| 1 |
commit: f7caa54d3afffe8220d1a5f237b8906a994a0792 |
| 2 |
Author: David Seifert <soap <AT> gentoo <DOT> org> |
| 3 |
AuthorDate: Sun Mar 27 22:39:22 2016 +0000 |
| 4 |
Commit: David Seifert <soap <AT> gentoo <DOT> org> |
| 5 |
CommitDate: Sun Mar 27 22:39:58 2016 +0000 |
| 6 |
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f7caa54d |
| 7 |
|
| 8 |
sci-biology/samtools: Version bump to 0.1.20 |
| 9 |
|
| 10 |
* EAPI=6 |
| 11 |
* samtools will be slotted with SLOT="legacy", in order |
| 12 |
to be able to install applications that rely on the old |
| 13 |
monolithic library. |
| 14 |
|
| 15 |
Package-Manager: portage-2.2.28 |
| 16 |
|
| 17 |
sci-biology/samtools/Manifest | 1 + |
| 18 |
.../files/samtools-0.1.20-buildsystem.patch | 206 +++++++++++++++++++++ |
| 19 |
sci-biology/samtools/samtools-0.1.20.ebuild | 64 +++++++ |
| 20 |
3 files changed, 271 insertions(+) |
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|
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diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest |
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index dae2fbd..fd88ba4 100644 |
| 24 |
--- a/sci-biology/samtools/Manifest |
| 25 |
+++ b/sci-biology/samtools/Manifest |
| 26 |
@@ -1,5 +1,6 @@ |
| 27 |
DIST samtools-0.1.12a.tar.bz2 355633 SHA256 377ed5cd2a4bb2b1ad572ca6fcafdd8ed644b67f01ab00fa020618fac11e59ac SHA512 8a3273c174fb478772f31a9c73183b5f7c6841ba4e20586aafc2cd3e966830d3a4ca8c7485ce5981fe85d7cd820170e2ac2e124d8cf077e35218a7381f305012 WHIRLPOOL da61692666dffbb32e172f87e77287e145a0c0f6d62d47e5d04d153ce478db5df1d4694bd93d654af11643f9b656551232b5cc085b619bb8d8536720de36984c |
| 28 |
DIST samtools-0.1.19.tar.bz2 514507 SHA256 d080c9d356e5f0ad334007e4461cbcee3c4ca97b8a7a5a48c44883cf9dee63d4 SHA512 d145f1d65eefefbdfb781945684b8b591419fb109ac7401a62cae65b9ca1e1271f001496e1038334ff9ab1c0e5bf9bcc059f70aaa273551193fbd68101fd188d WHIRLPOOL 7811388ae8b24c5d7a328d2da252b8d3afaefdab508bd97684d556d2d4ee60d9c8846ffa562beaa9d0c6a5e6bfac24fcd9d211dfee20383cf452609badc8ecd5 |
| 29 |
+DIST samtools-0.1.20.tar.gz 566387 SHA256 500019b4d1886ad995513d5ce8b413b14b51f16f251ce76bc0b35a446b182a47 SHA512 15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5 WHIRLPOOL 3ea05df172ea6afe31bd3880f918e0b286f65839f78ed846a0d3aef84ec70df1e3741ff6dcad5f70d62a06687f07b35609829aabd33c6688fac0d59effd979e0 |
| 30 |
DIST samtools-1.0.tar.bz2 4459669 SHA256 7340b843663c3f54a902a06f2f73c68198f3a62d29a2ed20671139957f7fd7c0 SHA512 5b80995c522d08b06a4c559f60a5e200d9085be7f44c3c9618db91e3de85e36c1473e42715eae8175520d7da3df8245bafa82e625d2fc08e0197adb395851693 WHIRLPOOL 2aa0f8639da9b0b828ca7296969e5c600b0e5452ad3231b914e4a7be418700906a4d695c928eaf837b643255567ec82cfadf0b53007e0f1e3a956856f6c4c832 |
| 31 |
DIST samtools-1.1.tar.bz2 4495373 SHA256 c24d26c303153d72b5bf3cc11f72c6c375a4ca1140cc485648c8c5473414b7f8 SHA512 a5552a6c8c4b0808b725b39ddb2fafa36c4f6623bfc7f84faadae7690223e4eec8d722af09c77145796ad9b3f01e04115dd0207207ccfafbb52ffc22d5fc09f0 WHIRLPOOL ed3131b2a8d8b4dab40b53d35a9b00b657670a949dc1597c91fbcd00392c1c1715a85a1d1e49bf0c73ae082738ccfb13d2c6809dbbeba17ff3028f6023ebc449 |
| 32 |
DIST samtools-1.2.tar.bz2 4547126 SHA256 420e7a4a107fe37619b9d300b6379452eb8eb04a4a9b65c3ec69de82ccc26daa SHA512 4849c3274e732267516b63799f5430c5415d575d46eddf6b704dac51053281094b03b90dd9f5367bcd14c22fb0fb1bd6a412f7d4225f7be5f5385437c5d2101d WHIRLPOOL 273185764a807365a20c381769f987ef02d14ae8e20a3a7fd5af4344769c5fab68d7155523e8c0c8c3cc86092898c2c8454cce8f1560d415bc2b41549cdf04f4 |
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|
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diff --git a/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch b/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch |
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new file mode 100644 |
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index 0000000..dfdd890 |
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--- /dev/null |
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+++ b/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch |
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@@ -0,0 +1,206 @@ |
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+--- samtools-0.1.20/bcftools/Makefile |
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++++ samtools-0.1.20/bcftools/Makefile |
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+@@ -1,6 +1,6 @@ |
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+-CC= gcc |
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+-CFLAGS= -g -Wall -O2 #-m64 #-arch ppc |
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+-DFLAGS= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE |
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++CC?= gcc |
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++CFLAGS?= -g -Wall -O2 #-m64 #-arch ppc |
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++CPPFLAGS+= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE |
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+ LOBJS= bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o |
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+ OMISC= .. |
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+ AOBJS= call1.o main.o $(OMISC)/kstring.o $(OMISC)/bgzf.o $(OMISC)/knetfile.o $(OMISC)/bedidx.o |
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+@@ -11,14 +11,14 @@ |
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+ .SUFFIXES:.c .o |
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+ |
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+ .c.o: |
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+- $(CC) -c $(CFLAGS) $(DFLAGS) -I.. $(INCLUDES) $< -o $@ |
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++ $(CC) -c $(CFLAGS) $(CPPFLAGS) -I.. $(INCLUDES) $< -o $@ |
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+ |
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+ all-recur lib-recur clean-recur cleanlocal-recur install-recur: |
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+ @target=`echo $@ | sed s/-recur//`; \ |
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+ wdir=`pwd`; \ |
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+ list='$(SUBDIRS)'; for subdir in $$list; do \ |
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+ cd $$subdir; \ |
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+- $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \ |
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++ $(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \ |
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+ INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \ |
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+ cd $$wdir; \ |
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+ done; |
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+@@ -31,7 +31,7 @@ |
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+ $(AR) -csru $@ $(LOBJS) |
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+ |
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+ bcftools:lib $(AOBJS) |
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+- $(CC) $(CFLAGS) -o $@ $(AOBJS) -L. $(LIBPATH) -lbcf -lm -lz -lpthread |
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++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) -L. $(LIBPATH) -lbcf -lm -lz -lpthread |
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+ |
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+ bcf.o:bcf.h |
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+ vcf.o:bcf.h |
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+--- samtools-0.1.20/Makefile |
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++++ samtools-0.1.20/Makefile |
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+@@ -4,10 +4,10 @@ |
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+ # make git-stamp |
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+ VERSION= |
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+ |
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+-CC= gcc |
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+-CFLAGS= -g -Wall $(VERSION) -O2 |
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+-#LDFLAGS= -Wl,-rpath,\$$ORIGIN/../lib |
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+-DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 |
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++CC?= gcc |
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++CFLAGS?= -g -Wall $(VERSION) -O2 |
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++#LDFLAGS+= -Wl,-rpath,\$$ORIGIN/../lib |
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++CPPFLAGS+= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 |
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+ KNETFILE_O= knetfile.o |
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+ LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \ |
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+ bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o \ |
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+@@ -28,14 +28,14 @@ |
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+ .PHONY: all lib |
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+ |
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+ .c.o: |
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+- $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@ |
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++ $(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@ |
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+ |
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+ all-recur lib-recur clean-recur cleanlocal-recur install-recur: |
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+ @target=`echo $@ | sed s/-recur//`; \ |
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+ wdir=`pwd`; \ |
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+ list='$(SUBDIRS)'; for subdir in $$list; do \ |
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+ cd $$subdir; \ |
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+- $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \ |
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++ $(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \ |
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+ INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \ |
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+ cd $$wdir; \ |
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+ done; |
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+@@ -48,22 +48,22 @@ |
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+ .PHONY:all lib clean cleanlocal |
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+ .PHONY:all-recur lib-recur clean-recur cleanlocal-recur install-recur |
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+ |
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+-lib:libbam.a |
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++lib:libbam-legacy.a |
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+ |
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+-libbam.a:$(LOBJS) |
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++libbam-legacy.a:$(LOBJS) |
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+ $(AR) -csru $@ $(LOBJS) |
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+ |
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+ samtools:lib-recur $(AOBJS) |
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+- $(CC) $(CFLAGS) -o $@ $(AOBJS) $(LDFLAGS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread |
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++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) libbam-legacy.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread |
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+ |
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+ razip:razip.o razf.o $(KNETFILE_O) |
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+- $(CC) $(CFLAGS) -o $@ $^ -lz |
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++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ -lz |
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+ |
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+ bgzip:bgzip.o bgzf.o $(KNETFILE_O) |
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+- $(CC) $(CFLAGS) -o $@ $^ -lz -lpthread |
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++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ -lz -lpthread |
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+ |
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+ bgzf.o:bgzf.c bgzf.h |
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+- $(CC) -c $(CFLAGS) $(DFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@ |
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++ $(CC) -c $(CFLAGS) $(CPPFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@ |
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+ |
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+ razip.o:razf.h |
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+ bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h |
| 141 |
+@@ -90,17 +90,17 @@ |
| 142 |
+ faidx_main.o:faidx.h razf.h |
| 143 |
+ |
| 144 |
+ |
| 145 |
+-libbam.1.dylib-local:$(LOBJS) |
| 146 |
+- libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz |
| 147 |
++libbam-legacy.1.dylib-local:$(LOBJS) |
| 148 |
++ libtool -dynamic $(LOBJS) -o libbam-legacy.1.dylib -lc -lz |
| 149 |
+ |
| 150 |
+-libbam.so.1-local:$(LOBJS) |
| 151 |
+- $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz |
| 152 |
++libbam-legacy.so.1-local:$(LOBJS) |
| 153 |
++ $(CC) $(LDFLAGS) -shared -Wl,-soname,libbam-legacy.so -o libbam-legacy.so.1 $(LOBJS) -lc -lz -lm -lpthread |
| 154 |
+ |
| 155 |
+ dylib: |
| 156 |
+ @$(MAKE) cleanlocal; \ |
| 157 |
+ case `uname` in \ |
| 158 |
+- Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.so.1-local;; \ |
| 159 |
+- Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.1.dylib-local;; \ |
| 160 |
++ Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam-legacy.so.1-local;; \ |
| 161 |
++ Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam-legacy.1.dylib-local;; \ |
| 162 |
+ *) echo 'Unknown OS';; \ |
| 163 |
+ esac |
| 164 |
+ |
| 165 |
+--- samtools-0.1.20/misc/Makefile |
| 166 |
++++ samtools-0.1.20/misc/Makefile |
| 167 |
+@@ -1,8 +1,8 @@ |
| 168 |
+-CC= gcc |
| 169 |
+-CXX= g++ |
| 170 |
+-CFLAGS= -g -Wall -O2 #-m64 #-arch ppc |
| 171 |
+-CXXFLAGS= $(CFLAGS) |
| 172 |
+-DFLAGS= -D_FILE_OFFSET_BITS=64 |
| 173 |
++CC?= gcc |
| 174 |
++CXX?= g++ |
| 175 |
++CFLAGS?= -g -Wall -O2 #-m64 #-arch ppc |
| 176 |
++CXXFLAGS?= $(CFLAGS) |
| 177 |
++CPPFLAGS+= -D_FILE_OFFSET_BITS=64 |
| 178 |
+ OBJS= |
| 179 |
+ PROG= md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck |
| 180 |
+ INCLUDES= -I.. |
| 181 |
+@@ -11,7 +11,7 @@ |
| 182 |
+ .SUFFIXES:.c .o |
| 183 |
+ |
| 184 |
+ .c.o: |
| 185 |
+- $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@ |
| 186 |
++ $(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@ |
| 187 |
+ |
| 188 |
+ all:$(PROG) |
| 189 |
+ |
| 190 |
+@@ -20,7 +20,7 @@ |
| 191 |
+ wdir=`pwd`; \ |
| 192 |
+ list='$(SUBDIRS)'; for subdir in $$list; do \ |
| 193 |
+ cd $$subdir; \ |
| 194 |
+- $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \ |
| 195 |
++ $(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \ |
| 196 |
+ INCLUDES="$(INCLUDES)" $$target || exit 1; \ |
| 197 |
+ cd $$wdir; \ |
| 198 |
+ done; |
| 199 |
+@@ -28,31 +28,31 @@ |
| 200 |
+ lib: |
| 201 |
+ |
| 202 |
+ bamcheck:bamcheck.o |
| 203 |
+- $(CC) $(CFLAGS) -o $@ bamcheck.o -L.. -lm -lbam -lpthread -lz |
| 204 |
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ bamcheck.o -L.. -lm -lbam-legacy -lpthread -lz |
| 205 |
+ |
| 206 |
+ bamcheck.o:bamcheck.c ../faidx.h ../khash.h ../sam.h ../razf.h |
| 207 |
+ $(CC) $(CFLAGS) -c -I.. -o $@ bamcheck.c |
| 208 |
+ |
| 209 |
+ ace2sam:ace2sam.o |
| 210 |
+- $(CC) $(CFLAGS) -o $@ ace2sam.o -lz |
| 211 |
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ ace2sam.o -lz |
| 212 |
+ |
| 213 |
+ wgsim:wgsim.o |
| 214 |
+- $(CC) $(CFLAGS) -o $@ wgsim.o -lm -lz |
| 215 |
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ wgsim.o -lm -lz |
| 216 |
+ |
| 217 |
+ md5fa:md5.o md5fa.o md5.h ../kseq.h |
| 218 |
+- $(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz |
| 219 |
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ md5.o md5fa.o -lz |
| 220 |
+ |
| 221 |
+ md5sum-lite:md5sum-lite.o |
| 222 |
+- $(CC) $(CFLAGS) -o $@ md5sum-lite.o |
| 223 |
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ md5sum-lite.o |
| 224 |
+ |
| 225 |
+ md5sum-lite.o:md5.c md5.h |
| 226 |
+ $(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c |
| 227 |
+ |
| 228 |
+ maq2sam-short:maq2sam.c |
| 229 |
+- $(CC) $(CFLAGS) -o $@ maq2sam.c -lz |
| 230 |
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ maq2sam.c -lz |
| 231 |
+ |
| 232 |
+ maq2sam-long:maq2sam.c |
| 233 |
+- $(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -lz |
| 234 |
++ $(CC) $(CFLAGS) -DMAQ_LONGREADS $(LDFLAGS) -o $@ maq2sam.c -lz |
| 235 |
+ |
| 236 |
+ md5fa.o:md5.h md5fa.c |
| 237 |
+ $(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c |
| 238 |
+--- samtools-0.1.20/misc/varfilter.py |
| 239 |
++++ samtools-0.1.20/misc/varfilter.py |
| 240 |
+@@ -1,4 +1,4 @@ |
| 241 |
+-#!/software/bin/python |
| 242 |
++#!/usr/bin/env python |
| 243 |
+ |
| 244 |
+ # Author: lh3, converted to python and modified to add -C option by Aylwyn Scally |
| 245 |
+ # |
| 246 |
|
| 247 |
diff --git a/sci-biology/samtools/samtools-0.1.20.ebuild b/sci-biology/samtools/samtools-0.1.20.ebuild |
| 248 |
new file mode 100644 |
| 249 |
index 0000000..50ee0b3 |
| 250 |
--- /dev/null |
| 251 |
+++ b/sci-biology/samtools/samtools-0.1.20.ebuild |
| 252 |
@@ -0,0 +1,64 @@ |
| 253 |
+# Copyright 1999-2016 Gentoo Foundation |
| 254 |
+# Distributed under the terms of the GNU General Public License v2 |
| 255 |
+# $Id$ |
| 256 |
+ |
| 257 |
+EAPI=6 |
| 258 |
+ |
| 259 |
+PYTHON_COMPAT=( python2_7 ) |
| 260 |
+ |
| 261 |
+inherit eutils python-r1 toolchain-funcs |
| 262 |
+ |
| 263 |
+DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats" |
| 264 |
+HOMEPAGE="http://samtools.sourceforge.net/" |
| 265 |
+SRC_URI="https://github.com/samtools/samtools/archive/${PV}.tar.gz -> ${P}.tar.gz" |
| 266 |
+ |
| 267 |
+LICENSE="MIT" |
| 268 |
+SLOT="legacy" |
| 269 |
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" |
| 270 |
+IUSE="examples" |
| 271 |
+ |
| 272 |
+REQUIRED_USE="${PYTHON_REQUIRED_USE}" |
| 273 |
+ |
| 274 |
+RDEPEND="sys-libs/ncurses:0= |
| 275 |
+ dev-lang/lua:0 |
| 276 |
+ dev-lang/perl" |
| 277 |
+DEPEND="${RDEPEND} |
| 278 |
+ virtual/pkgconfig" |
| 279 |
+ |
| 280 |
+PATCHES=( |
| 281 |
+ "${FILESDIR}/${P}-buildsystem.patch" |
| 282 |
+) |
| 283 |
+ |
| 284 |
+src_prepare() { |
| 285 |
+ default |
| 286 |
+ sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die |
| 287 |
+ tc-export CC AR |
| 288 |
+} |
| 289 |
+ |
| 290 |
+src_compile() { |
| 291 |
+ local _ncurses="$($(tc-getPKG_CONFIG) --libs ncurses)" |
| 292 |
+ emake dylib LIBCURSES="${_ncurses}" |
| 293 |
+ emake LIBCURSES="${_ncurses}" |
| 294 |
+} |
| 295 |
+ |
| 296 |
+src_install() { |
| 297 |
+ dobin samtools $(find bcftools misc -type f -executable) |
| 298 |
+ mv "${ED}"/usr/{bin,${PN}-${SLOT}} || die |
| 299 |
+ mkdir "${ED}"/usr/bin || die |
| 300 |
+ mv "${ED}"/usr/{${PN}-${SLOT},bin/} || die |
| 301 |
+ |
| 302 |
+ mv "${ED}"/usr/bin/${PN}-${SLOT}/varfilter{,-${SLOT}}.py || die |
| 303 |
+ python_replicate_script "${ED}"/usr/bin/${PN}-${SLOT}/varfilter-${SLOT}.py |
| 304 |
+ |
| 305 |
+ dolib.so libbam-${SLOT}$(get_libname 1) |
| 306 |
+ dosym libbam-${SLOT}$(get_libname 1) /usr/$(get_libdir)/libbam-${SLOT}$(get_libname) |
| 307 |
+ |
| 308 |
+ insinto /usr/include/bam-${SLOT} |
| 309 |
+ doins *.h |
| 310 |
+ |
| 311 |
+ mv ${PN}{,-${SLOT}}.1 || die |
| 312 |
+ doman ${PN}-${SLOT}.1 |
| 313 |
+ dodoc AUTHORS NEWS |
| 314 |
+ |
| 315 |
+ use examples && dodoc -r examples |
| 316 |
+} |
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