bz2 4459669 SHA256 7340b843663c3f54a902a06f2f73c68198f3a62d29a2ed20671139957f7fd7c0 SHA512 5b80995c522d08b06a4c559f60a5e200d9085be7f44c3c9618db91e3de85e36c1473e42715eae8175520d7da3df8245bafa82e625d2fc08e0197adb395851693 WHIRLPOOL 2aa0f8639da9b0b828ca7296969e5c600b0e5452ad3231b914e4a7be418700906a4d695c928eaf837b643255567ec82cfadf0b53007e0f1e3a956856f6c4c832 |
| 41 |
-DIST samtools-1.1.tar.bz2 4495373 SHA256 c24d26c303153d72b5bf3cc11f72c6c375a4ca1140cc485648c8c5473414b7f8 SHA512 a5552a6c8c4b0808b725b39ddb2fafa36c4f6623bfc7f84faadae7690223e4eec8d722af09c77145796ad9b3f01e04115dd0207207ccfafbb52ffc22d5fc09f0 WHIRLPOOL ed3131b2a8d8b4dab40b53d35a9b00b657670a949dc1597c91fbcd00392c1c1715a85a1d1e49bf0c73ae082738ccfb13d2c6809dbbeba17ff3028f6023ebc449 |
| 42 |
-DIST samtools-1.2.tar.bz2 4547126 SHA256 420e7a4a107fe37619b9d300b6379452eb8eb04a4a9b65c3ec69de82ccc26daa SHA512 4849c3274e732267516b63799f5430c5415d575d46eddf6b704dac51053281094b03b90dd9f5367bcd14c22fb0fb1bd6a412f7d4225f7be5f5385437c5d2101d WHIRLPOOL 273185764a807365a20c381769f987ef02d14ae8e20a3a7fd5af4344769c5fab68d7155523e8c0c8c3cc86092898c2c8454cce8f1560d415bc2b41549cdf04f4 |
| 43 |
-DIST samtools-1.3.tar.bz2 3978333 SHA256 beea4003c795a0a25224656815b4036f6864b8753053ed30c590bb052b70b60e SHA512 72920d4f0f10aa7b54ef448e03e6e769e1e07abd07388a2307d0e52548fa2909c03ca2c7eec5c63cf5b67724b2356833accb0079ce1486bb2ac66a45963a24ea WHIRLPOOL 3f798078100b4ed164f6c89d18cc8f62159437e2cfb2a228ac00f8d08313f7c39ef546214c0796c25a419c0a1065dc21d14b966fed769726b9b1975ec07e3b3e |
| 44 |
DIST samtools-1.5.tar.bz2 4190142 SHA256 8542da26832ee08c1978713f5f6188ff750635b50d8ab126a0c7bb2ac1ae2df6 SHA512 ff3e39ba867ecbd88f3363b038508c1557e349ea4223483f8f4ecb17ff8864fb53cd193bc2059a147e30f07395bbf53c8518d0f70219e454375c8bffe56e3059 WHIRLPOOL 1a88c9617857f1f6d146df179aef5b5c6bb83de8c9d127c405e5756842ced84c194a3f09f69a4757a8adf6ca623c9fdc972f4bf609649d3e991dda8f616e3582 |
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|
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diff --git a/sci-biology/samtools/files/samtools-0.1.19-buildsystem.patch b/sci-biology/samtools/files/samtools-0.1.19-buildsystem.patch |
| 47 |
deleted file mode 100644 |
| 48 |
index d5ff3bd45da..00000000000 |
| 49 |
--- a/sci-biology/samtools/files/samtools-0.1.19-buildsystem.patch |
| 50 |
+++ /dev/null |
| 51 |
@@ -1,183 +0,0 @@ |
| 52 |
- Makefile | 22 +++++++++++----------- |
| 53 |
- bcftools/Makefile | 12 ++++++------ |
| 54 |
- misc/Makefile | 28 ++++++++++++++-------------- |
| 55 |
- 3 files changed, 31 insertions(+), 31 deletions(-) |
| 56 |
- |
| 57 |
-diff --git a/Makefile b/Makefile |
| 58 |
-index 2f51bfc..4dda5a4 100644 |
| 59 |
---- a/Makefile |
| 60 |
-+++ b/Makefile |
| 61 |
-@@ -1,7 +1,7 @@ |
| 62 |
--CC= gcc |
| 63 |
--CFLAGS= -g -Wall -O2 |
| 64 |
--#LDFLAGS= -Wl,-rpath,\$$ORIGIN/../lib |
| 65 |
--DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 |
| 66 |
-+CC?= gcc |
| 67 |
-+CFLAGS?= -g -Wall -O2 |
| 68 |
-+#LDFLAGS+= -Wl,-rpath,\$$ORIGIN/../lib |
| 69 |
-+CPPFLAGS+= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 |
| 70 |
- KNETFILE_O= knetfile.o |
| 71 |
- LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \ |
| 72 |
- bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o \ |
| 73 |
-@@ -21,14 +21,14 @@ LIBCURSES= -lcurses # -lXCurses |
| 74 |
- .PHONY: all lib |
| 75 |
- |
| 76 |
- .c.o: |
| 77 |
-- $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@ |
| 78 |
-+ $(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@ |
| 79 |
- |
| 80 |
- all-recur lib-recur clean-recur cleanlocal-recur install-recur: |
| 81 |
- @target=`echo $@ | sed s/-recur//`; \ |
| 82 |
- wdir=`pwd`; \ |
| 83 |
- list='$(SUBDIRS)'; for subdir in $$list; do \ |
| 84 |
- cd $$subdir; \ |
| 85 |
-- $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \ |
| 86 |
-+ $(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \ |
| 87 |
- INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \ |
| 88 |
- cd $$wdir; \ |
| 89 |
- done; |
| 90 |
-@@ -44,16 +44,16 @@ libbam.a:$(LOBJS) |
| 91 |
- $(AR) -csru $@ $(LOBJS) |
| 92 |
- |
| 93 |
- samtools:lib-recur $(AOBJS) |
| 94 |
-- $(CC) $(CFLAGS) -o $@ $(AOBJS) $(LDFLAGS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread |
| 95 |
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread |
| 96 |
- |
| 97 |
- razip:razip.o razf.o $(KNETFILE_O) |
| 98 |
-- $(CC) $(CFLAGS) -o $@ $^ -lz |
| 99 |
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ -lz |
| 100 |
- |
| 101 |
- bgzip:bgzip.o bgzf.o $(KNETFILE_O) |
| 102 |
-- $(CC) $(CFLAGS) -o $@ $^ -lz -lpthread |
| 103 |
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ -lz -lpthread |
| 104 |
- |
| 105 |
- bgzf.o:bgzf.c bgzf.h |
| 106 |
-- $(CC) -c $(CFLAGS) $(DFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@ |
| 107 |
-+ $(CC) -c $(CFLAGS) $(CPPFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@ |
| 108 |
- |
| 109 |
- razip.o:razf.h |
| 110 |
- bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h |
| 111 |
-@@ -84,7 +84,7 @@ libbam.1.dylib-local:$(LOBJS) |
| 112 |
- libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz |
| 113 |
- |
| 114 |
- libbam.so.1-local:$(LOBJS) |
| 115 |
-- $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz |
| 116 |
-+ $(CC) $(LDFLAGS) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz -lm -lpthread |
| 117 |
- |
| 118 |
- dylib: |
| 119 |
- @$(MAKE) cleanlocal; \ |
| 120 |
-diff --git a/bcftools/Makefile b/bcftools/Makefile |
| 121 |
-index be831de..7ef796c 100644 |
| 122 |
---- a/bcftools/Makefile |
| 123 |
-+++ b/bcftools/Makefile |
| 124 |
-@@ -1,6 +1,6 @@ |
| 125 |
--CC= gcc |
| 126 |
--CFLAGS= -g -Wall -O2 #-m64 #-arch ppc |
| 127 |
--DFLAGS= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE |
| 128 |
-+CC?= gcc |
| 129 |
-+CFLAGS?= -g -Wall -O2 #-m64 #-arch ppc |
| 130 |
-+CPPFLAGS+= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE |
| 131 |
- LOBJS= bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o |
| 132 |
- OMISC= .. |
| 133 |
- AOBJS= call1.o main.o $(OMISC)/kstring.o $(OMISC)/bgzf.o $(OMISC)/knetfile.o $(OMISC)/bedidx.o |
| 134 |
-@@ -11,14 +11,14 @@ SUBDIRS= . |
| 135 |
- .SUFFIXES:.c .o |
| 136 |
- |
| 137 |
- .c.o: |
| 138 |
-- $(CC) -c $(CFLAGS) $(DFLAGS) -I.. $(INCLUDES) $< -o $@ |
| 139 |
-+ $(CC) -c $(CFLAGS) $(CPPFLAGS) -I.. $(INCLUDES) $< -o $@ |
| 140 |
- |
| 141 |
- all-recur lib-recur clean-recur cleanlocal-recur install-recur: |
| 142 |
- @target=`echo $@ | sed s/-recur//`; \ |
| 143 |
- wdir=`pwd`; \ |
| 144 |
- list='$(SUBDIRS)'; for subdir in $$list; do \ |
| 145 |
- cd $$subdir; \ |
| 146 |
-- $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \ |
| 147 |
-+ $(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \ |
| 148 |
- INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \ |
| 149 |
- cd $$wdir; \ |
| 150 |
- done; |
| 151 |
-@@ -31,7 +31,7 @@ libbcf.a:$(LOBJS) |
| 152 |
- $(AR) -csru $@ $(LOBJS) |
| 153 |
- |
| 154 |
- bcftools:lib $(AOBJS) |
| 155 |
-- $(CC) $(CFLAGS) -o $@ $(AOBJS) -L. $(LIBPATH) -lbcf -lm -lz -lpthread |
| 156 |
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) -L. $(LIBPATH) -lbcf -lm -lz -lpthread |
| 157 |
- |
| 158 |
- bcf.o:bcf.h |
| 159 |
- vcf.o:bcf.h |
| 160 |
-diff --git a/misc/Makefile b/misc/Makefile |
| 161 |
-index d36e7ac..7ae1dc3 100644 |
| 162 |
---- a/misc/Makefile |
| 163 |
-+++ b/misc/Makefile |
| 164 |
-@@ -1,8 +1,8 @@ |
| 165 |
--CC= gcc |
| 166 |
--CXX= g++ |
| 167 |
--CFLAGS= -g -Wall -O2 #-m64 #-arch ppc |
| 168 |
--CXXFLAGS= $(CFLAGS) |
| 169 |
--DFLAGS= -D_FILE_OFFSET_BITS=64 |
| 170 |
-+CC?= gcc |
| 171 |
-+CXX?= g++ |
| 172 |
-+CFLAGS?= -g -Wall -O2 #-m64 #-arch ppc |
| 173 |
-+CXXFLAGS?= $(CFLAGS) |
| 174 |
-+CPPFLAGS+= -D_FILE_OFFSET_BITS=64 |
| 175 |
- OBJS= |
| 176 |
- PROG= md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck |
| 177 |
- INCLUDES= -I.. |
| 178 |
-@@ -11,7 +11,7 @@ SUBDIRS= . |
| 179 |
- .SUFFIXES:.c .o |
| 180 |
- |
| 181 |
- .c.o: |
| 182 |
-- $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@ |
| 183 |
-+ $(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@ |
| 184 |
- |
| 185 |
- all:$(PROG) |
| 186 |
- |
| 187 |
-@@ -20,7 +20,7 @@ lib-recur all-recur clean-recur cleanlocal-recur install-recur: |
| 188 |
- wdir=`pwd`; \ |
| 189 |
- list='$(SUBDIRS)'; for subdir in $$list; do \ |
| 190 |
- cd $$subdir; \ |
| 191 |
-- $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \ |
| 192 |
-+ $(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \ |
| 193 |
- INCLUDES="$(INCLUDES)" $$target || exit 1; \ |
| 194 |
- cd $$wdir; \ |
| 195 |
- done; |
| 196 |
-@@ -28,31 +28,31 @@ lib-recur all-recur clean-recur cleanlocal-recur install-recur: |
| 197 |
- lib: |
| 198 |
- |
| 199 |
- bamcheck:bamcheck.o |
| 200 |
-- $(CC) $(CFLAGS) -o $@ bamcheck.o -L.. -lm -lbam -lpthread -lz |
| 201 |
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ bamcheck.o -L.. -lm -lbam -lpthread -lz |
| 202 |
- |
| 203 |
- bamcheck.o:bamcheck.c ../faidx.h ../khash.h ../sam.h ../razf.h |
| 204 |
- $(CC) $(CFLAGS) -c -I.. -o $@ bamcheck.c |
| 205 |
- |
| 206 |
- ace2sam:ace2sam.o |
| 207 |
-- $(CC) $(CFLAGS) -o $@ ace2sam.o -lz |
| 208 |
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ ace2sam.o -lz |
| 209 |
- |
| 210 |
- wgsim:wgsim.o |
| 211 |
-- $(CC) $(CFLAGS) -o $@ wgsim.o -lm -lz |
| 212 |
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ wgsim.o -lm -lz |
| 213 |
- |
| 214 |
- md5fa:md5.o md5fa.o md5.h ../kseq.h |
| 215 |
-- $(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz |
| 216 |
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ md5.o md5fa.o -lz |
| 217 |
- |
| 218 |
- md5sum-lite:md5sum-lite.o |
| 219 |
-- $(CC) $(CFLAGS) -o $@ md5sum-lite.o |
| 220 |
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ md5sum-lite.o |
| 221 |
- |
| 222 |
- md5sum-lite.o:md5.c md5.h |
| 223 |
- $(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c |
| 224 |
- |
| 225 |
- maq2sam-short:maq2sam.c |
| 226 |
-- $(CC) $(CFLAGS) -o $@ maq2sam.c -lz |
| 227 |
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ maq2sam.c -lz |
| 228 |
- |
| 229 |
- maq2sam-long:maq2sam.c |
| 230 |
-- $(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -lz |
| 231 |
-+ $(CC) $(CFLAGS) -DMAQ_LONGREADS $(LDFLAGS) -o $@ maq2sam.c -lz |
| 232 |
- |
| 233 |
- md5fa.o:md5.h md5fa.c |
| 234 |
- $(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c |
| 235 |
|
| 236 |
diff --git a/sci-biology/samtools/files/samtools-1.0-buildsystem.patch b/sci-biology/samtools/files/samtools-1.0-buildsystem.patch |
| 237 |
deleted file mode 100644 |
| 238 |
index 53a8b66f918..00000000000 |
| 239 |
--- a/sci-biology/samtools/files/samtools-1.0-buildsystem.patch |
| 240 |
+++ /dev/null |
| 241 |
@@ -1,59 +0,0 @@ |
| 242 |
- Makefile | 26 ++++++++++++++++++-------- |
| 243 |
- 1 file changed, 18 insertions(+), 8 deletions(-) |
| 244 |
- |
| 245 |
-diff --git a/Makefile b/Makefile |
| 246 |
-index ae59abf..0d2788c 100644 |
| 247 |
---- a/Makefile |
| 248 |
-+++ b/Makefile |
| 249 |
-@@ -21,11 +21,12 @@ |
| 250 |
- # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER |
| 251 |
- # DEALINGS IN THE SOFTWARE. |
| 252 |
- |
| 253 |
--CC = gcc |
| 254 |
--CPPFLAGS = $(DFLAGS) $(INCLUDES) |
| 255 |
--CFLAGS = -g -Wall -O2 |
| 256 |
--LDFLAGS = |
| 257 |
--LDLIBS = |
| 258 |
-+CC ?= gcc |
| 259 |
-+CPPFLAGS += $(DFLAGS) $(INCLUDES) |
| 260 |
-+CFLAGS ?= -g -Wall -O2 |
| 261 |
-+LDFLAGS += |
| 262 |
-+LDLIBS += |
| 263 |
-+BAMLIB ?= libbam.a |
| 264 |
- DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 |
| 265 |
- LOBJS= bam_aux.o bam.o bam_import.o sam.o \ |
| 266 |
- sam_header.o bam_plbuf.o |
| 267 |
-@@ -42,6 +43,7 @@ LIBCURSES= -lcurses # -lXCurses |
| 268 |
- prefix = /usr/local |
| 269 |
- exec_prefix = $(prefix) |
| 270 |
- bindir = $(exec_prefix)/bin |
| 271 |
-+bindir = $(exec_prefix)/lib |
| 272 |
- mandir = $(prefix)/share/man |
| 273 |
- man1dir = $(mandir)/man1 |
| 274 |
- |
| 275 |
-@@ -115,14 +117,22 @@ version.h: |
| 276 |
- .c.o: |
| 277 |
- $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ $< |
| 278 |
- |
| 279 |
-+$(LOBJS): |
| 280 |
-+ $(CC) $(CFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $< |
| 281 |
- |
| 282 |
--lib:libbam.a |
| 283 |
-+ |
| 284 |
-+lib:libbam.a libbam.so.1.0 |
| 285 |
- |
| 286 |
- libbam.a:$(LOBJS) |
| 287 |
- $(AR) -csru $@ $(LOBJS) |
| 288 |
- |
| 289 |
--samtools: $(AOBJS) libbam.a $(HTSLIB) |
| 290 |
-- $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz |
| 291 |
-+libbam.so.1.0:$(LOBJS) |
| 292 |
-+ $(CC) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB) -lz |
| 293 |
-+ ln -sf $@ libbam.so.0 |
| 294 |
-+ ln -sf $@ libbam.so |
| 295 |
-+ |
| 296 |
-+samtools: $(AOBJS) $(HTSLIB) lib |
| 297 |
-+ $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) $(BAMLIB) $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz |
| 298 |
- |
| 299 |
- bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h) |
| 300 |
- bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.h |
| 301 |
|
| 302 |
diff --git a/sci-biology/samtools/files/samtools-1.1-buildsystem.patch b/sci-biology/samtools/files/samtools-1.1-buildsystem.patch |
| 303 |
deleted file mode 100644 |
| 304 |
index b9ae77de67d..00000000000 |
| 305 |
--- a/sci-biology/samtools/files/samtools-1.1-buildsystem.patch |
| 306 |
+++ /dev/null |
| 307 |
@@ -1,153 +0,0 @@ |
| 308 |
- Makefile | 76 ++++++++++++++++++++++++++++++++++++---------------------------- |
| 309 |
- 1 file changed, 43 insertions(+), 33 deletions(-) |
| 310 |
- |
| 311 |
-diff --git a/Makefile b/Makefile |
| 312 |
-index 43cefc3..743dd07 100644 |
| 313 |
---- a/Makefile |
| 314 |
-+++ b/Makefile |
| 315 |
-@@ -21,11 +21,12 @@ |
| 316 |
- # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER |
| 317 |
- # DEALINGS IN THE SOFTWARE. |
| 318 |
- |
| 319 |
--CC = gcc |
| 320 |
--CPPFLAGS = $(DFLAGS) $(INCLUDES) |
| 321 |
--CFLAGS = -g -Wall -O2 |
| 322 |
--LDFLAGS = |
| 323 |
--LDLIBS = |
| 324 |
-+CC ?= gcc |
| 325 |
-+CPPFLAGS += $(DFLAGS) $(INCLUDES) |
| 326 |
-+CFLAGS ?= -g -Wall -O2 |
| 327 |
-+LDFLAGS += |
| 328 |
-+LDLIBS += |
| 329 |
-+BAMLIB ?= libbam.a |
| 330 |
- DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 |
| 331 |
- LOBJS= bam_aux.o bam.o bam_import.o sam.o \ |
| 332 |
- sam_header.o bam_plbuf.o |
| 333 |
-@@ -42,6 +43,7 @@ LIBCURSES= -lcurses # -lXCurses |
| 334 |
- prefix = /usr/local |
| 335 |
- exec_prefix = $(prefix) |
| 336 |
- bindir = $(exec_prefix)/bin |
| 337 |
-+libdir = $(exec_prefix)/lib |
| 338 |
- mandir = $(prefix)/share/man |
| 339 |
- man1dir = $(mandir)/man1 |
| 340 |
- |
| 341 |
-@@ -115,63 +117,71 @@ version.h: |
| 342 |
- .c.o: |
| 343 |
- $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ $< |
| 344 |
- |
| 345 |
-+$(LOBJS): |
| 346 |
-+ $(CC) $(CFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $< |
| 347 |
- |
| 348 |
--lib:libbam.a |
| 349 |
-+ |
| 350 |
-+lib:libbam.a libbam.so.1.0 |
| 351 |
- |
| 352 |
- libbam.a:$(LOBJS) |
| 353 |
- $(AR) -csru $@ $(LOBJS) |
| 354 |
- |
| 355 |
--samtools: $(AOBJS) libbam.a $(HTSLIB) |
| 356 |
-- $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz |
| 357 |
-+libbam.so.1.0:$(LOBJS) |
| 358 |
-+ $(CC) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB) -lz |
| 359 |
-+ ln -sf $@ libbam.so.0 |
| 360 |
-+ ln -sf $@ libbam.so |
| 361 |
-+ |
| 362 |
-+samtools: $(AOBJS) lib |
| 363 |
-+ $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) $(BAMLIB) $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz |
| 364 |
- |
| 365 |
- bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h) |
| 366 |
- bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.h |
| 367 |
- bam_lpileup_h = bam_lpileup.h $(htslib_sam_h) |
| 368 |
- bam_plbuf_h = bam_plbuf.h $(htslib_sam_h) |
| 369 |
--bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(HTSDIR)/htslib/khash.h $(bam_lpileup_h) |
| 370 |
-+bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(bam_lpileup_h) |
| 371 |
- sam_h = sam.h $(htslib_sam_h) $(bam_h) |
| 372 |
--sample_h = sample.h $(HTSDIR)/htslib/kstring.h |
| 373 |
-+sample_h = sample.h |
| 374 |
- |
| 375 |
- bam.o: bam.c $(bam_h) sam_header.h |
| 376 |
--bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kfunc.h $(bam2bcf_h) errmod.h |
| 377 |
-+bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(bam2bcf_h) errmod.h |
| 378 |
- bam2bcf_indel.o: bam2bcf_indel.c bam2bcf.h |
| 379 |
- bam2depth.o: bam2depth.c $(htslib_sam_h) samtools.h |
| 380 |
- bam_aux.o: bam_aux.c |
| 381 |
- bam_cat.o: bam_cat.c $(htslib_bgzf_h) $(bam_h) |
| 382 |
- bam_color.o: bam_color.c $(bam_h) |
| 383 |
--bam_import.o: bam_import.c $(HTSDIR)/htslib/kstring.h $(bam_h) $(HTSDIR)/htslib/kseq.h |
| 384 |
--bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) $(HTSDIR)/htslib/khash.h |
| 385 |
--bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) $(HTSDIR)/htslib/ksort.h |
| 386 |
-+bam_import.o: bam_import.c $(bam_h) |
| 387 |
-+bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) |
| 388 |
-+bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) |
| 389 |
- bam_mate.o: bam_mate.c $(bam_h) |
| 390 |
- bam_md.o: bam_md.c $(htslib_faidx_h) $(sam_h) kaln.h kprobaln.h |
| 391 |
- bam_pileup.o: bam_pileup.c $(sam_h) |
| 392 |
- bam_plbuf.o: bam_plbuf.c $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h) |
| 393 |
--bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/khash_str2int.h sam_header.h samtools.h $(bam2bcf_h) $(sample_h) |
| 394 |
-+bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) sam_header.h samtools.h $(bam2bcf_h) $(sample_h) |
| 395 |
- bam_reheader.o: bam_reheader.c $(htslib_bgzf_h) $(bam_h) |
| 396 |
--bam_rmdup.o: bam_rmdup.c $(sam_h) $(HTSDIR)/htslib/khash.h |
| 397 |
--bam_rmdupse.o: bam_rmdupse.c $(sam_h) $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/klist.h |
| 398 |
--bam_sort.o: bam_sort.c $(HTSDIR)/htslib/ksort.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/klist.h $(HTSDIR)/htslib/kstring.h $(htslib_sam_h) |
| 399 |
-+bam_rmdup.o: bam_rmdup.c $(sam_h) |
| 400 |
-+bam_rmdupse.o: bam_rmdupse.c $(sam_h) |
| 401 |
-+bam_sort.o: bam_sort.c $(htslib_sam_h) |
| 402 |
- bam_stat.o: bam_stat.c $(bam_h) samtools.h |
| 403 |
- bam_tview.o: bam_tview.c $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h) |
| 404 |
- bam_tview_curses.o: bam_tview_curses.c $(bam_tview_h) |
| 405 |
- bam_tview_html.o: bam_tview_html.c $(bam_tview_h) |
| 406 |
- bam_flags.o: bam_flags.c $(sam_h) |
| 407 |
--bamshuf.o: bamshuf.c $(htslib_sam_h) $(HTSDIR)/htslib/ksort.h samtools.h |
| 408 |
-+bamshuf.o: bamshuf.c $(htslib_sam_h) samtools.h |
| 409 |
- bamtk.o: bamtk.c $(bam_h) version.h samtools.h |
| 410 |
--bedcov.o: bedcov.c $(HTSDIR)/htslib/kstring.h $(htslib_sam_h) $(HTSDIR)/htslib/kseq.h |
| 411 |
--bedidx.o: bedidx.c $(HTSDIR)/htslib/ksort.h $(HTSDIR)/htslib/kseq.h $(HTSDIR)/htslib/khash.h |
| 412 |
-+bedcov.o: bedcov.c $(htslib_sam_h) |
| 413 |
-+bedidx.o: bedidx.c |
| 414 |
- cut_target.o: cut_target.c $(bam_h) errmod.h $(htslib_faidx_h) |
| 415 |
--errmod.o: errmod.c errmod.h $(HTSDIR)/htslib/ksort.h |
| 416 |
-+errmod.o: errmod.c errmod.h |
| 417 |
- kaln.o: kaln.c kaln.h |
| 418 |
- kprobaln.o: kprobaln.c kprobaln.h |
| 419 |
- padding.o: padding.c sam_header.h $(sam_h) $(bam_h) $(htslib_faidx_h) |
| 420 |
--phase.o: phase.c $(htslib_sam_h) errmod.h $(HTSDIR)/htslib/kseq.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/ksort.h |
| 421 |
-+phase.o: phase.c $(htslib_sam_h) errmod.h |
| 422 |
- sam.o: sam.c $(htslib_faidx_h) $(sam_h) |
| 423 |
--sam_header.o: sam_header.c sam_header.h $(HTSDIR)/htslib/khash.h |
| 424 |
--sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/khash.h samtools.h |
| 425 |
--sample.o: sample.c $(sample_h) $(HTSDIR)/htslib/khash.h |
| 426 |
--stats_isize.o: stats_isize.c stats_isize.h $(HTSDIR)/htslib/khash.h |
| 427 |
--stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/khash_str2int.h $(htslib_faidx_h) |
| 428 |
-+sam_header.o: sam_header.c sam_header.h |
| 429 |
-+sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) samtools.h |
| 430 |
-+sample.o: sample.c $(sample_h) |
| 431 |
-+stats_isize.o: stats_isize.c stats_isize.h |
| 432 |
-+stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(htslib_faidx_h) |
| 433 |
- |
| 434 |
- |
| 435 |
- # test programs |
| 436 |
-@@ -179,8 +189,8 @@ stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(HTSDIR)/htslib |
| 437 |
- # For tests that might use it, set $REF_PATH explicitly to use only reference |
| 438 |
- # areas within the test suite (or set it to ':' to use no reference areas). |
| 439 |
- # (regression.sh sets $REF_PATH to a subdirectory itself.) |
| 440 |
--check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS) |
| 441 |
-- REF_PATH=: test/test.pl --exec bgzip=$(BGZIP) |
| 442 |
-+check test: samtools $(BUILT_TEST_PROGRAMS) |
| 443 |
-+ REF_PATH=: test/test.pl --exec bgzip=bgzip |
| 444 |
- test/merge/test_bam_translate test/merge/test_bam_translate.tmp |
| 445 |
- test/merge/test_pretty_header |
| 446 |
- test/merge/test_rtrans_build |
| 447 |
-@@ -253,10 +263,10 @@ misc/md5sum-lite: misc/md5sum-lite.o |
| 448 |
- misc/wgsim: misc/wgsim.o |
| 449 |
- $(CC) $(LDFLAGS) -o $@ misc/wgsim.o $(LDLIBS) -lm -lz |
| 450 |
- |
| 451 |
--misc/ace2sam.o: misc/ace2sam.c $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kseq.h |
| 452 |
-+misc/ace2sam.o: misc/ace2sam.c |
| 453 |
- misc/md5.o: misc/md5.c misc/md5.h |
| 454 |
--misc/md5fa.o: misc/md5fa.c misc/md5.h $(HTSDIR)/htslib/kseq.h |
| 455 |
--misc/wgsim.o: misc/wgsim.c $(HTSDIR)/htslib/kseq.h |
| 456 |
-+misc/md5fa.o: misc/md5fa.c misc/md5.h |
| 457 |
-+misc/wgsim.o: misc/wgsim.c |
| 458 |
- |
| 459 |
- misc/maq2sam-short.o: misc/maq2sam.c |
| 460 |
- $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ misc/maq2sam.c |
| 461 |
|
| 462 |
diff --git a/sci-biology/samtools/files/samtools-1.2-buildsystem.patch b/sci-biology/samtools/files/samtools-1.2-buildsystem.patch |
| 463 |
deleted file mode 100644 |
| 464 |
index 2343b2245a2..00000000000 |
| 465 |
--- a/sci-biology/samtools/files/samtools-1.2-buildsystem.patch |
| 466 |
+++ /dev/null |
| 467 |
@@ -1,193 +0,0 @@ |
| 468 |
- Makefile | 94 +++++++++++++++++++++++++++++++++++----------------------------- |
| 469 |
- 1 file changed, 52 insertions(+), 42 deletions(-) |
| 470 |
- |
| 471 |
-diff --git a/Makefile b/Makefile |
| 472 |
-index e368cee..9054526 100644 |
| 473 |
---- a/Makefile |
| 474 |
-+++ b/Makefile |
| 475 |
-@@ -21,11 +21,12 @@ |
| 476 |
- # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER |
| 477 |
- # DEALINGS IN THE SOFTWARE. |
| 478 |
- |
| 479 |
--CC = gcc |
| 480 |
--CPPFLAGS = $(DFLAGS) $(INCLUDES) |
| 481 |
--CFLAGS = -g -Wall -O2 |
| 482 |
--LDFLAGS = |
| 483 |
--LDLIBS = |
| 484 |
-+CC ?= gcc |
| 485 |
-+CPPFLAGS += $(DFLAGS) $(INCLUDES) |
| 486 |
-+CFLAGS ?= -g -Wall -O2 |
| 487 |
-+LDFLAGS += |
| 488 |
-+LDLIBS += |
| 489 |
-+BAMLIB ?= libbam.a |
| 490 |
- DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 |
| 491 |
- LOBJS= bam_aux.o bam.o bam_import.o sam.o \ |
| 492 |
- sam_header.o bam_plbuf.o |
| 493 |
-@@ -42,6 +43,7 @@ LIBCURSES= -lcurses # -lXCurses |
| 494 |
- prefix = /usr/local |
| 495 |
- exec_prefix = $(prefix) |
| 496 |
- bindir = $(exec_prefix)/bin |
| 497 |
-+libdir = $(exec_prefix)/lib |
| 498 |
- mandir = $(prefix)/share/man |
| 499 |
- man1dir = $(mandir)/man1 |
| 500 |
- |
| 501 |
-@@ -115,62 +117,70 @@ version.h: |
| 502 |
- .c.o: |
| 503 |
- $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ $< |
| 504 |
- |
| 505 |
-+$(LOBJS): |
| 506 |
-+ $(CC) $(CFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $< |
| 507 |
- |
| 508 |
--lib:libbam.a |
| 509 |
-+ |
| 510 |
-+lib:libbam.a libbam.so.1.0 |
| 511 |
- |
| 512 |
- libbam.a:$(LOBJS) |
| 513 |
- $(AR) -csru $@ $(LOBJS) |
| 514 |
- |
| 515 |
--samtools: $(AOBJS) libbam.a $(HTSLIB) |
| 516 |
-- $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz |
| 517 |
-+libbam.so.1.0:$(LOBJS) |
| 518 |
-+ $(CC) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB) -lz |
| 519 |
-+ ln -sf $@ libbam.so.0 |
| 520 |
-+ ln -sf $@ libbam.so |
| 521 |
-+ |
| 522 |
-+samtools: $(AOBJS) lib |
| 523 |
-+ $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) $(BAMLIB) $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz |
| 524 |
- |
| 525 |
- bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h) |
| 526 |
- bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.h |
| 527 |
- bam_lpileup_h = bam_lpileup.h $(htslib_sam_h) |
| 528 |
- bam_plbuf_h = bam_plbuf.h $(htslib_sam_h) |
| 529 |
--bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(HTSDIR)/htslib/khash.h $(bam_lpileup_h) |
| 530 |
-+bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(bam_lpileup_h) |
| 531 |
- sam_h = sam.h $(htslib_sam_h) $(bam_h) |
| 532 |
--sample_h = sample.h $(HTSDIR)/htslib/kstring.h |
| 533 |
-+sample_h = sample.h |
| 534 |
- |
| 535 |
- bam.o: bam.c $(bam_h) sam_header.h |
| 536 |
--bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kfunc.h $(bam2bcf_h) errmod.h |
| 537 |
-+bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(bam2bcf_h) errmod.h |
| 538 |
- bam2bcf_indel.o: bam2bcf_indel.c $(htslib_sam_h) $(bam2bcf_h) kprobaln.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/ksort.h |
| 539 |
- bam2depth.o: bam2depth.c $(htslib_sam_h) samtools.h |
| 540 |
- bam_aux.o: bam_aux.c |
| 541 |
- bam_cat.o: bam_cat.c $(htslib_bgzf_h) $(bam_h) |
| 542 |
- bam_color.o: bam_color.c $(bam_h) |
| 543 |
--bam_import.o: bam_import.c $(HTSDIR)/htslib/kstring.h $(bam_h) $(HTSDIR)/htslib/kseq.h |
| 544 |
--bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) $(HTSDIR)/htslib/khash.h |
| 545 |
--bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) $(HTSDIR)/htslib/ksort.h |
| 546 |
-+bam_import.o: bam_import.c $(bam_h) |
| 547 |
-+bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) |
| 548 |
-+bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) |
| 549 |
- bam_mate.o: bam_mate.c $(bam_h) |
| 550 |
- bam_md.o: bam_md.c $(htslib_faidx_h) $(sam_h) kprobaln.h |
| 551 |
- bam_pileup.o: bam_pileup.c $(sam_h) |
| 552 |
- bam_plbuf.o: bam_plbuf.c $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h) |
| 553 |
--bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/khash_str2int.h sam_header.h samtools.h $(bam2bcf_h) $(sample_h) |
| 554 |
-+bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) sam_header.h samtools.h $(bam2bcf_h) $(sample_h) |
| 555 |
- bam_reheader.o: bam_reheader.c $(htslib_bgzf_h) $(bam_h) |
| 556 |
--bam_rmdup.o: bam_rmdup.c $(sam_h) $(HTSDIR)/htslib/khash.h |
| 557 |
--bam_rmdupse.o: bam_rmdupse.c $(sam_h) $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/klist.h |
| 558 |
--bam_sort.o: bam_sort.c $(HTSDIR)/htslib/ksort.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/klist.h $(HTSDIR)/htslib/kstring.h $(htslib_sam_h) |
| 559 |
-+bam_rmdup.o: bam_rmdup.c $(sam_h) |
| 560 |
-+bam_rmdupse.o: bam_rmdupse.c $(sam_h) |
| 561 |
-+bam_sort.o: bam_sort.c $(htslib_sam_h) |
| 562 |
- bam_stat.o: bam_stat.c $(bam_h) samtools.h |
| 563 |
- bam_tview.o: bam_tview.c $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h) |
| 564 |
- bam_tview_curses.o: bam_tview_curses.c $(bam_tview_h) |
| 565 |
- bam_tview_html.o: bam_tview_html.c $(bam_tview_h) |
| 566 |
- bam_flags.o: bam_flags.c $(sam_h) |
| 567 |
--bamshuf.o: bamshuf.c $(htslib_sam_h) $(HTSDIR)/htslib/ksort.h samtools.h |
| 568 |
-+bamshuf.o: bamshuf.c $(htslib_sam_h) samtools.h |
| 569 |
- bamtk.o: bamtk.c $(htslib_hts_h) version.h samtools.h |
| 570 |
--bedcov.o: bedcov.c $(HTSDIR)/htslib/kstring.h $(htslib_sam_h) $(HTSDIR)/htslib/kseq.h |
| 571 |
--bedidx.o: bedidx.c $(HTSDIR)/htslib/ksort.h $(HTSDIR)/htslib/kseq.h $(HTSDIR)/htslib/khash.h |
| 572 |
-+bedcov.o: bedcov.c $(htslib_sam_h) |
| 573 |
-+bedidx.o: bedidx.c |
| 574 |
- cut_target.o: cut_target.c $(bam_h) errmod.h $(htslib_faidx_h) |
| 575 |
--errmod.o: errmod.c errmod.h $(HTSDIR)/htslib/ksort.h |
| 576 |
-+errmod.o: errmod.c errmod.h |
| 577 |
- kprobaln.o: kprobaln.c kprobaln.h |
| 578 |
- padding.o: padding.c sam_header.h $(sam_h) $(bam_h) $(htslib_faidx_h) |
| 579 |
--phase.o: phase.c $(htslib_sam_h) errmod.h $(HTSDIR)/htslib/kseq.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/ksort.h |
| 580 |
-+phase.o: phase.c $(htslib_sam_h) errmod.h |
| 581 |
- sam.o: sam.c $(htslib_faidx_h) $(sam_h) |
| 582 |
--sam_header.o: sam_header.c sam_header.h $(HTSDIR)/htslib/khash.h |
| 583 |
--sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/khash.h samtools.h |
| 584 |
--sample.o: sample.c $(sample_h) $(HTSDIR)/htslib/khash.h |
| 585 |
--stats_isize.o: stats_isize.c stats_isize.h $(HTSDIR)/htslib/khash.h |
| 586 |
--stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/khash_str2int.h $(htslib_faidx_h) |
| 587 |
-+sam_header.o: sam_header.c sam_header.h |
| 588 |
-+sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) samtools.h |
| 589 |
-+sample.o: sample.c $(sample_h) |
| 590 |
-+stats_isize.o: stats_isize.c stats_isize.h |
| 591 |
-+stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(htslib_faidx_h) |
| 592 |
- |
| 593 |
- |
| 594 |
- # test programs |
| 595 |
-@@ -178,8 +188,8 @@ stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(HTSDIR)/htslib |
| 596 |
- # For tests that might use it, set $REF_PATH explicitly to use only reference |
| 597 |
- # areas within the test suite (or set it to ':' to use no reference areas). |
| 598 |
- # (regression.sh sets $REF_PATH to a subdirectory itself.) |
| 599 |
--check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS) |
| 600 |
-- REF_PATH=: test/test.pl --exec bgzip=$(BGZIP) |
| 601 |
-+check test: samtools $(BUILT_TEST_PROGRAMS) |
| 602 |
-+ REF_PATH=: test/test.pl --exec bgzip=bgzip |
| 603 |
- test/merge/test_bam_translate test/merge/test_bam_translate.tmp |
| 604 |
- test/merge/test_pretty_header |
| 605 |
- test/merge/test_rtrans_build |
| 606 |
-@@ -191,31 +201,31 @@ check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS) |
| 607 |
- test/split/test_parse_args |
| 608 |
- |
| 609 |
- |
| 610 |
--test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o $(HTSLIB) |
| 611 |
-+test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o |
| 612 |
- $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o $(HTSLIB) $(LDLIBS) -lz |
| 613 |
- |
| 614 |
--test/merge/test_pretty_header: test/merge/test_pretty_header.o $(HTSLIB) |
| 615 |
-+test/merge/test_pretty_header: test/merge/test_pretty_header.o |
| 616 |
- $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_pretty_header.o $(HTSLIB) $(LDLIBS) -lz |
| 617 |
- |
| 618 |
--test/merge/test_rtrans_build: test/merge/test_rtrans_build.o $(HTSLIB) |
| 619 |
-+test/merge/test_rtrans_build: test/merge/test_rtrans_build.o |
| 620 |
- $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_rtrans_build.o $(HTSLIB) $(LDLIBS) -lz |
| 621 |
- |
| 622 |
--test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o $(HTSLIB) |
| 623 |
-+test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o |
| 624 |
- $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o $(HTSLIB) $(LDLIBS) -lz |
| 625 |
- |
| 626 |
--test/split/test_count_rg: test/split/test_count_rg.o test/test.o $(HTSLIB) |
| 627 |
-+test/split/test_count_rg: test/split/test_count_rg.o test/test.o |
| 628 |
- $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o $(HTSLIB) $(LDLIBS) -lz |
| 629 |
- |
| 630 |
--test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o $(HTSLIB) |
| 631 |
-+test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o |
| 632 |
- $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o $(HTSLIB) $(LDLIBS) -lz |
| 633 |
- |
| 634 |
--test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o $(HTSLIB) |
| 635 |
-+test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o |
| 636 |
- $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o $(HTSLIB) $(LDLIBS) -lz |
| 637 |
- |
| 638 |
--test/split/test_parse_args: test/split/test_parse_args.o test/test.o $(HTSLIB) |
| 639 |
-+test/split/test_parse_args: test/split/test_parse_args.o test/test.o |
| 640 |
- $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o $(HTSLIB) $(LDLIBS) -lz |
| 641 |
- |
| 642 |
--test/vcf-miniview: test/vcf-miniview.o $(HTSLIB) |
| 643 |
-+test/vcf-miniview: test/vcf-miniview.o |
| 644 |
- $(CC) -pthread $(LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB) $(LDLIBS) -lz |
| 645 |
- |
| 646 |
- test_test_h = test/test.h $(htslib_sam_h) |
| 647 |
-@@ -252,10 +262,10 @@ misc/md5sum-lite: misc/md5sum-lite.o |
| 648 |
- misc/wgsim: misc/wgsim.o |
| 649 |
- $(CC) $(LDFLAGS) -o $@ misc/wgsim.o $(LDLIBS) -lm -lz |
| 650 |
- |
| 651 |
--misc/ace2sam.o: misc/ace2sam.c $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kseq.h |
| 652 |
-+misc/ace2sam.o: misc/ace2sam.c |
| 653 |
- misc/md5.o: misc/md5.c misc/md5.h |
| 654 |
--misc/md5fa.o: misc/md5fa.c misc/md5.h $(HTSDIR)/htslib/kseq.h |
| 655 |
--misc/wgsim.o: misc/wgsim.c $(HTSDIR)/htslib/kseq.h |
| 656 |
-+misc/md5fa.o: misc/md5fa.c misc/md5.h |
| 657 |
-+misc/wgsim.o: misc/wgsim.c |
| 658 |
- |
| 659 |
- misc/maq2sam-short.o: misc/maq2sam.c |
| 660 |
- $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ misc/maq2sam.c |
| 661 |
|
| 662 |
diff --git a/sci-biology/samtools/files/samtools-1.3-buildsystem.patch b/sci-biology/samtools/files/samtools-1.3-buildsystem.patch |
| 663 |
deleted file mode 100644 |
| 664 |
index 61f6b03bd8e..00000000000 |
| 665 |
--- a/sci-biology/samtools/files/samtools-1.3-buildsystem.patch |
| 666 |
+++ /dev/null |
| 667 |
@@ -1,174 +0,0 @@ |
| 668 |
---- samtools-1.3/Makefile |
| 669 |
-+++ samtools-1.3/Makefile |
| 670 |
-@@ -21,11 +21,12 @@ |
| 671 |
- # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER |
| 672 |
- # DEALINGS IN THE SOFTWARE. |
| 673 |
- |
| 674 |
--CC = gcc |
| 675 |
--CPPFLAGS = |
| 676 |
--CFLAGS = -g -Wall -O2 |
| 677 |
--LDFLAGS = |
| 678 |
--LIBS = |
| 679 |
-+CC ?= gcc |
| 680 |
-+CPPFLAGS += |
| 681 |
-+CFLAGS ?= -g -Wall -O2 |
| 682 |
-+LDFLAGS += |
| 683 |
-+LIBS += |
| 684 |
-+BAMLIB ?= libbam.a |
| 685 |
- |
| 686 |
- DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE |
| 687 |
- LOBJS= bam_aux.o bam.o bam_import.o sam.o \ |
| 688 |
-@@ -42,6 +43,7 @@ |
| 689 |
- prefix = /usr/local |
| 690 |
- exec_prefix = $(prefix) |
| 691 |
- bindir = $(exec_prefix)/bin |
| 692 |
-+libdir ?= $(exec_prefix)/lib |
| 693 |
- datarootdir = $(prefix)/share |
| 694 |
- mandir = $(datarootdir)/man |
| 695 |
- man1dir = $(mandir)/man1 |
| 696 |
-@@ -129,67 +131,74 @@ |
| 697 |
- .c.o: |
| 698 |
- $(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ $< |
| 699 |
- |
| 700 |
-+$(LOBJS): |
| 701 |
-+ $(CC) $(CFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $< |
| 702 |
- |
| 703 |
--lib:libbam.a |
| 704 |
-+lib:libbam.a libbam.so.1.0 |
| 705 |
- |
| 706 |
- libbam.a:$(LOBJS) |
| 707 |
- $(AR) -csru $@ $(LOBJS) |
| 708 |
- |
| 709 |
--samtools: $(AOBJS) libbam.a $(HTSLIB) |
| 710 |
-- $(CC) -pthread $(ALL_LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB_LIB) $(CURSES_LIB) -lm $(ALL_LIBS) |
| 711 |
-+libbam.so.1.0:$(LOBJS) |
| 712 |
-+ $(CC) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB) -lz |
| 713 |
-+ ln -sf $@ libbam.so.1 |
| 714 |
-+ ln -sf $@ libbam.so |
| 715 |
-+ |
| 716 |
-+samtools: $(AOBJS) lib |
| 717 |
-+ $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) $(BAMLIB) $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz |
| 718 |
- |
| 719 |
- bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h) |
| 720 |
- bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.h |
| 721 |
- bam_lpileup_h = bam_lpileup.h $(htslib_sam_h) |
| 722 |
- bam_plbuf_h = bam_plbuf.h $(htslib_sam_h) |
| 723 |
--bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(htslib_khash_h) $(bam_lpileup_h) |
| 724 |
-+bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(bam_lpileup_h) |
| 725 |
- sam_h = sam.h $(htslib_sam_h) $(bam_h) |
| 726 |
- sam_opts_h = sam_opts.h $(htslib_hts_h) |
| 727 |
--sample_h = sample.h $(htslib_kstring_h) |
| 728 |
-+sample_h = sample.h |
| 729 |
- |
| 730 |
- bam.o: bam.c $(bam_h) $(htslib_kstring_h) sam_header.h |
| 731 |
--bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(htslib_kstring_h) $(htslib_kfunc_h) $(bam2bcf_h) errmod.h |
| 732 |
-+bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(bam2bcf_h) errmod.h |
| 733 |
- bam2bcf_indel.o: bam2bcf_indel.c $(htslib_sam_h) $(bam2bcf_h) kprobaln.h $(htslib_khash_h) $(htslib_ksort_h) |
| 734 |
- bam2depth.o: bam2depth.c $(htslib_sam_h) samtools.h $(sam_opts_h) |
| 735 |
- bam_addrprg.o: bam_addrprg.c $(htslib_sam_h) $(htslib_kstring_h) samtools.h $(sam_opts_h) |
| 736 |
- bam_aux.o: bam_aux.c $(bam_h) |
| 737 |
- bam_cat.o: bam_cat.c $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_cram_h) $(htslib_khash_h) |
| 738 |
- bam_color.o: bam_color.c $(bam_h) |
| 739 |
--bam_import.o: bam_import.c $(htslib_kstring_h) $(bam_h) $(htslib_kseq_h) |
| 740 |
--bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_h) samtools.h |
| 741 |
--bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) $(htslib_ksort_h) |
| 742 |
-+bam_import.o: bam_import.c $(bam_h) |
| 743 |
-+bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) |
| 744 |
-+bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) |
| 745 |
- bam_mate.o: bam_mate.c $(sam_opts_h) $(htslib_kstring_h) $(htslib_sam_h) |
| 746 |
- bam_md.o: bam_md.c $(htslib_faidx_h) $(htslib_sam_h) $(htslib_kstring_h) kprobaln.h $(sam_opts_h) |
| 747 |
- bam_plbuf.o: bam_plbuf.c $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h) |
| 748 |
--bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) sam_header.h samtools.h $(sam_opts_h) $(bam2bcf_h) $(sample_h) |
| 749 |
-+bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) sam_header.h samtools.h $(bam2bcf_h) $(sample_h) |
| 750 |
- bam_quickcheck.o: bam_quickcheck.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_bgzf_h) |
| 751 |
- bam_reheader.o: bam_reheader.c $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_hfile_h) $(htslib_cram_h) samtools.h |
| 752 |
--bam_rmdup.o: bam_rmdup.c $(htslib_sam_h) $(sam_opts_h) $(bam_h) $(htslib_khash_h) |
| 753 |
--bam_rmdupse.o: bam_rmdupse.c $(bam_h) $(htslib_sam_h) $(htslib_khash_h) $(htslib_klist_h) |
| 754 |
--bam_sort.o: bam_sort.c $(htslib_ksort_h) $(htslib_khash_h) $(htslib_klist_h) $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) |
| 755 |
-+bam_rmdup.o: bam_rmdup.c $(sam_h) |
| 756 |
-+bam_rmdupse.o: bam_rmdupse.c $(sam_h) |
| 757 |
-+bam_sort.o: bam_sort.c $(htslib_sam_h) |
| 758 |
- bam_split.o: bam_split.c $(htslib_sam_h) $(htslib_khash_h) $(htslib_kstring_h) $(sam_opts_h) |
| 759 |
- bam_stat.o: bam_stat.c $(htslib_sam_h) samtools.h |
| 760 |
- bam_tview.o: bam_tview.c $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h) $(sam_opts_h) |
| 761 |
- bam_tview_curses.o: bam_tview_curses.c config.h $(bam_tview_h) |
| 762 |
- bam_tview_html.o: bam_tview_html.c $(bam_tview_h) |
| 763 |
- bam_flags.o: bam_flags.c $(htslib_sam_h) |
| 764 |
--bamshuf.o: bamshuf.c $(htslib_sam_h) $(htslib_hts_h) $(htslib_ksort_h) samtools.h $(sam_opts_h) |
| 765 |
-+bamshuf.o: bamshuf.c $(htslib_sam_h) samtools.h |
| 766 |
- bamtk.o: bamtk.c $(htslib_hts_h) samtools.h version.h |
| 767 |
--bedcov.o: bedcov.c $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) $(htslib_kseq_h) |
| 768 |
--bedidx.o: bedidx.c $(htslib_ksort_h) $(htslib_kseq_h) $(htslib_khash_h) |
| 769 |
-+bedcov.o: bedcov.c $(htslib_sam_h) |
| 770 |
-+bedidx.o: bedidx.c |
| 771 |
- cut_target.o: cut_target.c $(htslib_sam_h) errmod.h $(htslib_faidx_h) $(sam_opts_h) |
| 772 |
- dict.o: dict.c $(htslib_kseq_h) $(htslib_hts_h) |
| 773 |
--errmod.o: errmod.c errmod.h $(htslib_ksort_h) |
| 774 |
-+errmod.o: errmod.c errmod.h |
| 775 |
- kprobaln.o: kprobaln.c kprobaln.h |
| 776 |
- padding.o: padding.c $(htslib_kstring_h) $(htslib_sam_h) $(htslib_faidx_h) sam_header.h $(sam_opts_h) |
| 777 |
--phase.o: phase.c $(htslib_sam_h) errmod.h $(sam_opts_h) $(htslib_kseq_h) $(htslib_khash_h) $(htslib_ksort_h) |
| 778 |
-+phase.o: phase.c $(htslib_sam_h) errmod.h |
| 779 |
- sam.o: sam.c $(htslib_faidx_h) $(sam_h) |
| 780 |
--sam_header.o: sam_header.c sam_header.h $(htslib_khash_h) |
| 781 |
-+sam_header.o: sam_header.c sam_header.h |
| 782 |
- sam_opts.o: sam_opts.c $(sam_opts_h) |
| 783 |
--sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_h) samtools.h $(sam_opts_h) |
| 784 |
--sample.o: sample.c $(sample_h) $(htslib_khash_h) |
| 785 |
--stats_isize.o: stats_isize.c stats_isize.h $(htslib_khash_h) |
| 786 |
--stats.o: stats.c $(htslib_faidx_h) $(htslib_sam_h) $(htslib_hts_h) sam_header.h $(htslib_khash_str2int_h) samtools.h $(htslib_khash_h) $(htslib_kstring_h) stats_isize.h $(sam_opts_h) |
| 787 |
-+sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) samtools.h |
| 788 |
-+sample.o: sample.c $(sample_h) |
| 789 |
-+stats_isize.o: stats_isize.c stats_isize.h |
| 790 |
-+stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(htslib_faidx_h) |
| 791 |
- |
| 792 |
- |
| 793 |
- # test programs |
| 794 |
-@@ -197,8 +206,8 @@ |
| 795 |
- # For tests that might use it, set $REF_PATH explicitly to use only reference |
| 796 |
- # areas within the test suite (or set it to ':' to use no reference areas). |
| 797 |
- # (regression.sh sets $REF_PATH to a subdirectory itself.) |
| 798 |
--check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS) |
| 799 |
-- REF_PATH=: test/test.pl --exec bgzip=$(BGZIP) |
| 800 |
-+check test: samtools $(BUILT_TEST_PROGRAMS) |
| 801 |
-+ REF_PATH=: test/test.pl --exec bgzip=bgzip |
| 802 |
- test/merge/test_bam_translate test/merge/test_bam_translate.tmp |
| 803 |
- test/merge/test_rtrans_build |
| 804 |
- test/merge/test_trans_tbl_init |
| 805 |
-@@ -210,28 +219,28 @@ |
| 806 |
- test/split/test_parse_args |
| 807 |
- |
| 808 |
- |
| 809 |
--test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o sam_opts.o $(HTSLIB) |
| 810 |
-+test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o |
| 811 |
- $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) |
| 812 |
- |
| 813 |
--test/merge/test_rtrans_build: test/merge/test_rtrans_build.o sam_opts.o $(HTSLIB) |
| 814 |
-+test/merge/test_rtrans_build: test/merge/test_rtrans_build.o |
| 815 |
- $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_rtrans_build.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) |
| 816 |
- |
| 817 |
--test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o sam_opts.o $(HTSLIB) |
| 818 |
-+test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o |
| 819 |
- $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) |
| 820 |
- |
| 821 |
--test/split/test_count_rg: test/split/test_count_rg.o test/test.o sam_opts.o $(HTSLIB) |
| 822 |
-+test/split/test_count_rg: test/split/test_count_rg.o test/test.o |
| 823 |
- $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) |
| 824 |
- |
| 825 |
--test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o sam_opts.o $(HTSLIB) |
| 826 |
-+test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o |
| 827 |
- $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) |
| 828 |
- |
| 829 |
--test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o sam_opts.o $(HTSLIB) |
| 830 |
-+test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o |
| 831 |
- $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) |
| 832 |
- |
| 833 |
--test/split/test_parse_args: test/split/test_parse_args.o test/test.o sam_opts.o $(HTSLIB) |
| 834 |
-+test/split/test_parse_args: test/split/test_parse_args.o test/test.o |
| 835 |
- $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) |
| 836 |
- |
| 837 |
--test/vcf-miniview: test/vcf-miniview.o $(HTSLIB) |
| 838 |
-+test/vcf-miniview: test/vcf-miniview.o |
| 839 |
- $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB_LIB) $(ALL_LIBS) |
| 840 |
- |
| 841 |
- test_test_h = test/test.h $(htslib_sam_h) |
| 842 |
|
| 843 |
diff --git a/sci-biology/samtools/files/samtools-1.3-ncurses.patch b/sci-biology/samtools/files/samtools-1.3-ncurses.patch |
| 844 |
deleted file mode 100644 |
| 845 |
index baeb6701cd2..00000000000 |
| 846 |
--- a/sci-biology/samtools/files/samtools-1.3-ncurses.patch |
| 847 |
+++ /dev/null |
| 848 |
@@ -1,737 +0,0 @@ |
| 849 |
-* Add modern AX_WITH_CURSES that prefers using pkg-config for detecting ncurses |
| 850 |
-* Change macro structure by moving AX_WITH_HTSLIB into its own file |
| 851 |
- |
| 852 |
---- samtools-1.3/configure.ac |
| 853 |
-+++ samtools-1.3/configure.ac |
| 854 |
-@@ -28,6 +28,7 @@ |
| 855 |
- AC_PREREQ([2.63]) dnl This version introduced 4-argument AC_CHECK_HEADER |
| 856 |
- AC_CONFIG_SRCDIR([bamtk.c]) |
| 857 |
- AC_CONFIG_HEADERS([config.h]) |
| 858 |
-+AC_CONFIG_MACRO_DIR([m4]) |
| 859 |
- |
| 860 |
- dnl Copyright notice to be copied into the generated configure script |
| 861 |
- AC_COPYRIGHT([Portions copyright (C) 2015 Genome Research Ltd. |
| 862 |
---- samtools-1.3/m4/ax_with_curses.m4 |
| 863 |
-+++ samtools-1.3/m4/ax_with_curses.m4 |
| 864 |
-@@ -0,0 +1,578 @@ |
| 865 |
-+# =========================================================================== |
| 866 |
-+# http://www.gnu.org/software/autoconf-archive/ax_with_curses.html |
| 867 |
-+# =========================================================================== |
| 868 |
-+# |
| 869 |
-+# SYNOPSIS |
| 870 |
-+# |
| 871 |
-+# AX_WITH_CURSES |
| 872 |
-+# |
| 873 |
-+# DESCRIPTION |
| 874 |
-+# |
| 875 |
-+# This macro checks whether a SysV or X/Open-compatible Curses library is |
| 876 |
-+# present, along with the associated header file. The NcursesW |
| 877 |
-+# (wide-character) library is searched for first, followed by Ncurses, |
| 878 |
-+# then the system-default plain Curses. The first library found is the |
| 879 |
-+# one returned. Finding libraries will first be attempted by using |
| 880 |
-+# pkg-config, and should the pkg-config files not be available, will |
| 881 |
-+# fallback to combinations of known flags itself. |
| 882 |
-+# |
| 883 |
-+# The following options are understood: --with-ncursesw, --with-ncurses, |
| 884 |
-+# --without-ncursesw, --without-ncurses. The "--with" options force the |
| 885 |
-+# macro to use that particular library, terminating with an error if not |
| 886 |
-+# found. The "--without" options simply skip the check for that library. |
| 887 |
-+# The effect on the search pattern is: |
| 888 |
-+# |
| 889 |
-+# (no options) - NcursesW, Ncurses, Curses |
| 890 |
-+# --with-ncurses --with-ncursesw - NcursesW only [*] |
| 891 |
-+# --without-ncurses --with-ncursesw - NcursesW only [*] |
| 892 |
-+# --with-ncursesw - NcursesW only [*] |
| 893 |
-+# --with-ncurses --without-ncursesw - Ncurses only [*] |
| 894 |
-+# --with-ncurses - NcursesW, Ncurses [**] |
| 895 |
-+# --without-ncurses --without-ncursesw - Curses only |
| 896 |
-+# --without-ncursesw - Ncurses, Curses |
| 897 |
-+# --without-ncurses - NcursesW, Curses |
| 898 |
-+# |
| 899 |
-+# [*] If the library is not found, abort the configure script. |
| 900 |
-+# |
| 901 |
-+# [**] If the second library (Ncurses) is not found, abort configure. |
| 902 |
-+# |
| 903 |
-+# The following preprocessor symbols may be defined by this macro if the |
| 904 |
-+# appropriate conditions are met: |
| 905 |
-+# |
| 906 |
-+# HAVE_CURSES - if any SysV or X/Open Curses library found |
| 907 |
-+# HAVE_CURSES_ENHANCED - if library supports X/Open Enhanced functions |
| 908 |
-+# HAVE_CURSES_COLOR - if library supports color (enhanced functions) |
| 909 |
-+# HAVE_CURSES_OBSOLETE - if library supports certain obsolete features |
| 910 |
-+# HAVE_NCURSESW - if NcursesW (wide char) library is to be used |
| 911 |
-+# HAVE_NCURSES - if the Ncurses library is to be used |
| 912 |
-+# |
| 913 |
-+# HAVE_CURSES_H - if <curses.h> is present and should be used |
| 914 |
-+# HAVE_NCURSESW_H - if <ncursesw.h> should be used |
| 915 |
-+# HAVE_NCURSES_H - if <ncurses.h> should be used |
| 916 |
-+# HAVE_NCURSESW_CURSES_H - if <ncursesw/curses.h> should be used |
| 917 |
-+# HAVE_NCURSES_CURSES_H - if <ncurses/curses.h> should be used |
| 918 |
-+# |
| 919 |
-+# (These preprocessor symbols are discussed later in this document.) |
| 920 |
-+# |
| 921 |
-+# The following output variables are defined by this macro; they are |
| 922 |
-+# precious and may be overridden on the ./configure command line: |
| 923 |
-+# |
| 924 |
-+# CURSES_LIB - library to add to xxx_LDADD |
| 925 |
-+# CURSES_CPPFLAGS - include paths to add to xxx_CPPFLAGS |
| 926 |
-+# |
| 927 |
-+# Neither the library listed in CURSES_LIB, nor the flags in |
| 928 |
-+# CURSES_CPPFLAGS are added to LIBS, respectively CPPFLAGS, by default. |
| 929 |
-+# You need to add both to the appropriate xxx_LDADD/xxx_CPPFLAGS line in |
| 930 |
-+# your Makefile.am. For example: |
| 931 |
-+# |
| 932 |
-+# prog_LDADD = @CURSES_LIB@ |
| 933 |
-+# prog_CPPFLAGS = @CURSES_CPPFLAGS@ |
| 934 |
-+# |
| 935 |
-+# If CURSES_LIB is set on the configure command line (such as by running |
| 936 |
-+# "./configure CURSES_LIB=-lmycurses"), then the only header searched for |
| 937 |
-+# is <curses.h>. If the user needs to specify an alternative path for a |
| 938 |
-+# library (such as for a non-standard NcurseW), the user should use the |
| 939 |
-+# LDFLAGS variable. |
| 940 |
-+# |
| 941 |
-+# The following shell variables may be defined by this macro: |
| 942 |
-+# |
| 943 |
-+# ax_cv_curses - set to "yes" if any Curses library found |
| 944 |
-+# ax_cv_curses_enhanced - set to "yes" if Enhanced functions present |
| 945 |
-+# ax_cv_curses_color - set to "yes" if color functions present |
| 946 |
-+# ax_cv_curses_obsolete - set to "yes" if obsolete features present |
| 947 |
-+# |
| 948 |
-+# ax_cv_ncursesw - set to "yes" if NcursesW library found |
| 949 |
-+# ax_cv_ncurses - set to "yes" if Ncurses library found |
| 950 |
-+# ax_cv_plaincurses - set to "yes" if plain Curses library found |
| 951 |
-+# ax_cv_curses_which - set to "ncursesw", "ncurses", "plaincurses" or "no" |
| 952 |
-+# |
| 953 |
-+# These variables can be used in your configure.ac to determine the level |
| 954 |
-+# of support you need from the Curses library. For example, if you must |
| 955 |
-+# have either Ncurses or NcursesW, you could include: |
| 956 |
-+# |
| 957 |
-+# AX_WITH_CURSES |
| 958 |
-+# if test "x$ax_cv_ncursesw" != xyes && test "x$ax_cv_ncurses" != xyes; then |
| 959 |
-+# AC_MSG_ERROR([requires either NcursesW or Ncurses library]) |
| 960 |
-+# fi |
| 961 |
-+# |
| 962 |
-+# If any Curses library will do (but one must be present and must support |
| 963 |
-+# color), you could use: |
| 964 |
-+# |
| 965 |
-+# AX_WITH_CURSES |
| 966 |
-+# if test "x$ax_cv_curses" != xyes || test "x$ax_cv_curses_color" != xyes; then |
| 967 |
-+# AC_MSG_ERROR([requires an X/Open-compatible Curses library with color]) |
| 968 |
-+# fi |
| 969 |
-+# |
| 970 |
-+# Certain preprocessor symbols and shell variables defined by this macro |
| 971 |
-+# can be used to determine various features of the Curses library. In |
| 972 |
-+# particular, HAVE_CURSES and ax_cv_curses are defined if the Curses |
| 973 |
-+# library found conforms to the traditional SysV and/or X/Open Base Curses |
| 974 |
-+# definition. Any working Curses library conforms to this level. |
| 975 |
-+# |
| 976 |
-+# HAVE_CURSES_ENHANCED and ax_cv_curses_enhanced are defined if the |
| 977 |
-+# library supports the X/Open Enhanced Curses definition. In particular, |
| 978 |
-+# the wide-character types attr_t, cchar_t and wint_t, the functions |
| 979 |
-+# wattr_set() and wget_wch() and the macros WA_NORMAL and _XOPEN_CURSES |
| 980 |
-+# are checked. The Ncurses library does NOT conform to this definition, |
| 981 |
-+# although NcursesW does. |
| 982 |
-+# |
| 983 |
-+# HAVE_CURSES_COLOR and ax_cv_curses_color are defined if the library |
| 984 |
-+# supports color functions and macros such as COLOR_PAIR, A_COLOR, |
| 985 |
-+# COLOR_WHITE, COLOR_RED and init_pair(). These are NOT part of the |
| 986 |
-+# X/Open Base Curses definition, but are part of the Enhanced set of |
| 987 |
-+# functions. The Ncurses library DOES support these functions, as does |
| 988 |
-+# NcursesW. |
| 989 |
-+# |
| 990 |
-+# HAVE_CURSES_OBSOLETE and ax_cv_curses_obsolete are defined if the |
| 991 |
-+# library supports certain features present in SysV and BSD Curses but not |
| 992 |
-+# defined in the X/Open definition. In particular, the functions |
| 993 |
-+# getattrs(), getcurx() and getmaxx() are checked. |
| 994 |
-+# |
| 995 |
-+# To use the HAVE_xxx_H preprocessor symbols, insert the following into |
| 996 |
-+# your system.h (or equivalent) header file: |
| 997 |
-+# |
| 998 |
-+# #if defined HAVE_NCURSESW_CURSES_H |
| 999 |
-+# # include <ncursesw/curses.h> |
| 1000 |
-+# #elif defined HAVE_NCURSESW_H |
| 1001 |
-+# # include <ncursesw.h> |
| 1002 |
-+# #elif defined HAVE_NCURSES_CURSES_H |
| 1003 |
-+# # include <ncurses/curses.h> |
| 1004 |
-+# #elif defined HAVE_NCURSES_H |
| 1005 |
-+# # include <ncurses.h> |
| 1006 |
-+# #elif defined HAVE_CURSES_H |
| 1007 |
-+# # include <curses.h> |
| 1008 |
-+# #else |
| 1009 |
-+# # error "SysV or X/Open-compatible Curses header file required" |
| 1010 |
-+# #endif |
| 1011 |
-+# |
| 1012 |
-+# For previous users of this macro: you should not need to change anything |
| 1013 |
-+# in your configure.ac or Makefile.am, as the previous (serial 10) |
| 1014 |
-+# semantics are still valid. However, you should update your system.h (or |
| 1015 |
-+# equivalent) header file to the fragment shown above. You are encouraged |
| 1016 |
-+# also to make use of the extended functionality provided by this version |
| 1017 |
-+# of AX_WITH_CURSES, as well as in the additional macros |
| 1018 |
-+# AX_WITH_CURSES_PANEL, AX_WITH_CURSES_MENU and AX_WITH_CURSES_FORM. |
| 1019 |
-+# |
| 1020 |
-+# LICENSE |
| 1021 |
-+# |
| 1022 |
-+# Copyright (c) 2009 Mark Pulford <mark@××××××××.au> |
| 1023 |
-+# Copyright (c) 2009 Damian Pietras <daper@×××××.net> |
| 1024 |
-+# Copyright (c) 2012 Reuben Thomas <rrt@××××.org> |
| 1025 |
-+# Copyright (c) 2011 John Zaitseff <J.Zaitseff@×××××××.au> |
| 1026 |
-+# |
| 1027 |
-+# This program is free software: you can redistribute it and/or modify it |
| 1028 |
-+# under the terms of the GNU General Public License as published by the |
| 1029 |
-+# Free Software Foundation, either version 3 of the License, or (at your |
| 1030 |
-+# option) any later version. |
| 1031 |
-+# |
| 1032 |
-+# This program is distributed in the hope that it will be useful, but |
| 1033 |
-+# WITHOUT ANY WARRANTY; without even the implied warranty of |
| 1034 |
-+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General |
| 1035 |
-+# Public License for more details. |
| 1036 |
-+# |
| 1037 |
-+# You should have received a copy of the GNU General Public License along |
| 1038 |
-+# with this program. If not, see <http://www.gnu.org/licenses/>. |
| 1039 |
-+# |
| 1040 |
-+# As a special exception, the respective Autoconf Macro's copyright owner |
| 1041 |
-+# gives unlimited permission to copy, distribute and modify the configure |
| 1042 |
-+# scripts that are the output of Autoconf when processing the Macro. You |
| 1043 |
-+# need not follow the terms of the GNU General Public License when using |
| 1044 |
-+# or distributing such scripts, even though portions of the text of the |
| 1045 |
-+# Macro appear in them. The GNU General Public License (GPL) does govern |
| 1046 |
-+# all other use of the material that constitutes the Autoconf Macro. |
| 1047 |
-+# |
| 1048 |
-+# This special exception to the GPL applies to versions of the Autoconf |
| 1049 |
-+# Macro released by the Autoconf Archive. When you make and distribute a |
| 1050 |
-+# modified version of the Autoconf Macro, you may extend this special |
| 1051 |
-+# exception to the GPL to apply to your modified version as well. |
| 1052 |
-+ |
| 1053 |
-+#serial 16 |
| 1054 |
-+ |
| 1055 |
-+# internal function to factorize common code that is used by both ncurses |
| 1056 |
-+# and ncursesw |
| 1057 |
-+AC_DEFUN([_FIND_CURSES_FLAGS], [ |
| 1058 |
-+ AC_MSG_CHECKING([for $1 via pkg-config]) |
| 1059 |
-+ |
| 1060 |
-+ _PKG_CONFIG([_ax_cv_$1_lib], [libs], [$1]) |
| 1061 |
-+ _PKG_CONFIG([_ax_cv_$1_cppflags], [cflags], [$1]) |
| 1062 |
-+ |
| 1063 |
-+ AS_IF([test "x$pkg_failed" = "xyes" || test "x$pkg_failed" = "xuntried"],[ |
| 1064 |
-+ AC_MSG_RESULT([no]) |
| 1065 |
-+ # No suitable .pc file found, have to find flags via fallback |
| 1066 |
-+ AC_CACHE_CHECK([for $1 via fallback], [ax_cv_$1], [ |
| 1067 |
-+ AS_ECHO() |
| 1068 |
-+ pkg_cv__ax_cv_$1_lib="-l$1" |
| 1069 |
-+ pkg_cv__ax_cv_$1_cppflags="$CURSES_CPPFLAGS" |
| 1070 |
-+ LIBS="$ax_saved_LIBS $pkg_cv__ax_cv_$1_lib" |
| 1071 |
-+ CPPFLAGS="$ax_saved_CPPFLAGS $pkg_cv__ax_cv_$1_cppflags" |
| 1072 |
-+ |
| 1073 |
-+ AC_MSG_CHECKING([for initscr() with $pkg_cv__ax_cv_$1_lib]) |
| 1074 |
-+ AC_LINK_IFELSE([AC_LANG_CALL([], [initscr])], |
| 1075 |
-+ [ |
| 1076 |
-+ AC_MSG_RESULT([yes]) |
| 1077 |
-+ AC_MSG_CHECKING([for nodelay() with $pkg_cv__ax_cv_$1_lib]) |
| 1078 |
-+ AC_LINK_IFELSE([AC_LANG_CALL([], [nodelay])],[ |
| 1079 |
-+ ax_cv_$1=yes |
| 1080 |
-+ ],[ |
| 1081 |
-+ AC_MSG_RESULT([no]) |
| 1082 |
-+ m4_if( |
| 1083 |
-+ [$1],[ncursesw],[pkg_cv__ax_cv_$1_lib="$pkg_cv__ax_cv_$1_lib -ltinfow"], |
| 1084 |
-+ [$1],[ncurses],[pkg_cv__ax_cv_$1_lib="$pkg_cv__ax_cv_$1_lib -ltinfo"] |
| 1085 |
-+ ) |
| 1086 |
-+ LIBS="$ax_saved_LIBS $pkg_cv__ax_cv_$1_lib" |
| 1087 |
-+ |
| 1088 |
-+ AC_MSG_CHECKING([for nodelay() with $pkg_cv__ax_cv_$1_lib]) |
| 1089 |
-+ AC_LINK_IFELSE([AC_LANG_CALL([], [nodelay])],[ |
| 1090 |
-+ ax_cv_$1=yes |
| 1091 |
-+ ],[ |
| 1092 |
-+ ax_cv_$1=no |
| 1093 |
-+ ]) |
| 1094 |
-+ ]) |
| 1095 |
-+ ],[ |
| 1096 |
-+ ax_cv_$1=no |
| 1097 |
-+ ]) |
| 1098 |
-+ ]) |
| 1099 |
-+ ],[ |
| 1100 |
-+ AC_MSG_RESULT([yes]) |
| 1101 |
-+ # Found .pc file, using its information |
| 1102 |
-+ LIBS="$ax_saved_LIBS $pkg_cv__ax_cv_$1_lib" |
| 1103 |
-+ CPPFLAGS="$ax_saved_CPPFLAGS $pkg_cv__ax_cv_$1_cppflags" |
| 1104 |
-+ ax_cv_$1=yes |
| 1105 |
-+ ]) |
| 1106 |
-+]) |
| 1107 |
-+ |
| 1108 |
-+AU_ALIAS([MP_WITH_CURSES], [AX_WITH_CURSES]) |
| 1109 |
-+AC_DEFUN([AX_WITH_CURSES], [ |
| 1110 |
-+ AC_ARG_VAR([CURSES_LIB], [linker library for Curses, e.g. -lcurses]) |
| 1111 |
-+ AC_ARG_VAR([CURSES_CPPFLAGS], [preprocessor flags for Curses, e.g. -I/usr/include/ncursesw]) |
| 1112 |
-+ AC_ARG_WITH([ncurses], [AS_HELP_STRING([--with-ncurses], |
| 1113 |
-+ [force the use of Ncurses or NcursesW])], |
| 1114 |
-+ [], [with_ncurses=check]) |
| 1115 |
-+ AC_ARG_WITH([ncursesw], [AS_HELP_STRING([--without-ncursesw], |
| 1116 |
-+ [do not use NcursesW (wide character support)])], |
| 1117 |
-+ [], [with_ncursesw=check]) |
| 1118 |
-+ AC_REQUIRE([PKG_PROG_PKG_CONFIG]) |
| 1119 |
-+ |
| 1120 |
-+ ax_saved_LIBS=$LIBS |
| 1121 |
-+ ax_saved_CPPFLAGS=$CPPFLAGS |
| 1122 |
-+ |
| 1123 |
-+ AS_IF([test "x$with_ncurses" = xyes || test "x$with_ncursesw" = xyes], |
| 1124 |
-+ [ax_with_plaincurses=no], [ax_with_plaincurses=check]) |
| 1125 |
-+ |
| 1126 |
-+ ax_cv_curses_which=no |
| 1127 |
-+ |
| 1128 |
-+ # Test for NcursesW |
| 1129 |
-+ AS_IF([test "x$CURSES_LIB" = x && test "x$with_ncursesw" != xno], [ |
| 1130 |
-+ _FIND_CURSES_FLAGS([ncursesw]) |
| 1131 |
-+ |
| 1132 |
-+ AS_IF([test "x$ax_cv_ncursesw" = xno && test "x$with_ncursesw" = xyes], [ |
| 1133 |
-+ AC_MSG_ERROR([--with-ncursesw specified but could not find NcursesW library]) |
| 1134 |
-+ ]) |
| 1135 |
-+ |
| 1136 |
-+ AS_IF([test "x$ax_cv_ncursesw" = xyes], [ |
| 1137 |
-+ ax_cv_curses=yes |
| 1138 |
-+ ax_cv_curses_which=ncursesw |
| 1139 |
-+ CURSES_LIB="$pkg_cv__ax_cv_ncursesw_lib" |
| 1140 |
-+ CURSES_CPPFLAGS="$pkg_cv__ax_cv_ncursesw_cppflags" |
| 1141 |
-+ AC_DEFINE([HAVE_NCURSESW], [1], [Define to 1 if the NcursesW library is present]) |
| 1142 |
-+ AC_DEFINE([HAVE_CURSES], [1], [Define to 1 if a SysV or X/Open compatible Curses library is present]) |
| 1143 |
-+ |
| 1144 |
-+ AC_CACHE_CHECK([for working ncursesw/curses.h], [ax_cv_header_ncursesw_curses_h], [ |
| 1145 |
-+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ |
| 1146 |
-+ @%:@define _XOPEN_SOURCE_EXTENDED 1 |
| 1147 |
-+ @%:@include <ncursesw/curses.h> |
| 1148 |
-+ ]], [[ |
| 1149 |
-+ chtype a = A_BOLD; |
| 1150 |
-+ int b = KEY_LEFT; |
| 1151 |
-+ chtype c = COLOR_PAIR(1) & A_COLOR; |
| 1152 |
-+ attr_t d = WA_NORMAL; |
| 1153 |
-+ cchar_t e; |
| 1154 |
-+ wint_t f; |
| 1155 |
-+ int g = getattrs(stdscr); |
| 1156 |
-+ int h = getcurx(stdscr) + getmaxx(stdscr); |
| 1157 |
-+ initscr(); |
| 1158 |
-+ init_pair(1, COLOR_WHITE, COLOR_RED); |
| 1159 |
-+ wattr_set(stdscr, d, 0, NULL); |
| 1160 |
-+ wget_wch(stdscr, &f); |
| 1161 |
-+ ]])], |
| 1162 |
-+ [ax_cv_header_ncursesw_curses_h=yes], |
| 1163 |
-+ [ax_cv_header_ncursesw_curses_h=no]) |
| 1164 |
-+ ]) |
| 1165 |
-+ AS_IF([test "x$ax_cv_header_ncursesw_curses_h" = xyes], [ |
| 1166 |
-+ ax_cv_curses_enhanced=yes |
| 1167 |
-+ ax_cv_curses_color=yes |
| 1168 |
-+ ax_cv_curses_obsolete=yes |
| 1169 |
-+ AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions]) |
| 1170 |
-+ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) |
| 1171 |
-+ AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features]) |
| 1172 |
-+ AC_DEFINE([HAVE_NCURSESW_CURSES_H], [1], [Define to 1 if <ncursesw/curses.h> is present]) |
| 1173 |
-+ ]) |
| 1174 |
-+ |
| 1175 |
-+ AC_CACHE_CHECK([for working ncursesw.h], [ax_cv_header_ncursesw_h], [ |
| 1176 |
-+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ |
| 1177 |
-+ @%:@define _XOPEN_SOURCE_EXTENDED 1 |
| 1178 |
-+ @%:@include <ncursesw.h> |
| 1179 |
-+ ]], [[ |
| 1180 |
-+ chtype a = A_BOLD; |
| 1181 |
-+ int b = KEY_LEFT; |
| 1182 |
-+ chtype c = COLOR_PAIR(1) & A_COLOR; |
| 1183 |
-+ attr_t d = WA_NORMAL; |
| 1184 |
-+ cchar_t e; |
| 1185 |
-+ wint_t f; |
| 1186 |
-+ int g = getattrs(stdscr); |
| 1187 |
-+ int h = getcurx(stdscr) + getmaxx(stdscr); |
| 1188 |
-+ initscr(); |
| 1189 |
-+ init_pair(1, COLOR_WHITE, COLOR_RED); |
| 1190 |
-+ wattr_set(stdscr, d, 0, NULL); |
| 1191 |
-+ wget_wch(stdscr, &f); |
| 1192 |
-+ ]])], |
| 1193 |
-+ [ax_cv_header_ncursesw_h=yes], |
| 1194 |
-+ [ax_cv_header_ncursesw_h=no]) |
| 1195 |
-+ ]) |
| 1196 |
-+ AS_IF([test "x$ax_cv_header_ncursesw_h" = xyes], [ |
| 1197 |
-+ ax_cv_curses_enhanced=yes |
| 1198 |
-+ ax_cv_curses_color=yes |
| 1199 |
-+ ax_cv_curses_obsolete=yes |
| 1200 |
-+ AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions]) |
| 1201 |
-+ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) |
| 1202 |
-+ AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features]) |
| 1203 |
-+ AC_DEFINE([HAVE_NCURSESW_H], [1], [Define to 1 if <ncursesw.h> is present]) |
| 1204 |
-+ ]) |
| 1205 |
-+ |
| 1206 |
-+ AC_CACHE_CHECK([for working ncurses.h], [ax_cv_header_ncurses_h_with_ncursesw], [ |
| 1207 |
-+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ |
| 1208 |
-+ @%:@define _XOPEN_SOURCE_EXTENDED 1 |
| 1209 |
-+ @%:@include <ncurses.h> |
| 1210 |
-+ ]], [[ |
| 1211 |
-+ chtype a = A_BOLD; |
| 1212 |
-+ int b = KEY_LEFT; |
| 1213 |
-+ chtype c = COLOR_PAIR(1) & A_COLOR; |
| 1214 |
-+ attr_t d = WA_NORMAL; |
| 1215 |
-+ cchar_t e; |
| 1216 |
-+ wint_t f; |
| 1217 |
-+ int g = getattrs(stdscr); |
| 1218 |
-+ int h = getcurx(stdscr) + getmaxx(stdscr); |
| 1219 |
-+ initscr(); |
| 1220 |
-+ init_pair(1, COLOR_WHITE, COLOR_RED); |
| 1221 |
-+ wattr_set(stdscr, d, 0, NULL); |
| 1222 |
-+ wget_wch(stdscr, &f); |
| 1223 |
-+ ]])], |
| 1224 |
-+ [ax_cv_header_ncurses_h_with_ncursesw=yes], |
| 1225 |
-+ [ax_cv_header_ncurses_h_with_ncursesw=no]) |
| 1226 |
-+ ]) |
| 1227 |
-+ AS_IF([test "x$ax_cv_header_ncurses_h_with_ncursesw" = xyes], [ |
| 1228 |
-+ ax_cv_curses_enhanced=yes |
| 1229 |
-+ ax_cv_curses_color=yes |
| 1230 |
-+ ax_cv_curses_obsolete=yes |
| 1231 |
-+ AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions]) |
| 1232 |
-+ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) |
| 1233 |
-+ AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features]) |
| 1234 |
-+ AC_DEFINE([HAVE_NCURSES_H], [1], [Define to 1 if <ncurses.h> is present]) |
| 1235 |
-+ ]) |
| 1236 |
-+ |
| 1237 |
-+ AS_IF([test "x$ax_cv_header_ncursesw_curses_h" = xno && test "x$ax_cv_header_ncursesw_h" = xno && test "x$ax_cv_header_ncurses_h_with_ncursesw" = xno], [ |
| 1238 |
-+ AC_MSG_WARN([could not find a working ncursesw/curses.h, ncursesw.h or ncurses.h]) |
| 1239 |
-+ ]) |
| 1240 |
-+ ]) |
| 1241 |
-+ ]) |
| 1242 |
-+ unset pkg_cv__ax_cv_ncursesw_lib |
| 1243 |
-+ unset pkg_cv__ax_cv_ncursesw_cppflags |
| 1244 |
-+ |
| 1245 |
-+ # Test for Ncurses |
| 1246 |
-+ AS_IF([test "x$CURSES_LIB" = x && test "x$with_ncurses" != xno && test "x$ax_cv_curses_which" = xno], [ |
| 1247 |
-+ _FIND_CURSES_FLAGS([ncurses]) |
| 1248 |
-+ |
| 1249 |
-+ AS_IF([test "x$ax_cv_ncurses" = xno && test "x$with_ncurses" = xyes], [ |
| 1250 |
-+ AC_MSG_ERROR([--with-ncurses specified but could not find Ncurses library]) |
| 1251 |
-+ ]) |
| 1252 |
-+ |
| 1253 |
-+ AS_IF([test "x$ax_cv_ncurses" = xyes], [ |
| 1254 |
-+ ax_cv_curses=yes |
| 1255 |
-+ ax_cv_curses_which=ncurses |
| 1256 |
-+ CURSES_LIB="$pkg_cv__ax_cv_ncurses_lib" |
| 1257 |
-+ CURSES_CPPFLAGS="$pkg_cv__ax_cv_ncurses_cppflags" |
| 1258 |
-+ AC_DEFINE([HAVE_NCURSES], [1], [Define to 1 if the Ncurses library is present]) |
| 1259 |
-+ AC_DEFINE([HAVE_CURSES], [1], [Define to 1 if a SysV or X/Open compatible Curses library is present]) |
| 1260 |
-+ |
| 1261 |
-+ AC_CACHE_CHECK([for working ncurses/curses.h], [ax_cv_header_ncurses_curses_h], [ |
| 1262 |
-+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ |
| 1263 |
-+ @%:@include <ncurses/curses.h> |
| 1264 |
-+ ]], [[ |
| 1265 |
-+ chtype a = A_BOLD; |
| 1266 |
-+ int b = KEY_LEFT; |
| 1267 |
-+ chtype c = COLOR_PAIR(1) & A_COLOR; |
| 1268 |
-+ int g = getattrs(stdscr); |
| 1269 |
-+ int h = getcurx(stdscr) + getmaxx(stdscr); |
| 1270 |
-+ initscr(); |
| 1271 |
-+ init_pair(1, COLOR_WHITE, COLOR_RED); |
| 1272 |
-+ ]])], |
| 1273 |
-+ [ax_cv_header_ncurses_curses_h=yes], |
| 1274 |
-+ [ax_cv_header_ncurses_curses_h=no]) |
| 1275 |
-+ ]) |
| 1276 |
-+ AS_IF([test "x$ax_cv_header_ncurses_curses_h" = xyes], [ |
| 1277 |
-+ ax_cv_curses_color=yes |
| 1278 |
-+ ax_cv_curses_obsolete=yes |
| 1279 |
-+ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) |
| 1280 |
-+ AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features]) |
| 1281 |
-+ AC_DEFINE([HAVE_NCURSES_CURSES_H], [1], [Define to 1 if <ncurses/curses.h> is present]) |
| 1282 |
-+ ]) |
| 1283 |
-+ |
| 1284 |
-+ AC_CACHE_CHECK([for working ncurses.h], [ax_cv_header_ncurses_h], [ |
| 1285 |
-+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ |
| 1286 |
-+ @%:@include <ncurses.h> |
| 1287 |
-+ ]], [[ |
| 1288 |
-+ chtype a = A_BOLD; |
| 1289 |
-+ int b = KEY_LEFT; |
| 1290 |
-+ chtype c = COLOR_PAIR(1) & A_COLOR; |
| 1291 |
-+ int g = getattrs(stdscr); |
| 1292 |
-+ int h = getcurx(stdscr) + getmaxx(stdscr); |
| 1293 |
-+ initscr(); |
| 1294 |
-+ init_pair(1, COLOR_WHITE, COLOR_RED); |
| 1295 |
-+ ]])], |
| 1296 |
-+ [ax_cv_header_ncurses_h=yes], |
| 1297 |
-+ [ax_cv_header_ncurses_h=no]) |
| 1298 |
-+ ]) |
| 1299 |
-+ AS_IF([test "x$ax_cv_header_ncurses_h" = xyes], [ |
| 1300 |
-+ ax_cv_curses_color=yes |
| 1301 |
-+ ax_cv_curses_obsolete=yes |
| 1302 |
-+ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) |
| 1303 |
-+ AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features]) |
| 1304 |
-+ AC_DEFINE([HAVE_NCURSES_H], [1], [Define to 1 if <ncurses.h> is present]) |
| 1305 |
-+ ]) |
| 1306 |
-+ |
| 1307 |
-+ AS_IF([test "x$ax_cv_header_ncurses_curses_h" = xno && test "x$ax_cv_header_ncurses_h" = xno], [ |
| 1308 |
-+ AC_MSG_WARN([could not find a working ncurses/curses.h or ncurses.h]) |
| 1309 |
-+ ]) |
| 1310 |
-+ ]) |
| 1311 |
-+ ]) |
| 1312 |
-+ unset pkg_cv__ax_cv_ncurses_lib |
| 1313 |
-+ unset pkg_cv__ax_cv_ncurses_cppflags |
| 1314 |
-+ |
| 1315 |
-+ # Test for plain Curses (or if CURSES_LIB was set by user) |
| 1316 |
-+ AS_IF([test "x$with_plaincurses" != xno && test "x$ax_cv_curses_which" = xno], [ |
| 1317 |
-+ AS_IF([test "x$CURSES_LIB" != x], [ |
| 1318 |
-+ LIBS="$ax_saved_LIBS $CURSES_LIB" |
| 1319 |
-+ ], [ |
| 1320 |
-+ LIBS="$ax_saved_LIBS -lcurses" |
| 1321 |
-+ ]) |
| 1322 |
-+ |
| 1323 |
-+ AC_CACHE_CHECK([for Curses library], [ax_cv_plaincurses], [ |
| 1324 |
-+ AC_LINK_IFELSE([AC_LANG_CALL([], [initscr])], |
| 1325 |
-+ [ax_cv_plaincurses=yes], [ax_cv_plaincurses=no]) |
| 1326 |
-+ ]) |
| 1327 |
-+ |
| 1328 |
-+ AS_IF([test "x$ax_cv_plaincurses" = xyes], [ |
| 1329 |
-+ ax_cv_curses=yes |
| 1330 |
-+ ax_cv_curses_which=plaincurses |
| 1331 |
-+ AS_IF([test "x$CURSES_LIB" = x], [ |
| 1332 |
-+ CURSES_LIB="-lcurses" |
| 1333 |
-+ ]) |
| 1334 |
-+ AC_DEFINE([HAVE_CURSES], [1], [Define to 1 if a SysV or X/Open compatible Curses library is present]) |
| 1335 |
-+ |
| 1336 |
-+ # Check for base conformance (and header file) |
| 1337 |
-+ |
| 1338 |
-+ AC_CACHE_CHECK([for working curses.h], [ax_cv_header_curses_h], [ |
| 1339 |
-+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ |
| 1340 |
-+ @%:@include <curses.h> |
| 1341 |
-+ ]], [[ |
| 1342 |
-+ chtype a = A_BOLD; |
| 1343 |
-+ int b = KEY_LEFT; |
| 1344 |
-+ initscr(); |
| 1345 |
-+ ]])], |
| 1346 |
-+ [ax_cv_header_curses_h=yes], |
| 1347 |
-+ [ax_cv_header_curses_h=no]) |
| 1348 |
-+ ]) |
| 1349 |
-+ AS_IF([test "x$ax_cv_header_curses_h" = xyes], [ |
| 1350 |
-+ AC_DEFINE([HAVE_CURSES_H], [1], [Define to 1 if <curses.h> is present]) |
| 1351 |
-+ |
| 1352 |
-+ # Check for X/Open Enhanced conformance |
| 1353 |
-+ |
| 1354 |
-+ AC_CACHE_CHECK([for X/Open Enhanced Curses conformance], [ax_cv_plaincurses_enhanced], [ |
| 1355 |
-+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ |
| 1356 |
-+ @%:@define _XOPEN_SOURCE_EXTENDED 1 |
| 1357 |
-+ @%:@include <curses.h> |
| 1358 |
-+ @%:@ifndef _XOPEN_CURSES |
| 1359 |
-+ @%:@error "this Curses library is not enhanced" |
| 1360 |
-+ "this Curses library is not enhanced" |
| 1361 |
-+ @%:@endif |
| 1362 |
-+ ]], [[ |
| 1363 |
-+ chtype a = A_BOLD; |
| 1364 |
-+ int b = KEY_LEFT; |
| 1365 |
-+ chtype c = COLOR_PAIR(1) & A_COLOR; |
| 1366 |
-+ attr_t d = WA_NORMAL; |
| 1367 |
-+ cchar_t e; |
| 1368 |
-+ wint_t f; |
| 1369 |
-+ initscr(); |
| 1370 |
-+ init_pair(1, COLOR_WHITE, COLOR_RED); |
| 1371 |
-+ wattr_set(stdscr, d, 0, NULL); |
| 1372 |
-+ wget_wch(stdscr, &f); |
| 1373 |
-+ ]])], |
| 1374 |
-+ [ax_cv_plaincurses_enhanced=yes], |
| 1375 |
-+ [ax_cv_plaincurses_enhanced=no]) |
| 1376 |
-+ ]) |
| 1377 |
-+ AS_IF([test "x$ax_cv_plaincurses_enhanced" = xyes], [ |
| 1378 |
-+ ax_cv_curses_enhanced=yes |
| 1379 |
-+ ax_cv_curses_color=yes |
| 1380 |
-+ AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions]) |
| 1381 |
-+ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) |
| 1382 |
-+ ]) |
| 1383 |
-+ |
| 1384 |
-+ # Check for color functions |
| 1385 |
-+ |
| 1386 |
-+ AC_CACHE_CHECK([for Curses color functions], [ax_cv_plaincurses_color], [ |
| 1387 |
-+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ |
| 1388 |
-+ @%:@define _XOPEN_SOURCE_EXTENDED 1 |
| 1389 |
-+ @%:@include <curses.h> |
| 1390 |
-+ ]], [[ |
| 1391 |
-+ chtype a = A_BOLD; |
| 1392 |
-+ int b = KEY_LEFT; |
| 1393 |
-+ chtype c = COLOR_PAIR(1) & A_COLOR; |
| 1394 |
-+ initscr(); |
| 1395 |
-+ init_pair(1, COLOR_WHITE, COLOR_RED); |
| 1396 |
-+ ]])], |
| 1397 |
-+ [ax_cv_plaincurses_color=yes], |
| 1398 |
-+ [ax_cv_plaincurses_color=no]) |
| 1399 |
-+ ]) |
| 1400 |
-+ AS_IF([test "x$ax_cv_plaincurses_color" = xyes], [ |
| 1401 |
-+ ax_cv_curses_color=yes |
| 1402 |
-+ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) |
| 1403 |
-+ ]) |
| 1404 |
-+ |
| 1405 |
-+ # Check for obsolete functions |
| 1406 |
-+ |
| 1407 |
-+ AC_CACHE_CHECK([for obsolete Curses functions], [ax_cv_plaincurses_obsolete], [ |
| 1408 |
-+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ |
| 1409 |
-+ @%:@include <curses.h> |
| 1410 |
-+ ]], [[ |
| 1411 |
-+ chtype a = A_BOLD; |
| 1412 |
-+ int b = KEY_LEFT; |
| 1413 |
-+ int g = getattrs(stdscr); |
| 1414 |
-+ int h = getcurx(stdscr) + getmaxx(stdscr); |
| 1415 |
-+ initscr(); |
| 1416 |
-+ ]])], |
| 1417 |
-+ [ax_cv_plaincurses_obsolete=yes], |
| 1418 |
-+ [ax_cv_plaincurses_obsolete=no]) |
| 1419 |
-+ ]) |
| 1420 |
-+ AS_IF([test "x$ax_cv_plaincurses_obsolete" = xyes], [ |
| 1421 |
-+ ax_cv_curses_obsolete=yes |
| 1422 |
-+ AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features]) |
| 1423 |
-+ ]) |
| 1424 |
-+ ]) |
| 1425 |
-+ |
| 1426 |
-+ AS_IF([test "x$ax_cv_header_curses_h" = xno], [ |
| 1427 |
-+ AC_MSG_WARN([could not find a working curses.h]) |
| 1428 |
-+ ]) |
| 1429 |
-+ ]) |
| 1430 |
-+ ]) |
| 1431 |
-+ |
| 1432 |
-+ AS_IF([test "x$ax_cv_curses" != xyes], [ax_cv_curses=no]) |
| 1433 |
-+ AS_IF([test "x$ax_cv_curses_enhanced" != xyes], [ax_cv_curses_enhanced=no]) |
| 1434 |
-+ AS_IF([test "x$ax_cv_curses_color" != xyes], [ax_cv_curses_color=no]) |
| 1435 |
-+ AS_IF([test "x$ax_cv_curses_obsolete" != xyes], [ax_cv_curses_obsolete=no]) |
| 1436 |
-+ |
| 1437 |
-+ LIBS=$ax_saved_LIBS |
| 1438 |
-+ CPPFLAGS=$ax_saved_CPPFLAGS |
| 1439 |
-+ |
| 1440 |
-+ unset ax_saved_LIBS |
| 1441 |
-+ unset ax_saved_CPPFLAGS |
| 1442 |
-+])dnl |
| 1443 |
---- samtools-1.3/m4/ax_with_htslib.m4 |
| 1444 |
-+++ samtools-1.3/m4/ax_with_htslib.m4 |
| 1445 |
-@@ -0,0 +1,140 @@ |
| 1446 |
-+# =========================================================================== |
| 1447 |
-+# http://www.gnu.org/software/autoconf-archive/ax_with_htslib.html |
| 1448 |
-+# =========================================================================== |
| 1449 |
-+# |
| 1450 |
-+# SYNOPSIS |
| 1451 |
-+# |
| 1452 |
-+# AX_WITH_HTSLIB |
| 1453 |
-+# |
| 1454 |
-+# DESCRIPTION |
| 1455 |
-+# |
| 1456 |
-+# This macro checks whether HTSlib <http://www.htslib.org/> is installed |
| 1457 |
-+# or nearby, and adds a --with-htslib=DIR option to the configure script |
| 1458 |
-+# for specifying the location. It locates either an installation prefix |
| 1459 |
-+# (with 'include' and 'lib' subdirectories) or an HTSlib source tree, as |
| 1460 |
-+# HTSlib is fast-moving and users may wish to use an in-development tree. |
| 1461 |
-+# |
| 1462 |
-+# Different checks occur depending on the --with-htslib argument given: |
| 1463 |
-+# |
| 1464 |
-+# With --with-htslib=DIR, checks whether DIR is a source tree or contains |
| 1465 |
-+# a working installation. |
| 1466 |
-+# By default, searches for a source tree (with a name matching htslib*) |
| 1467 |
-+# within or alongside $srcdir. Produces AC_MSG_ERROR if there are |
| 1468 |
-+# several equally-likely candidates. If there are none, checks for |
| 1469 |
-+# a working default installation. |
| 1470 |
-+# With --with-htslib=system, checks for a working default installation. |
| 1471 |
-+# |
| 1472 |
-+# If a source tree is found or specified, it is added to AC_CONFIG_SUBDIRS |
| 1473 |
-+# (which unfortunately may cause a "you should use literals" warning when |
| 1474 |
-+# autoconf is run). |
| 1475 |
-+# |
| 1476 |
-+# The following output variables are set by this macro: |
| 1477 |
-+# |
| 1478 |
-+# HTSDIR Directory containing HTSlib source tree |
| 1479 |
-+# HTSLIB_CPPFLAGS Preprocessor flags for compiling with HTSlib |
| 1480 |
-+# HTSLIB_LDFLAGS Linker flags for linking with HTSlib |
| 1481 |
-+# |
| 1482 |
-+# The following shell variables may be defined: |
| 1483 |
-+# |
| 1484 |
-+# ax_cv_htslib Set to "yes" if HTSlib was found |
| 1485 |
-+# ax_cv_htslib_which Set to "source", "install", or "none" |
| 1486 |
-+# |
| 1487 |
-+# LICENSE |
| 1488 |
-+# |
| 1489 |
-+# Copyright (C) 2015 Genome Research Ltd |
| 1490 |
-+# |
| 1491 |
-+# Copying and distribution of this file, with or without modification, are |
| 1492 |
-+# permitted in any medium without royalty provided the copyright notice |
| 1493 |
-+# and this notice are preserved. This file is offered as-is, without any |
| 1494 |
-+# warranty. |
| 1495 |
-+ |
| 1496 |
-+#serial 1 |
| 1497 |
-+ |
| 1498 |
-+AC_DEFUN([AX_WITH_HTSLIB], |
| 1499 |
-+[AC_ARG_WITH([htslib], |
| 1500 |
-+ [AS_HELP_STRING([--with-htslib=DIR], |
| 1501 |
-+ [use the HTSlib source tree or installation in DIR]) |
| 1502 |
-+dnl Not indented, to avoid extra whitespace outwith AS_HELP_STRING() |
| 1503 |
-+AS_HELP_STRING([--with-htslib=system], |
| 1504 |
-+ [use only a system HTSlib installation])], |
| 1505 |
-+ [], [with_htslib=search]) |
| 1506 |
-+ |
| 1507 |
-+case $with_htslib in |
| 1508 |
-+yes|search) |
| 1509 |
-+ AC_MSG_CHECKING([location of HTSlib source tree]) |
| 1510 |
-+ case $srcdir in |
| 1511 |
-+ .) srcp= ;; |
| 1512 |
-+ *) srcp=$srcdir/ ;; |
| 1513 |
-+ esac |
| 1514 |
-+ found= |
| 1515 |
-+ for dir in ${srcp}htslib* -- ${srcp}../htslib -- ${srcp}../htslib* |
| 1516 |
-+ do |
| 1517 |
-+ if test "$dir" = "--"; then |
| 1518 |
-+ test -n "$found" && break |
| 1519 |
-+ elif test -f "$dir/hts.c" && test -f "$dir/htslib/hts.h"; then |
| 1520 |
-+ found="${found}1" |
| 1521 |
-+ HTSDIR=$dir |
| 1522 |
-+ fi |
| 1523 |
-+ done |
| 1524 |
-+ if test -z "$found"; then |
| 1525 |
-+ AC_MSG_RESULT([none found]) |
| 1526 |
-+ ax_cv_htslib_which=system |
| 1527 |
-+ elif test "$found" = 1; then |
| 1528 |
-+ AC_MSG_RESULT([$HTSDIR]) |
| 1529 |
-+ ax_cv_htslib_which=source |
| 1530 |
-+ else |
| 1531 |
-+ AC_MSG_RESULT([several directories found]) |
| 1532 |
-+ AC_MSG_ERROR([use --with-htslib=DIR to select which HTSlib to use]) |
| 1533 |
-+ fi |
| 1534 |
-+ ;; |
| 1535 |
-+no) ax_cv_htslib_which=none ;; |
| 1536 |
-+system) ax_cv_htslib_which=system ;; |
| 1537 |
-+*) |
| 1538 |
-+ HTSDIR=$with_htslib |
| 1539 |
-+ if test -f "$HTSDIR/hts.c" && test -f "$HTSDIR/htslib/hts.h"; then |
| 1540 |
-+ ax_cv_htslib_which=source |
| 1541 |
-+ else |
| 1542 |
-+ ax_cv_htslib_which=install |
| 1543 |
-+ fi |
| 1544 |
-+ ;; |
| 1545 |
-+esac |
| 1546 |
-+ |
| 1547 |
-+case $ax_cv_htslib_which in |
| 1548 |
-+source) |
| 1549 |
-+ ax_cv_htslib=yes |
| 1550 |
-+ HTSLIB_CPPFLAGS="-I$HTSDIR" |
| 1551 |
-+ HTSLIB_LDFLAGS="-L$HTSDIR" |
| 1552 |
-+ # We can't use a literal, because $HTSDIR is user-provided and variable |
| 1553 |
-+ AC_CONFIG_SUBDIRS($HTSDIR) |
| 1554 |
-+ ;; |
| 1555 |
-+system) |
| 1556 |
-+ AC_CHECK_HEADER([htslib/sam.h], |
| 1557 |
-+ [AC_CHECK_LIB(hts, hts_version, [ax_cv_htslib=yes], [ax_cv_htslib=no])], |
| 1558 |
-+ [ax_cv_htslib=no], [;]) |
| 1559 |
-+ ax_cv_htslib_which=install |
| 1560 |
-+ HTSDIR= |
| 1561 |
-+ HTSLIB_CPPFLAGS= |
| 1562 |
-+ HTSLIB_LDFLAGS= |
| 1563 |
-+ ;; |
| 1564 |
-+install) |
| 1565 |
-+ ax_saved_CPPFLAGS=$CPPFLAGS |
| 1566 |
-+ ax_saved_LDFLAGS=$LDFLAGS |
| 1567 |
-+ HTSLIB_CPPFLAGS="-I$HTSDIR/include" |
| 1568 |
-+ HTSLIB_LDFLAGS="-L$HTSDIR/lib" |
| 1569 |
-+ CPPFLAGS="$CPPFLAGS $HTSLIB_CPPFLAGS" |
| 1570 |
-+ LDFLAGS="$LDFLAGS $HTSLIB_LDFLAGS" |
| 1571 |
-+ AC_CHECK_HEADER([htslib/sam.h], |
| 1572 |
-+ [AC_CHECK_LIB(hts, hts_version, [ax_cv_htslib=yes], [ax_cv_htslib=no])], |
| 1573 |
-+ [ax_cv_htslib=no], [;]) |
| 1574 |
-+ HTSDIR= |
| 1575 |
-+ CPPFLAGS=$ax_saved_CPPFLAGS |
| 1576 |
-+ LDFLAGS=$ax_saved_LDFLAGS |
| 1577 |
-+ ;; |
| 1578 |
-+none) |
| 1579 |
-+ ax_cv_htslib=no |
| 1580 |
-+ ;; |
| 1581 |
-+esac |
| 1582 |
-+ |
| 1583 |
-+AC_SUBST([HTSDIR]) |
| 1584 |
-+AC_SUBST([HTSLIB_CPPFLAGS]) |
| 1585 |
-+AC_SUBST([HTSLIB_LDFLAGS])]) |
| 1586 |
|
| 1587 |
diff --git a/sci-biology/samtools/samtools-0.1.12.ebuild b/sci-biology/samtools/samtools-0.1.12.ebuild |
| 1588 |
deleted file mode 100644 |
| 1589 |
index d32746ae2ba..00000000000 |
| 1590 |
--- a/sci-biology/samtools/samtools-0.1.12.ebuild |
| 1591 |
+++ /dev/null |
| 1592 |
@@ -1,30 +0,0 @@ |
| 1593 |
-# Copyright 1999-2016 Gentoo Foundation |
| 1594 |
-# Distributed under the terms of the GNU General Public License v2 |
| 1595 |
- |
| 1596 |
-EAPI=2 |
| 1597 |
- |
| 1598 |
-MY_P="${P}a" |
| 1599 |
- |
| 1600 |
-DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats" |
| 1601 |
-HOMEPAGE="http://samtools.sourceforge.net/" |
| 1602 |
-SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.bz2" |
| 1603 |
- |
| 1604 |
-LICENSE="MIT" |
| 1605 |
-SLOT="0" |
| 1606 |
-IUSE="" |
| 1607 |
-KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" |
| 1608 |
- |
| 1609 |
-S="${WORKDIR}/${MY_P}" |
| 1610 |
- |
| 1611 |
-src_prepare() { |
| 1612 |
- sed -i 's/^CFLAGS=/CFLAGS+=/' "${S}"/{Makefile,misc/Makefile} |
| 1613 |
-} |
| 1614 |
- |
| 1615 |
-src_install() { |
| 1616 |
- dobin samtools || die |
| 1617 |
- dobin $(find misc -type f -executable) || die |
| 1618 |
- insinto /usr/share/${PN} |
| 1619 |
- doins -r examples || die |
| 1620 |
- doman ${PN}.1 || die |
| 1621 |
- dodoc AUTHORS ChangeLog NEWS |
| 1622 |
-} |
| 1623 |
|
| 1624 |
diff --git a/sci-biology/samtools/samtools-0.1.19-r2.ebuild b/sci-biology/samtools/samtools-0.1.19-r2.ebuild |
| 1625 |
deleted file mode 100644 |
| 1626 |
index a401e5f9df8..00000000000 |
| 1627 |
--- a/sci-biology/samtools/samtools-0.1.19-r2.ebuild |
| 1628 |
+++ /dev/null |
| 1629 |
@@ -1,60 +0,0 @@ |
| 1630 |
-# Copyright 1999-2017 Gentoo Foundation |
| 1631 |
-# Distributed under the terms of the GNU General Public License v2 |
| 1632 |
- |
| 1633 |
-EAPI=5 |
| 1634 |
- |
| 1635 |
-PYTHON_COMPAT=( python2_7 ) |
| 1636 |
- |
| 1637 |
-inherit eutils multilib python-r1 toolchain-funcs |
| 1638 |
- |
| 1639 |
-DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats" |
| 1640 |
-HOMEPAGE="http://samtools.sourceforge.net/" |
| 1641 |
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" |
| 1642 |
- |
| 1643 |
-LICENSE="MIT" |
| 1644 |
-SLOT="0" |
| 1645 |
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" |
| 1646 |
-IUSE="examples" |
| 1647 |
-REQUIRED_USE="${PYTHON_REQUIRED_USE}" |
| 1648 |
- |
| 1649 |
-CDEPEND="sys-libs/ncurses:0=" |
| 1650 |
-RDEPEND="${CDEPEND} |
| 1651 |
- dev-lang/lua |
| 1652 |
- dev-lang/perl |
| 1653 |
- ${PYTHON_DEPS}" |
| 1654 |
-DEPEND="${CDEPEND} |
| 1655 |
- virtual/pkgconfig" |
| 1656 |
- |
| 1657 |
-src_prepare() { |
| 1658 |
- epatch "${FILESDIR}"/${P}-buildsystem.patch |
| 1659 |
- |
| 1660 |
- sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die |
| 1661 |
- |
| 1662 |
- tc-export CC AR |
| 1663 |
-} |
| 1664 |
- |
| 1665 |
-src_compile() { |
| 1666 |
- local _ncurses="$($(tc-getPKG_CONFIG) --libs ncurses)" |
| 1667 |
- emake dylib LIBCURSES="${_ncurses}" |
| 1668 |
- emake LIBCURSES="${_ncurses}" |
| 1669 |
-} |
| 1670 |
- |
| 1671 |
-src_install() { |
| 1672 |
- dobin samtools $(find bcftools misc -type f -executable) |
| 1673 |
- |
| 1674 |
- python_replicate_script "${ED}"/usr/bin/varfilter.py |
| 1675 |
- |
| 1676 |
- dolib.so libbam$(get_libname 1) |
| 1677 |
- dosym libbam$(get_libname 1) /usr/$(get_libdir)/libbam$(get_libname) |
| 1678 |
- |
| 1679 |
- insinto /usr/include/bam |
| 1680 |
- doins *.h |
| 1681 |
- |
| 1682 |
- doman ${PN}.1 |
| 1683 |
- dodoc AUTHORS NEWS |
| 1684 |
- |
| 1685 |
- if use examples; then |
| 1686 |
- insinto /usr/share/${PN} |
| 1687 |
- doins -r examples |
| 1688 |
- fi |
| 1689 |
-} |
| 1690 |
|
| 1691 |
diff --git a/sci-biology/samtools/samtools-1.0-r1.ebuild b/sci-biology/samtools/samtools-1.0-r1.ebuild |
| 1692 |
deleted file mode 100644 |
| 1693 |
index b6e1aeb5831..00000000000 |
| 1694 |
--- a/sci-biology/samtools/samtools-1.0-r1.ebuild |
| 1695 |
+++ /dev/null |
| 1696 |
@@ -1,72 +0,0 @@ |
| 1697 |
-# Copyright 1999-2017 Gentoo Foundation |
| 1698 |
-# Distributed under the terms of the GNU General Public License v2 |
| 1699 |
- |
| 1700 |
-EAPI=5 |
| 1701 |
- |
| 1702 |
-PYTHON_COMPAT=( python2_7 ) |
| 1703 |
- |
| 1704 |
-inherit eutils multilib python-r1 toolchain-funcs |
| 1705 |
- |
| 1706 |
-DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats" |
| 1707 |
-HOMEPAGE="http://www.htslib.org/" |
| 1708 |
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" |
| 1709 |
- |
| 1710 |
-LICENSE="MIT" |
| 1711 |
-SLOT="0" |
| 1712 |
-KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~x64-macos" |
| 1713 |
-IUSE="examples" |
| 1714 |
-REQUIRED_USE="${PYTHON_REQUIRED_USE}" |
| 1715 |
- |
| 1716 |
-CDEPEND=" |
| 1717 |
- sys-libs/ncurses:0= |
| 1718 |
- sci-libs/htslib" |
| 1719 |
- |
| 1720 |
-RDEPEND="${CDEPEND} |
| 1721 |
- dev-lang/lua |
| 1722 |
- dev-lang/perl |
| 1723 |
- ${PYTHON_DEPS}" |
| 1724 |
-DEPEND="${CDEPEND} |
| 1725 |
- virtual/pkgconfig" |
| 1726 |
- |
| 1727 |
-src_prepare() { |
| 1728 |
- find htslib-1.0 -delete || die |
| 1729 |
- |
| 1730 |
- sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die |
| 1731 |
- |
| 1732 |
- epatch "${FILESDIR}"/${P}-buildsystem.patch |
| 1733 |
- |
| 1734 |
- tc-export CC AR |
| 1735 |
- |
| 1736 |
- sed \ |
| 1737 |
- -e '/htslib.mk/d' \ |
| 1738 |
- -i Makefile || die |
| 1739 |
- |
| 1740 |
-} |
| 1741 |
- |
| 1742 |
-src_compile() { |
| 1743 |
- local mymakeargs=( |
| 1744 |
- LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" |
| 1745 |
- HTSDIR="${EPREFIX}/usr/include" |
| 1746 |
- HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) |
| 1747 |
- BAMLIB="libbam.so" |
| 1748 |
- ) |
| 1749 |
- emake "${mymakeargs[@]}" |
| 1750 |
-} |
| 1751 |
- |
| 1752 |
-src_install() { |
| 1753 |
- dobin samtools $(find misc -type f -executable) |
| 1754 |
- |
| 1755 |
- python_replicate_script "${ED}"/usr/bin/varfilter.py |
| 1756 |
- dolib.so libbam.so* |
| 1757 |
- |
| 1758 |
- insinto /usr/include/bam |
| 1759 |
- doins *.h |
| 1760 |
- |
| 1761 |
- doman ${PN}.1 |
| 1762 |
- dodoc AUTHORS NEWS README |
| 1763 |
- |
| 1764 |
- if use examples; then |
| 1765 |
- insinto /usr/share/${PN} |
| 1766 |
- doins -r examples |
| 1767 |
- fi |
| 1768 |
-} |
| 1769 |
|
| 1770 |
diff --git a/sci-biology/samtools/samtools-1.0.ebuild b/sci-biology/samtools/samtools-1.0.ebuild |
| 1771 |
deleted file mode 100644 |
| 1772 |
index 0fb9d04344b..00000000000 |
| 1773 |
--- a/sci-biology/samtools/samtools-1.0.ebuild |
| 1774 |
+++ /dev/null |
| 1775 |
@@ -1,68 +0,0 @@ |
| 1776 |
-# Copyright 1999-2017 Gentoo Foundation |
| 1777 |
-# Distributed under the terms of the GNU General Public License v2 |
| 1778 |
- |
| 1779 |
-EAPI=5 |
| 1780 |
- |
| 1781 |
-PYTHON_COMPAT=( python2_7 ) |
| 1782 |
- |
| 1783 |
-inherit eutils multilib python-r1 toolchain-funcs |
| 1784 |
- |
| 1785 |
-DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats" |
| 1786 |
-HOMEPAGE="http://www.htslib.org/" |
| 1787 |
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" |
| 1788 |
- |
| 1789 |
-LICENSE="MIT" |
| 1790 |
-SLOT="0" |
| 1791 |
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" |
| 1792 |
-IUSE="examples" |
| 1793 |
-REQUIRED_USE="${PYTHON_REQUIRED_USE}" |
| 1794 |
- |
| 1795 |
-CDEPEND=" |
| 1796 |
- sys-libs/ncurses:0= |
| 1797 |
- sci-libs/htslib" |
| 1798 |
- |
| 1799 |
-RDEPEND="${CDEPEND} |
| 1800 |
- dev-lang/lua |
| 1801 |
- dev-lang/perl |
| 1802 |
- ${PYTHON_DEPS}" |
| 1803 |
-DEPEND="${CDEPEND} |
| 1804 |
- virtual/pkgconfig" |
| 1805 |
- |
| 1806 |
-src_prepare() { |
| 1807 |
- find htslib-1.0 -delete || die |
| 1808 |
- |
| 1809 |
- sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die |
| 1810 |
- |
| 1811 |
- tc-export CC AR |
| 1812 |
- |
| 1813 |
- sed \ |
| 1814 |
- -e '/htslib.mk/d' \ |
| 1815 |
- -i Makefile || die |
| 1816 |
- |
| 1817 |
-} |
| 1818 |
- |
| 1819 |
-src_compile() { |
| 1820 |
- local mymakeargs=( |
| 1821 |
- LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" |
| 1822 |
- CC="$(tc-getCC)" |
| 1823 |
- LDFLAGS="${LDFLAGS}" |
| 1824 |
- CFLAGS="${CFLAGS}" |
| 1825 |
- HTSDIR="${EPREFIX}/usr/include" |
| 1826 |
- HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) |
| 1827 |
- ) |
| 1828 |
- emake "${mymakeargs[@]}" |
| 1829 |
-} |
| 1830 |
- |
| 1831 |
-src_install() { |
| 1832 |
- dobin samtools $(find misc -type f -executable) |
| 1833 |
- |
| 1834 |
- python_replicate_script "${ED}"/usr/bin/varfilter.py |
| 1835 |
- |
| 1836 |
- doman ${PN}.1 |
| 1837 |
- dodoc AUTHORS NEWS README |
| 1838 |
- |
| 1839 |
- if use examples; then |
| 1840 |
- insinto /usr/share/${PN} |
| 1841 |
- doins -r examples |
| 1842 |
- fi |
| 1843 |
-} |
| 1844 |
|
| 1845 |
diff --git a/sci-biology/samtools/samtools-1.1.ebuild b/sci-biology/samtools/samtools-1.1.ebuild |
| 1846 |
deleted file mode 100644 |
| 1847 |
index ca3e4b46c22..00000000000 |
| 1848 |
--- a/sci-biology/samtools/samtools-1.1.ebuild |
| 1849 |
+++ /dev/null |
| 1850 |
@@ -1,82 +0,0 @@ |
| 1851 |
-# Copyright 1999-2017 Gentoo Foundation |
| 1852 |
-# Distributed under the terms of the GNU General Public License v2 |
| 1853 |
- |
| 1854 |
-EAPI=5 |
| 1855 |
- |
| 1856 |
-PYTHON_COMPAT=( python2_7 ) |
| 1857 |
- |
| 1858 |
-inherit eutils multilib python-r1 toolchain-funcs |
| 1859 |
- |
| 1860 |
-DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats" |
| 1861 |
-HOMEPAGE="http://www.htslib.org/" |
| 1862 |
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" |
| 1863 |
- |
| 1864 |
-LICENSE="MIT" |
| 1865 |
-SLOT="0" |
| 1866 |
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" |
| 1867 |
-IUSE="examples" |
| 1868 |
-REQUIRED_USE="${PYTHON_REQUIRED_USE}" |
| 1869 |
- |
| 1870 |
-CDEPEND=" |
| 1871 |
- sys-libs/ncurses:0= |
| 1872 |
- ~sci-libs/htslib-${PV}" |
| 1873 |
- |
| 1874 |
-RDEPEND="${CDEPEND} |
| 1875 |
- dev-lang/lua |
| 1876 |
- dev-lang/perl |
| 1877 |
- ${PYTHON_DEPS}" |
| 1878 |
-DEPEND="${CDEPEND} |
| 1879 |
- virtual/pkgconfig" |
| 1880 |
- |
| 1881 |
-src_prepare() { |
| 1882 |
- find htslib-* -delete || die |
| 1883 |
- |
| 1884 |
- sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die |
| 1885 |
- |
| 1886 |
- epatch "${FILESDIR}"/${P}-buildsystem.patch |
| 1887 |
- |
| 1888 |
- tc-export CC AR |
| 1889 |
- |
| 1890 |
- sed \ |
| 1891 |
- -e '/htslib.mk/d' \ |
| 1892 |
- -i Makefile || die |
| 1893 |
- |
| 1894 |
-} |
| 1895 |
- |
| 1896 |
-src_compile() { |
| 1897 |
- local mymakeargs=( |
| 1898 |
- LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" |
| 1899 |
- HTSDIR="${EPREFIX}/usr/include" |
| 1900 |
- HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) |
| 1901 |
- BAMLIB="libbam.so" |
| 1902 |
- ) |
| 1903 |
- emake "${mymakeargs[@]}" |
| 1904 |
-} |
| 1905 |
- |
| 1906 |
-src_test() { |
| 1907 |
- local mymakeargs=( |
| 1908 |
- LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" |
| 1909 |
- HTSDIR="${EPREFIX}/usr/include" |
| 1910 |
- HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) |
| 1911 |
- BAMLIB="libbam.so" |
| 1912 |
- ) |
| 1913 |
- emake "${mymakeargs[@]}" test |
| 1914 |
-} |
| 1915 |
- |
| 1916 |
-src_install() { |
| 1917 |
- dobin samtools $(find misc -type f -executable) |
| 1918 |
- |
| 1919 |
- python_replicate_script "${ED}"/usr/bin/varfilter.py |
| 1920 |
- dolib.so libbam.so* |
| 1921 |
- |
| 1922 |
- insinto /usr/include/bam |
| 1923 |
- doins *.h |
| 1924 |
- |
| 1925 |
- doman ${PN}.1 |
| 1926 |
- dodoc AUTHORS NEWS README |
| 1927 |
- |
| 1928 |
- if use examples; then |
| 1929 |
- insinto /usr/share/${PN} |
| 1930 |
- doins -r examples |
| 1931 |
- fi |
| 1932 |
-} |
| 1933 |
|
| 1934 |
diff --git a/sci-biology/samtools/samtools-1.2.ebuild b/sci-biology/samtools/samtools-1.2.ebuild |
| 1935 |
deleted file mode 100644 |
| 1936 |
index 75dfbfae1f2..00000000000 |
| 1937 |
--- a/sci-biology/samtools/samtools-1.2.ebuild |
| 1938 |
+++ /dev/null |
| 1939 |
@@ -1,82 +0,0 @@ |
| 1940 |
-# Copyright 1999-2017 Gentoo Foundation |
| 1941 |
-# Distributed under the terms of the GNU General Public License v2 |
| 1942 |
- |
| 1943 |
-EAPI=5 |
| 1944 |
- |
| 1945 |
-PYTHON_COMPAT=( python2_7 ) |
| 1946 |
- |
| 1947 |
-inherit eutils multilib python-r1 toolchain-funcs |
| 1948 |
- |
| 1949 |
-DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats" |
| 1950 |
-HOMEPAGE="http://www.htslib.org/" |
| 1951 |
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" |
| 1952 |
- |
| 1953 |
-LICENSE="MIT" |
| 1954 |
-SLOT="0" |
| 1955 |
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" |
| 1956 |
-IUSE="examples" |
| 1957 |
-REQUIRED_USE="${PYTHON_REQUIRED_USE}" |
| 1958 |
- |
| 1959 |
-CDEPEND=" |
| 1960 |
- sys-libs/ncurses:0= |
| 1961 |
- >=sci-libs/htslib-${PV}" |
| 1962 |
- |
| 1963 |
-RDEPEND="${CDEPEND} |
| 1964 |
- dev-lang/lua |
| 1965 |
- dev-lang/perl |
| 1966 |
- ${PYTHON_DEPS}" |
| 1967 |
-DEPEND="${CDEPEND} |
| 1968 |
- virtual/pkgconfig" |
| 1969 |
- |
| 1970 |
-src_prepare() { |
| 1971 |
- find htslib-* -delete || die |
| 1972 |
- |
| 1973 |
- sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die |
| 1974 |
- |
| 1975 |
- epatch "${FILESDIR}"/${P}-buildsystem.patch |
| 1976 |
- |
| 1977 |
- tc-export CC AR |
| 1978 |
- |
| 1979 |
- sed \ |
| 1980 |
- -e '/htslib.mk/d' \ |
| 1981 |
- -i Makefile || die |
| 1982 |
- |
| 1983 |
-} |
| 1984 |
- |
| 1985 |
-src_compile() { |
| 1986 |
- local mymakeargs=( |
| 1987 |
- LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" |
| 1988 |
- HTSDIR="${EPREFIX}/usr/include" |
| 1989 |
- HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) |
| 1990 |
- BAMLIB="libbam.so" |
| 1991 |
- ) |
| 1992 |
- emake "${mymakeargs[@]}" |
| 1993 |
-} |
| 1994 |
- |
| 1995 |
-src_test() { |
| 1996 |
- local mymakeargs=( |
| 1997 |
- LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" |
| 1998 |
- HTSDIR="${EPREFIX}/usr/include" |
| 1999 |
- HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) |
| 2000 |
- BAMLIB="libbam.so" |
| 2001 |
- ) |
| 2002 |
- LD_LIBRARY_PATH="${S}" emake "${mymakeargs[@]}" test |
| 2003 |
-} |
| 2004 |
- |
| 2005 |
-src_install() { |
| 2006 |
- dobin samtools $(find misc -type f -executable) |
| 2007 |
- |
| 2008 |
- python_replicate_script "${ED}"/usr/bin/varfilter.py |
| 2009 |
- dolib.so libbam.so* |
| 2010 |
- |
| 2011 |
- insinto /usr/include/bam |
| 2012 |
- doins *.h |
| 2013 |
- |
| 2014 |
- doman ${PN}.1 |
| 2015 |
- dodoc AUTHORS NEWS README |
| 2016 |
- |
| 2017 |
- if use examples; then |
| 2018 |
- insinto /usr/share/${PN} |
| 2019 |
- doins -r examples |
| 2020 |
- fi |
| 2021 |
-} |
| 2022 |
|
| 2023 |
diff --git a/sci-biology/samtools/samtools-1.3-r1.ebuild b/sci-biology/samtools/samtools-1.3-r1.ebuild |
| 2024 |
deleted file mode 100644 |
| 2025 |
index 8d25bf84ad3..00000000000 |
| 2026 |
--- a/sci-biology/samtools/samtools-1.3-r1.ebuild |
| 2027 |
+++ /dev/null |
| 2028 |
@@ -1,96 +0,0 @@ |
| 2029 |
-# Copyright 1999-2017 Gentoo Foundation |
| 2030 |
-# Distributed under the terms of the GNU General Public License v2 |
| 2031 |
- |
| 2032 |
-EAPI=6 |
| 2033 |
- |
| 2034 |
-PYTHON_COMPAT=( python2_7 ) |
| 2035 |
- |
| 2036 |
-inherit autotools python-r1 toolchain-funcs |
| 2037 |
- |
| 2038 |
-DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats" |
| 2039 |
-HOMEPAGE="http://www.htslib.org/" |
| 2040 |
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" |
| 2041 |
- |
| 2042 |
-LICENSE="MIT" |
| 2043 |
-SLOT="0" |
| 2044 |
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" |
| 2045 |
-IUSE="examples" |
| 2046 |
-REQUIRED_USE="${PYTHON_REQUIRED_USE}" |
| 2047 |
- |
| 2048 |
-RDEPEND="sys-libs/ncurses:0= |
| 2049 |
- =sci-libs/htslib-${PV}* |
| 2050 |
- dev-lang/perl |
| 2051 |
- ${PYTHON_DEPS}" |
| 2052 |
-DEPEND="${RDEPEND} |
| 2053 |
- virtual/pkgconfig" |
| 2054 |
- |
| 2055 |
-PATCHES=( |
| 2056 |
- "${FILESDIR}/${P}-buildsystem.patch" |
| 2057 |
- "${FILESDIR}/${P}-ncurses.patch" |
| 2058 |
-) |
| 2059 |
- |
| 2060 |
-src_prepare() { |
| 2061 |
- default |
| 2062 |
- |
| 2063 |
- # unbundle libs |
| 2064 |
- find htslib-* -delete || die |
| 2065 |
- |
| 2066 |
- sed -i -e 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die |
| 2067 |
- sed -i -e '/htslib.mk/d' -i Makefile || die |
| 2068 |
- |
| 2069 |
- tc-export CC AR |
| 2070 |
- |
| 2071 |
- rm -f aclocal.m4 || die |
| 2072 |
- eautoreconf |
| 2073 |
-} |
| 2074 |
- |
| 2075 |
-src_compile() { |
| 2076 |
- local mymakeargs=( |
| 2077 |
- LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" |
| 2078 |
- HTSDIR="${EPREFIX}/usr/include" |
| 2079 |
- HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) |
| 2080 |
- BAMLIB="libbam.so" |
| 2081 |
- libdir=/usr/$(get_libdir) |
| 2082 |
- ) |
| 2083 |
- emake "${mymakeargs[@]}" |
| 2084 |
-} |
| 2085 |
- |
| 2086 |
-src_test() { |
| 2087 |
- local mymakeargs=( |
| 2088 |
- LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" |
| 2089 |
- HTSDIR="${EPREFIX}/usr/include" |
| 2090 |
- HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) |
| 2091 |
- BAMLIB="libbam.so" |
| 2092 |
- ) |
| 2093 |
- LD_LIBRARY_PATH="${S}" emake "${mymakeargs[@]}" test |
| 2094 |
-} |
| 2095 |
- |
| 2096 |
-src_install() { |
| 2097 |
- dobin samtools $(find misc -type f -executable) |
| 2098 |
- |
| 2099 |
- python_replicate_script "${ED}"usr/bin/varfilter.py |
| 2100 |
- |
| 2101 |
- # fix perl shebangs |
| 2102 |
- pushd "${ED}"usr/bin/ >> /dev/null |
| 2103 |
- local i |
| 2104 |
- for i in plot-bamstats *.pl; do |
| 2105 |
- sed -e '1s:.*:#!/usr/bin/env perl:' -i "${i}" || die |
| 2106 |
- done |
| 2107 |
- |
| 2108 |
- # remove lua scripts |
| 2109 |
- rm -f r2plot.lua vcfutils.lua || die |
| 2110 |
- popd >> /dev/null |
| 2111 |
- |
| 2112 |
- dolib.so libbam.so* |
| 2113 |
- |
| 2114 |
- insinto /usr/include/bam |
| 2115 |
- doins *.h |
| 2116 |
- |
| 2117 |
- doman ${PN}.1 |
| 2118 |
- dodoc AUTHORS NEWS README |
| 2119 |
- |
| 2120 |
- if use examples; then |
| 2121 |
- insinto /usr/share/${PN} |
| 2122 |
- doins -r examples |
| 2123 |
- fi |
| 2124 |
-} |
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