| 1 |
commit: 767b616524e6b171ed4775fe35ecd068f58abc22 |
| 2 |
Author: David Seifert <soap <AT> gentoo <DOT> org> |
| 3 |
AuthorDate: Mon Mar 28 19:59:02 2016 +0000 |
| 4 |
Commit: David Seifert <soap <AT> gentoo <DOT> org> |
| 5 |
CommitDate: Mon Mar 28 19:59:24 2016 +0000 |
| 6 |
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=767b6165 |
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|
| 8 |
sci-biology/samtools: version bump to 1.3, to match htslib |
| 9 |
|
| 10 |
* EAPI=6 |
| 11 |
* Added modern AX_WITH_CURSES that works with pkg-config |
| 12 |
* Fixed incorrect symlinks for libbam.so |
| 13 |
|
| 14 |
Package-Manager: portage-2.2.28 |
| 15 |
|
| 16 |
sci-biology/samtools/Manifest | 1 + |
| 17 |
.../samtools/files/samtools-1.3-buildsystem.patch | 174 +++++ |
| 18 |
.../samtools/files/samtools-1.3-ncurses.patch | 737 +++++++++++++++++++++ |
| 19 |
sci-biology/samtools/samtools-1.3.ebuild | 86 +++ |
| 20 |
4 files changed, 998 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 fd88ba4..d25774f 100644 |
| 24 |
--- a/sci-biology/samtools/Manifest |
| 25 |
+++ b/sci-biology/samtools/Manifest |
| 26 |
@@ -4,3 +4,4 @@ DIST samtools-0.1.20.tar.gz 566387 SHA256 500019b4d1886ad995513d5ce8b413b14b51f1 |
| 27 |
DIST samtools-1.0.tar.bz2 4459669 SHA256 7340b843663c3f54a902a06f2f73c68198f3a62d29a2ed20671139957f7fd7c0 SHA512 5b80995c522d08b06a4c559f60a5e200d9085be7f44c3c9618db91e3de85e36c1473e42715eae8175520d7da3df8245bafa82e625d2fc08e0197adb395851693 WHIRLPOOL 2aa0f8639da9b0b828ca7296969e5c600b0e5452ad3231b914e4a7be418700906a4d695c928eaf837b643255567ec82cfadf0b53007e0f1e3a956856f6c4c832 |
| 28 |
DIST samtools-1.1.tar.bz2 4495373 SHA256 c24d26c303153d72b5bf3cc11f72c6c375a4ca1140cc485648c8c5473414b7f8 SHA512 a5552a6c8c4b0808b725b39ddb2fafa36c4f6623bfc7f84faadae7690223e4eec8d722af09c77145796ad9b3f01e04115dd0207207ccfafbb52ffc22d5fc09f0 WHIRLPOOL ed3131b2a8d8b4dab40b53d35a9b00b657670a949dc1597c91fbcd00392c1c1715a85a1d1e49bf0c73ae082738ccfb13d2c6809dbbeba17ff3028f6023ebc449 |
| 29 |
DIST samtools-1.2.tar.bz2 4547126 SHA256 420e7a4a107fe37619b9d300b6379452eb8eb04a4a9b65c3ec69de82ccc26daa SHA512 4849c3274e732267516b63799f5430c5415d575d46eddf6b704dac51053281094b03b90dd9f5367bcd14c22fb0fb1bd6a412f7d4225f7be5f5385437c5d2101d WHIRLPOOL 273185764a807365a20c381769f987ef02d14ae8e20a3a7fd5af4344769c5fab68d7155523e8c0c8c3cc86092898c2c8454cce8f1560d415bc2b41549cdf04f4 |
| 30 |
+DIST samtools-1.3.tar.bz2 3978333 SHA256 beea4003c795a0a25224656815b4036f6864b8753053ed30c590bb052b70b60e SHA512 72920d4f0f10aa7b54ef448e03e6e769e1e07abd07388a2307d0e52548fa2909c03ca2c7eec5c63cf5b67724b2356833accb0079ce1486bb2ac66a45963a24ea WHIRLPOOL 3f798078100b4ed164f6c89d18cc8f62159437e2cfb2a228ac00f8d08313f7c39ef546214c0796c25a419c0a1065dc21d14b966fed769726b9b1975ec07e3b3e |
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|
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diff --git a/sci-biology/samtools/files/samtools-1.3-buildsystem.patch b/sci-biology/samtools/files/samtools-1.3-buildsystem.patch |
| 33 |
new file mode 100644 |
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index 0000000..61f6b03 |
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--- /dev/null |
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+++ b/sci-biology/samtools/files/samtools-1.3-buildsystem.patch |
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@@ -0,0 +1,174 @@ |
| 38 |
+--- samtools-1.3/Makefile |
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++++ samtools-1.3/Makefile |
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+@@ -21,11 +21,12 @@ |
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+ # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER |
| 42 |
+ # DEALINGS IN THE SOFTWARE. |
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+ |
| 44 |
+-CC = gcc |
| 45 |
+-CPPFLAGS = |
| 46 |
+-CFLAGS = -g -Wall -O2 |
| 47 |
+-LDFLAGS = |
| 48 |
+-LIBS = |
| 49 |
++CC ?= gcc |
| 50 |
++CPPFLAGS += |
| 51 |
++CFLAGS ?= -g -Wall -O2 |
| 52 |
++LDFLAGS += |
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++LIBS += |
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++BAMLIB ?= libbam.a |
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+ |
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+ DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE |
| 57 |
+ LOBJS= bam_aux.o bam.o bam_import.o sam.o \ |
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+@@ -42,6 +43,7 @@ |
| 59 |
+ prefix = /usr/local |
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+ exec_prefix = $(prefix) |
| 61 |
+ bindir = $(exec_prefix)/bin |
| 62 |
++libdir ?= $(exec_prefix)/lib |
| 63 |
+ datarootdir = $(prefix)/share |
| 64 |
+ mandir = $(datarootdir)/man |
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+ man1dir = $(mandir)/man1 |
| 66 |
+@@ -129,67 +131,74 @@ |
| 67 |
+ .c.o: |
| 68 |
+ $(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ $< |
| 69 |
+ |
| 70 |
++$(LOBJS): |
| 71 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $< |
| 72 |
+ |
| 73 |
+-lib:libbam.a |
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++lib:libbam.a libbam.so.1.0 |
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+ |
| 76 |
+ libbam.a:$(LOBJS) |
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+ $(AR) -csru $@ $(LOBJS) |
| 78 |
+ |
| 79 |
+-samtools: $(AOBJS) libbam.a $(HTSLIB) |
| 80 |
+- $(CC) -pthread $(ALL_LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB_LIB) $(CURSES_LIB) -lm $(ALL_LIBS) |
| 81 |
++libbam.so.1.0:$(LOBJS) |
| 82 |
++ $(CC) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB) -lz |
| 83 |
++ ln -sf $@ libbam.so.1 |
| 84 |
++ ln -sf $@ libbam.so |
| 85 |
++ |
| 86 |
++samtools: $(AOBJS) lib |
| 87 |
++ $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) $(BAMLIB) $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz |
| 88 |
+ |
| 89 |
+ bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h) |
| 90 |
+ bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.h |
| 91 |
+ bam_lpileup_h = bam_lpileup.h $(htslib_sam_h) |
| 92 |
+ bam_plbuf_h = bam_plbuf.h $(htslib_sam_h) |
| 93 |
+-bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(htslib_khash_h) $(bam_lpileup_h) |
| 94 |
++bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(bam_lpileup_h) |
| 95 |
+ sam_h = sam.h $(htslib_sam_h) $(bam_h) |
| 96 |
+ sam_opts_h = sam_opts.h $(htslib_hts_h) |
| 97 |
+-sample_h = sample.h $(htslib_kstring_h) |
| 98 |
++sample_h = sample.h |
| 99 |
+ |
| 100 |
+ bam.o: bam.c $(bam_h) $(htslib_kstring_h) sam_header.h |
| 101 |
+-bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(htslib_kstring_h) $(htslib_kfunc_h) $(bam2bcf_h) errmod.h |
| 102 |
++bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(bam2bcf_h) errmod.h |
| 103 |
+ bam2bcf_indel.o: bam2bcf_indel.c $(htslib_sam_h) $(bam2bcf_h) kprobaln.h $(htslib_khash_h) $(htslib_ksort_h) |
| 104 |
+ bam2depth.o: bam2depth.c $(htslib_sam_h) samtools.h $(sam_opts_h) |
| 105 |
+ bam_addrprg.o: bam_addrprg.c $(htslib_sam_h) $(htslib_kstring_h) samtools.h $(sam_opts_h) |
| 106 |
+ bam_aux.o: bam_aux.c $(bam_h) |
| 107 |
+ bam_cat.o: bam_cat.c $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_cram_h) $(htslib_khash_h) |
| 108 |
+ bam_color.o: bam_color.c $(bam_h) |
| 109 |
+-bam_import.o: bam_import.c $(htslib_kstring_h) $(bam_h) $(htslib_kseq_h) |
| 110 |
+-bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_h) samtools.h |
| 111 |
+-bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) $(htslib_ksort_h) |
| 112 |
++bam_import.o: bam_import.c $(bam_h) |
| 113 |
++bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) |
| 114 |
++bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) |
| 115 |
+ bam_mate.o: bam_mate.c $(sam_opts_h) $(htslib_kstring_h) $(htslib_sam_h) |
| 116 |
+ bam_md.o: bam_md.c $(htslib_faidx_h) $(htslib_sam_h) $(htslib_kstring_h) kprobaln.h $(sam_opts_h) |
| 117 |
+ bam_plbuf.o: bam_plbuf.c $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h) |
| 118 |
+-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) |
| 119 |
++bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) sam_header.h samtools.h $(bam2bcf_h) $(sample_h) |
| 120 |
+ bam_quickcheck.o: bam_quickcheck.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_bgzf_h) |
| 121 |
+ bam_reheader.o: bam_reheader.c $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_hfile_h) $(htslib_cram_h) samtools.h |
| 122 |
+-bam_rmdup.o: bam_rmdup.c $(htslib_sam_h) $(sam_opts_h) $(bam_h) $(htslib_khash_h) |
| 123 |
+-bam_rmdupse.o: bam_rmdupse.c $(bam_h) $(htslib_sam_h) $(htslib_khash_h) $(htslib_klist_h) |
| 124 |
+-bam_sort.o: bam_sort.c $(htslib_ksort_h) $(htslib_khash_h) $(htslib_klist_h) $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) |
| 125 |
++bam_rmdup.o: bam_rmdup.c $(sam_h) |
| 126 |
++bam_rmdupse.o: bam_rmdupse.c $(sam_h) |
| 127 |
++bam_sort.o: bam_sort.c $(htslib_sam_h) |
| 128 |
+ bam_split.o: bam_split.c $(htslib_sam_h) $(htslib_khash_h) $(htslib_kstring_h) $(sam_opts_h) |
| 129 |
+ bam_stat.o: bam_stat.c $(htslib_sam_h) samtools.h |
| 130 |
+ bam_tview.o: bam_tview.c $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h) $(sam_opts_h) |
| 131 |
+ bam_tview_curses.o: bam_tview_curses.c config.h $(bam_tview_h) |
| 132 |
+ bam_tview_html.o: bam_tview_html.c $(bam_tview_h) |
| 133 |
+ bam_flags.o: bam_flags.c $(htslib_sam_h) |
| 134 |
+-bamshuf.o: bamshuf.c $(htslib_sam_h) $(htslib_hts_h) $(htslib_ksort_h) samtools.h $(sam_opts_h) |
| 135 |
++bamshuf.o: bamshuf.c $(htslib_sam_h) samtools.h |
| 136 |
+ bamtk.o: bamtk.c $(htslib_hts_h) samtools.h version.h |
| 137 |
+-bedcov.o: bedcov.c $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) $(htslib_kseq_h) |
| 138 |
+-bedidx.o: bedidx.c $(htslib_ksort_h) $(htslib_kseq_h) $(htslib_khash_h) |
| 139 |
++bedcov.o: bedcov.c $(htslib_sam_h) |
| 140 |
++bedidx.o: bedidx.c |
| 141 |
+ cut_target.o: cut_target.c $(htslib_sam_h) errmod.h $(htslib_faidx_h) $(sam_opts_h) |
| 142 |
+ dict.o: dict.c $(htslib_kseq_h) $(htslib_hts_h) |
| 143 |
+-errmod.o: errmod.c errmod.h $(htslib_ksort_h) |
| 144 |
++errmod.o: errmod.c errmod.h |
| 145 |
+ kprobaln.o: kprobaln.c kprobaln.h |
| 146 |
+ padding.o: padding.c $(htslib_kstring_h) $(htslib_sam_h) $(htslib_faidx_h) sam_header.h $(sam_opts_h) |
| 147 |
+-phase.o: phase.c $(htslib_sam_h) errmod.h $(sam_opts_h) $(htslib_kseq_h) $(htslib_khash_h) $(htslib_ksort_h) |
| 148 |
++phase.o: phase.c $(htslib_sam_h) errmod.h |
| 149 |
+ sam.o: sam.c $(htslib_faidx_h) $(sam_h) |
| 150 |
+-sam_header.o: sam_header.c sam_header.h $(htslib_khash_h) |
| 151 |
++sam_header.o: sam_header.c sam_header.h |
| 152 |
+ sam_opts.o: sam_opts.c $(sam_opts_h) |
| 153 |
+-sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_h) samtools.h $(sam_opts_h) |
| 154 |
+-sample.o: sample.c $(sample_h) $(htslib_khash_h) |
| 155 |
+-stats_isize.o: stats_isize.c stats_isize.h $(htslib_khash_h) |
| 156 |
+-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) |
| 157 |
++sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) samtools.h |
| 158 |
++sample.o: sample.c $(sample_h) |
| 159 |
++stats_isize.o: stats_isize.c stats_isize.h |
| 160 |
++stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(htslib_faidx_h) |
| 161 |
+ |
| 162 |
+ |
| 163 |
+ # test programs |
| 164 |
+@@ -197,8 +206,8 @@ |
| 165 |
+ # For tests that might use it, set $REF_PATH explicitly to use only reference |
| 166 |
+ # areas within the test suite (or set it to ':' to use no reference areas). |
| 167 |
+ # (regression.sh sets $REF_PATH to a subdirectory itself.) |
| 168 |
+-check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS) |
| 169 |
+- REF_PATH=: test/test.pl --exec bgzip=$(BGZIP) |
| 170 |
++check test: samtools $(BUILT_TEST_PROGRAMS) |
| 171 |
++ REF_PATH=: test/test.pl --exec bgzip=bgzip |
| 172 |
+ test/merge/test_bam_translate test/merge/test_bam_translate.tmp |
| 173 |
+ test/merge/test_rtrans_build |
| 174 |
+ test/merge/test_trans_tbl_init |
| 175 |
+@@ -210,28 +219,28 @@ |
| 176 |
+ test/split/test_parse_args |
| 177 |
+ |
| 178 |
+ |
| 179 |
+-test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o sam_opts.o $(HTSLIB) |
| 180 |
++test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o |
| 181 |
+ $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) |
| 182 |
+ |
| 183 |
+-test/merge/test_rtrans_build: test/merge/test_rtrans_build.o sam_opts.o $(HTSLIB) |
| 184 |
++test/merge/test_rtrans_build: test/merge/test_rtrans_build.o |
| 185 |
+ $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_rtrans_build.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) |
| 186 |
+ |
| 187 |
+-test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o sam_opts.o $(HTSLIB) |
| 188 |
++test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o |
| 189 |
+ $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) |
| 190 |
+ |
| 191 |
+-test/split/test_count_rg: test/split/test_count_rg.o test/test.o sam_opts.o $(HTSLIB) |
| 192 |
++test/split/test_count_rg: test/split/test_count_rg.o test/test.o |
| 193 |
+ $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) |
| 194 |
+ |
| 195 |
+-test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o sam_opts.o $(HTSLIB) |
| 196 |
++test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o |
| 197 |
+ $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) |
| 198 |
+ |
| 199 |
+-test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o sam_opts.o $(HTSLIB) |
| 200 |
++test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o |
| 201 |
+ $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) |
| 202 |
+ |
| 203 |
+-test/split/test_parse_args: test/split/test_parse_args.o test/test.o sam_opts.o $(HTSLIB) |
| 204 |
++test/split/test_parse_args: test/split/test_parse_args.o test/test.o |
| 205 |
+ $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) |
| 206 |
+ |
| 207 |
+-test/vcf-miniview: test/vcf-miniview.o $(HTSLIB) |
| 208 |
++test/vcf-miniview: test/vcf-miniview.o |
| 209 |
+ $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB_LIB) $(ALL_LIBS) |
| 210 |
+ |
| 211 |
+ test_test_h = test/test.h $(htslib_sam_h) |
| 212 |
|
| 213 |
diff --git a/sci-biology/samtools/files/samtools-1.3-ncurses.patch b/sci-biology/samtools/files/samtools-1.3-ncurses.patch |
| 214 |
new file mode 100644 |
| 215 |
index 0000000..baeb670 |
| 216 |
--- /dev/null |
| 217 |
+++ b/sci-biology/samtools/files/samtools-1.3-ncurses.patch |
| 218 |
@@ -0,0 +1,737 @@ |
| 219 |
+* Add modern AX_WITH_CURSES that prefers using pkg-config for detecting ncurses |
| 220 |
+* Change macro structure by moving AX_WITH_HTSLIB into its own file |
| 221 |
+ |
| 222 |
+--- samtools-1.3/configure.ac |
| 223 |
++++ samtools-1.3/configure.ac |
| 224 |
+@@ -28,6 +28,7 @@ |
| 225 |
+ AC_PREREQ([2.63]) dnl This version introduced 4-argument AC_CHECK_HEADER |
| 226 |
+ AC_CONFIG_SRCDIR([bamtk.c]) |
| 227 |
+ AC_CONFIG_HEADERS([config.h]) |
| 228 |
++AC_CONFIG_MACRO_DIR([m4]) |
| 229 |
+ |
| 230 |
+ dnl Copyright notice to be copied into the generated configure script |
| 231 |
+ AC_COPYRIGHT([Portions copyright (C) 2015 Genome Research Ltd. |
| 232 |
+--- samtools-1.3/m4/ax_with_curses.m4 |
| 233 |
++++ samtools-1.3/m4/ax_with_curses.m4 |
| 234 |
+@@ -0,0 +1,578 @@ |
| 235 |
++# =========================================================================== |
| 236 |
++# http://www.gnu.org/software/autoconf-archive/ax_with_curses.html |
| 237 |
++# =========================================================================== |
| 238 |
++# |
| 239 |
++# SYNOPSIS |
| 240 |
++# |
| 241 |
++# AX_WITH_CURSES |
| 242 |
++# |
| 243 |
++# DESCRIPTION |
| 244 |
++# |
| 245 |
++# This macro checks whether a SysV or X/Open-compatible Curses library is |
| 246 |
++# present, along with the associated header file. The NcursesW |
| 247 |
++# (wide-character) library is searched for first, followed by Ncurses, |
| 248 |
++# then the system-default plain Curses. The first library found is the |
| 249 |
++# one returned. Finding libraries will first be attempted by using |
| 250 |
++# pkg-config, and should the pkg-config files not be available, will |
| 251 |
++# fallback to combinations of known flags itself. |
| 252 |
++# |
| 253 |
++# The following options are understood: --with-ncursesw, --with-ncurses, |
| 254 |
++# --without-ncursesw, --without-ncurses. The "--with" options force the |
| 255 |
++# macro to use that particular library, terminating with an error if not |
| 256 |
++# found. The "--without" options simply skip the check for that library. |
| 257 |
++# The effect on the search pattern is: |
| 258 |
++# |
| 259 |
++# (no options) - NcursesW, Ncurses, Curses |
| 260 |
++# --with-ncurses --with-ncursesw - NcursesW only [*] |
| 261 |
++# --without-ncurses --with-ncursesw - NcursesW only [*] |
| 262 |
++# --with-ncursesw - NcursesW only [*] |
| 263 |
++# --with-ncurses --without-ncursesw - Ncurses only [*] |
| 264 |
++# --with-ncurses - NcursesW, Ncurses [**] |
| 265 |
++# --without-ncurses --without-ncursesw - Curses only |
| 266 |
++# --without-ncursesw - Ncurses, Curses |
| 267 |
++# --without-ncurses - NcursesW, Curses |
| 268 |
++# |
| 269 |
++# [*] If the library is not found, abort the configure script. |
| 270 |
++# |
| 271 |
++# [**] If the second library (Ncurses) is not found, abort configure. |
| 272 |
++# |
| 273 |
++# The following preprocessor symbols may be defined by this macro if the |
| 274 |
++# appropriate conditions are met: |
| 275 |
++# |
| 276 |
++# HAVE_CURSES - if any SysV or X/Open Curses library found |
| 277 |
++# HAVE_CURSES_ENHANCED - if library supports X/Open Enhanced functions |
| 278 |
++# HAVE_CURSES_COLOR - if library supports color (enhanced functions) |
| 279 |
++# HAVE_CURSES_OBSOLETE - if library supports certain obsolete features |
| 280 |
++# HAVE_NCURSESW - if NcursesW (wide char) library is to be used |
| 281 |
++# HAVE_NCURSES - if the Ncurses library is to be used |
| 282 |
++# |
| 283 |
++# HAVE_CURSES_H - if <curses.h> is present and should be used |
| 284 |
++# HAVE_NCURSESW_H - if <ncursesw.h> should be used |
| 285 |
++# HAVE_NCURSES_H - if <ncurses.h> should be used |
| 286 |
++# HAVE_NCURSESW_CURSES_H - if <ncursesw/curses.h> should be used |
| 287 |
++# HAVE_NCURSES_CURSES_H - if <ncurses/curses.h> should be used |
| 288 |
++# |
| 289 |
++# (These preprocessor symbols are discussed later in this document.) |
| 290 |
++# |
| 291 |
++# The following output variables are defined by this macro; they are |
| 292 |
++# precious and may be overridden on the ./configure command line: |
| 293 |
++# |
| 294 |
++# CURSES_LIB - library to add to xxx_LDADD |
| 295 |
++# CURSES_CPPFLAGS - include paths to add to xxx_CPPFLAGS |
| 296 |
++# |
| 297 |
++# Neither the library listed in CURSES_LIB, nor the flags in |
| 298 |
++# CURSES_CPPFLAGS are added to LIBS, respectively CPPFLAGS, by default. |
| 299 |
++# You need to add both to the appropriate xxx_LDADD/xxx_CPPFLAGS line in |
| 300 |
++# your Makefile.am. For example: |
| 301 |
++# |
| 302 |
++# prog_LDADD = @CURSES_LIB@ |
| 303 |
++# prog_CPPFLAGS = @CURSES_CPPFLAGS@ |
| 304 |
++# |
| 305 |
++# If CURSES_LIB is set on the configure command line (such as by running |
| 306 |
++# "./configure CURSES_LIB=-lmycurses"), then the only header searched for |
| 307 |
++# is <curses.h>. If the user needs to specify an alternative path for a |
| 308 |
++# library (such as for a non-standard NcurseW), the user should use the |
| 309 |
++# LDFLAGS variable. |
| 310 |
++# |
| 311 |
++# The following shell variables may be defined by this macro: |
| 312 |
++# |
| 313 |
++# ax_cv_curses - set to "yes" if any Curses library found |
| 314 |
++# ax_cv_curses_enhanced - set to "yes" if Enhanced functions present |
| 315 |
++# ax_cv_curses_color - set to "yes" if color functions present |
| 316 |
++# ax_cv_curses_obsolete - set to "yes" if obsolete features present |
| 317 |
++# |
| 318 |
++# ax_cv_ncursesw - set to "yes" if NcursesW library found |
| 319 |
++# ax_cv_ncurses - set to "yes" if Ncurses library found |
| 320 |
++# ax_cv_plaincurses - set to "yes" if plain Curses library found |
| 321 |
++# ax_cv_curses_which - set to "ncursesw", "ncurses", "plaincurses" or "no" |
| 322 |
++# |
| 323 |
++# These variables can be used in your configure.ac to determine the level |
| 324 |
++# of support you need from the Curses library. For example, if you must |
| 325 |
++# have either Ncurses or NcursesW, you could include: |
| 326 |
++# |
| 327 |
++# AX_WITH_CURSES |
| 328 |
++# if test "x$ax_cv_ncursesw" != xyes && test "x$ax_cv_ncurses" != xyes; then |
| 329 |
++# AC_MSG_ERROR([requires either NcursesW or Ncurses library]) |
| 330 |
++# fi |
| 331 |
++# |
| 332 |
++# If any Curses library will do (but one must be present and must support |
| 333 |
++# color), you could use: |
| 334 |
++# |
| 335 |
++# AX_WITH_CURSES |
| 336 |
++# if test "x$ax_cv_curses" != xyes || test "x$ax_cv_curses_color" != xyes; then |
| 337 |
++# AC_MSG_ERROR([requires an X/Open-compatible Curses library with color]) |
| 338 |
++# fi |
| 339 |
++# |
| 340 |
++# Certain preprocessor symbols and shell variables defined by this macro |
| 341 |
++# can be used to determine various features of the Curses library. In |
| 342 |
++# particular, HAVE_CURSES and ax_cv_curses are defined if the Curses |
| 343 |
++# library found conforms to the traditional SysV and/or X/Open Base Curses |
| 344 |
++# definition. Any working Curses library conforms to this level. |
| 345 |
++# |
| 346 |
++# HAVE_CURSES_ENHANCED and ax_cv_curses_enhanced are defined if the |
| 347 |
++# library supports the X/Open Enhanced Curses definition. In particular, |
| 348 |
++# the wide-character types attr_t, cchar_t and wint_t, the functions |
| 349 |
++# wattr_set() and wget_wch() and the macros WA_NORMAL and _XOPEN_CURSES |
| 350 |
++# are checked. The Ncurses library does NOT conform to this definition, |
| 351 |
++# although NcursesW does. |
| 352 |
++# |
| 353 |
++# HAVE_CURSES_COLOR and ax_cv_curses_color are defined if the library |
| 354 |
++# supports color functions and macros such as COLOR_PAIR, A_COLOR, |
| 355 |
++# COLOR_WHITE, COLOR_RED and init_pair(). These are NOT part of the |
| 356 |
++# X/Open Base Curses definition, but are part of the Enhanced set of |
| 357 |
++# functions. The Ncurses library DOES support these functions, as does |
| 358 |
++# NcursesW. |
| 359 |
++# |
| 360 |
++# HAVE_CURSES_OBSOLETE and ax_cv_curses_obsolete are defined if the |
| 361 |
++# library supports certain features present in SysV and BSD Curses but not |
| 362 |
++# defined in the X/Open definition. In particular, the functions |
| 363 |
++# getattrs(), getcurx() and getmaxx() are checked. |
| 364 |
++# |
| 365 |
++# To use the HAVE_xxx_H preprocessor symbols, insert the following into |
| 366 |
++# your system.h (or equivalent) header file: |
| 367 |
++# |
| 368 |
++# #if defined HAVE_NCURSESW_CURSES_H |
| 369 |
++# # include <ncursesw/curses.h> |
| 370 |
++# #elif defined HAVE_NCURSESW_H |
| 371 |
++# # include <ncursesw.h> |
| 372 |
++# #elif defined HAVE_NCURSES_CURSES_H |
| 373 |
++# # include <ncurses/curses.h> |
| 374 |
++# #elif defined HAVE_NCURSES_H |
| 375 |
++# # include <ncurses.h> |
| 376 |
++# #elif defined HAVE_CURSES_H |
| 377 |
++# # include <curses.h> |
| 378 |
++# #else |
| 379 |
++# # error "SysV or X/Open-compatible Curses header file required" |
| 380 |
++# #endif |
| 381 |
++# |
| 382 |
++# For previous users of this macro: you should not need to change anything |
| 383 |
++# in your configure.ac or Makefile.am, as the previous (serial 10) |
| 384 |
++# semantics are still valid. However, you should update your system.h (or |
| 385 |
++# equivalent) header file to the fragment shown above. You are encouraged |
| 386 |
++# also to make use of the extended functionality provided by this version |
| 387 |
++# of AX_WITH_CURSES, as well as in the additional macros |
| 388 |
++# AX_WITH_CURSES_PANEL, AX_WITH_CURSES_MENU and AX_WITH_CURSES_FORM. |
| 389 |
++# |
| 390 |
++# LICENSE |
| 391 |
++# |
| 392 |
++# Copyright (c) 2009 Mark Pulford <mark@××××××××.au> |
| 393 |
++# Copyright (c) 2009 Damian Pietras <daper@×××××.net> |
| 394 |
++# Copyright (c) 2012 Reuben Thomas <rrt@××××.org> |
| 395 |
++# Copyright (c) 2011 John Zaitseff <J.Zaitseff@×××××××.au> |
| 396 |
++# |
| 397 |
++# This program is free software: you can redistribute it and/or modify it |
| 398 |
++# under the terms of the GNU General Public License as published by the |
| 399 |
++# Free Software Foundation, either version 3 of the License, or (at your |
| 400 |
++# option) any later version. |
| 401 |
++# |
| 402 |
++# This program is distributed in the hope that it will be useful, but |
| 403 |
++# WITHOUT ANY WARRANTY; without even the implied warranty of |
| 404 |
++# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General |
| 405 |
++# Public License for more details. |
| 406 |
++# |
| 407 |
++# You should have received a copy of the GNU General Public License along |
| 408 |
++# with this program. If not, see <http://www.gnu.org/licenses/>. |
| 409 |
++# |
| 410 |
++# As a special exception, the respective Autoconf Macro's copyright owner |
| 411 |
++# gives unlimited permission to copy, distribute and modify the configure |
| 412 |
++# scripts that are the output of Autoconf when processing the Macro. You |
| 413 |
++# need not follow the terms of the GNU General Public License when using |
| 414 |
++# or distributing such scripts, even though portions of the text of the |
| 415 |
++# Macro appear in them. The GNU General Public License (GPL) does govern |
| 416 |
++# all other use of the material that constitutes the Autoconf Macro. |
| 417 |
++# |
| 418 |
++# This special exception to the GPL applies to versions of the Autoconf |
| 419 |
++# Macro released by the Autoconf Archive. When you make and distribute a |
| 420 |
++# modified version of the Autoconf Macro, you may extend this special |
| 421 |
++# exception to the GPL to apply to your modified version as well. |
| 422 |
++ |
| 423 |
++#serial 16 |
| 424 |
++ |
| 425 |
++# internal function to factorize common code that is used by both ncurses |
| 426 |
++# and ncursesw |
| 427 |
++AC_DEFUN([_FIND_CURSES_FLAGS], [ |
| 428 |
++ AC_MSG_CHECKING([for $1 via pkg-config]) |
| 429 |
++ |
| 430 |
++ _PKG_CONFIG([_ax_cv_$1_lib], [libs], [$1]) |
| 431 |
++ _PKG_CONFIG([_ax_cv_$1_cppflags], [cflags], [$1]) |
| 432 |
++ |
| 433 |
++ AS_IF([test "x$pkg_failed" = "xyes" || test "x$pkg_failed" = "xuntried"],[ |
| 434 |
++ AC_MSG_RESULT([no]) |
| 435 |
++ # No suitable .pc file found, have to find flags via fallback |
| 436 |
++ AC_CACHE_CHECK([for $1 via fallback], [ax_cv_$1], [ |
| 437 |
++ AS_ECHO() |
| 438 |
++ pkg_cv__ax_cv_$1_lib="-l$1" |
| 439 |
++ pkg_cv__ax_cv_$1_cppflags="$CURSES_CPPFLAGS" |
| 440 |
++ LIBS="$ax_saved_LIBS $pkg_cv__ax_cv_$1_lib" |
| 441 |
++ CPPFLAGS="$ax_saved_CPPFLAGS $pkg_cv__ax_cv_$1_cppflags" |
| 442 |
++ |
| 443 |
++ AC_MSG_CHECKING([for initscr() with $pkg_cv__ax_cv_$1_lib]) |
| 444 |
++ AC_LINK_IFELSE([AC_LANG_CALL([], [initscr])], |
| 445 |
++ [ |
| 446 |
++ AC_MSG_RESULT([yes]) |
| 447 |
++ AC_MSG_CHECKING([for nodelay() with $pkg_cv__ax_cv_$1_lib]) |
| 448 |
++ AC_LINK_IFELSE([AC_LANG_CALL([], [nodelay])],[ |
| 449 |
++ ax_cv_$1=yes |
| 450 |
++ ],[ |
| 451 |
++ AC_MSG_RESULT([no]) |
| 452 |
++ m4_if( |
| 453 |
++ [$1],[ncursesw],[pkg_cv__ax_cv_$1_lib="$pkg_cv__ax_cv_$1_lib -ltinfow"], |
| 454 |
++ [$1],[ncurses],[pkg_cv__ax_cv_$1_lib="$pkg_cv__ax_cv_$1_lib -ltinfo"] |
| 455 |
++ ) |
| 456 |
++ LIBS="$ax_saved_LIBS $pkg_cv__ax_cv_$1_lib" |
| 457 |
++ |
| 458 |
++ AC_MSG_CHECKING([for nodelay() with $pkg_cv__ax_cv_$1_lib]) |
| 459 |
++ AC_LINK_IFELSE([AC_LANG_CALL([], [nodelay])],[ |
| 460 |
++ ax_cv_$1=yes |
| 461 |
++ ],[ |
| 462 |
++ ax_cv_$1=no |
| 463 |
++ ]) |
| 464 |
++ ]) |
| 465 |
++ ],[ |
| 466 |
++ ax_cv_$1=no |
| 467 |
++ ]) |
| 468 |
++ ]) |
| 469 |
++ ],[ |
| 470 |
++ AC_MSG_RESULT([yes]) |
| 471 |
++ # Found .pc file, using its information |
| 472 |
++ LIBS="$ax_saved_LIBS $pkg_cv__ax_cv_$1_lib" |
| 473 |
++ CPPFLAGS="$ax_saved_CPPFLAGS $pkg_cv__ax_cv_$1_cppflags" |
| 474 |
++ ax_cv_$1=yes |
| 475 |
++ ]) |
| 476 |
++]) |
| 477 |
++ |
| 478 |
++AU_ALIAS([MP_WITH_CURSES], [AX_WITH_CURSES]) |
| 479 |
++AC_DEFUN([AX_WITH_CURSES], [ |
| 480 |
++ AC_ARG_VAR([CURSES_LIB], [linker library for Curses, e.g. -lcurses]) |
| 481 |
++ AC_ARG_VAR([CURSES_CPPFLAGS], [preprocessor flags for Curses, e.g. -I/usr/include/ncursesw]) |
| 482 |
++ AC_ARG_WITH([ncurses], [AS_HELP_STRING([--with-ncurses], |
| 483 |
++ [force the use of Ncurses or NcursesW])], |
| 484 |
++ [], [with_ncurses=check]) |
| 485 |
++ AC_ARG_WITH([ncursesw], [AS_HELP_STRING([--without-ncursesw], |
| 486 |
++ [do not use NcursesW (wide character support)])], |
| 487 |
++ [], [with_ncursesw=check]) |
| 488 |
++ AC_REQUIRE([PKG_PROG_PKG_CONFIG]) |
| 489 |
++ |
| 490 |
++ ax_saved_LIBS=$LIBS |
| 491 |
++ ax_saved_CPPFLAGS=$CPPFLAGS |
| 492 |
++ |
| 493 |
++ AS_IF([test "x$with_ncurses" = xyes || test "x$with_ncursesw" = xyes], |
| 494 |
++ [ax_with_plaincurses=no], [ax_with_plaincurses=check]) |
| 495 |
++ |
| 496 |
++ ax_cv_curses_which=no |
| 497 |
++ |
| 498 |
++ # Test for NcursesW |
| 499 |
++ AS_IF([test "x$CURSES_LIB" = x && test "x$with_ncursesw" != xno], [ |
| 500 |
++ _FIND_CURSES_FLAGS([ncursesw]) |
| 501 |
++ |
| 502 |
++ AS_IF([test "x$ax_cv_ncursesw" = xno && test "x$with_ncursesw" = xyes], [ |
| 503 |
++ AC_MSG_ERROR([--with-ncursesw specified but could not find NcursesW library]) |
| 504 |
++ ]) |
| 505 |
++ |
| 506 |
++ AS_IF([test "x$ax_cv_ncursesw" = xyes], [ |
| 507 |
++ ax_cv_curses=yes |
| 508 |
++ ax_cv_curses_which=ncursesw |
| 509 |
++ CURSES_LIB="$pkg_cv__ax_cv_ncursesw_lib" |
| 510 |
++ CURSES_CPPFLAGS="$pkg_cv__ax_cv_ncursesw_cppflags" |
| 511 |
++ AC_DEFINE([HAVE_NCURSESW], [1], [Define to 1 if the NcursesW library is present]) |
| 512 |
++ AC_DEFINE([HAVE_CURSES], [1], [Define to 1 if a SysV or X/Open compatible Curses library is present]) |
| 513 |
++ |
| 514 |
++ AC_CACHE_CHECK([for working ncursesw/curses.h], [ax_cv_header_ncursesw_curses_h], [ |
| 515 |
++ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ |
| 516 |
++ @%:@define _XOPEN_SOURCE_EXTENDED 1 |
| 517 |
++ @%:@include <ncursesw/curses.h> |
| 518 |
++ ]], [[ |
| 519 |
++ chtype a = A_BOLD; |
| 520 |
++ int b = KEY_LEFT; |
| 521 |
++ chtype c = COLOR_PAIR(1) & A_COLOR; |
| 522 |
++ attr_t d = WA_NORMAL; |
| 523 |
++ cchar_t e; |
| 524 |
++ wint_t f; |
| 525 |
++ int g = getattrs(stdscr); |
| 526 |
++ int h = getcurx(stdscr) + getmaxx(stdscr); |
| 527 |
++ initscr(); |
| 528 |
++ init_pair(1, COLOR_WHITE, COLOR_RED); |
| 529 |
++ wattr_set(stdscr, d, 0, NULL); |
| 530 |
++ wget_wch(stdscr, &f); |
| 531 |
++ ]])], |
| 532 |
++ [ax_cv_header_ncursesw_curses_h=yes], |
| 533 |
++ [ax_cv_header_ncursesw_curses_h=no]) |
| 534 |
++ ]) |
| 535 |
++ AS_IF([test "x$ax_cv_header_ncursesw_curses_h" = xyes], [ |
| 536 |
++ ax_cv_curses_enhanced=yes |
| 537 |
++ ax_cv_curses_color=yes |
| 538 |
++ ax_cv_curses_obsolete=yes |
| 539 |
++ AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions]) |
| 540 |
++ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) |
| 541 |
++ AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features]) |
| 542 |
++ AC_DEFINE([HAVE_NCURSESW_CURSES_H], [1], [Define to 1 if <ncursesw/curses.h> is present]) |
| 543 |
++ ]) |
| 544 |
++ |
| 545 |
++ AC_CACHE_CHECK([for working ncursesw.h], [ax_cv_header_ncursesw_h], [ |
| 546 |
++ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ |
| 547 |
++ @%:@define _XOPEN_SOURCE_EXTENDED 1 |
| 548 |
++ @%:@include <ncursesw.h> |
| 549 |
++ ]], [[ |
| 550 |
++ chtype a = A_BOLD; |
| 551 |
++ int b = KEY_LEFT; |
| 552 |
++ chtype c = COLOR_PAIR(1) & A_COLOR; |
| 553 |
++ attr_t d = WA_NORMAL; |
| 554 |
++ cchar_t e; |
| 555 |
++ wint_t f; |
| 556 |
++ int g = getattrs(stdscr); |
| 557 |
++ int h = getcurx(stdscr) + getmaxx(stdscr); |
| 558 |
++ initscr(); |
| 559 |
++ init_pair(1, COLOR_WHITE, COLOR_RED); |
| 560 |
++ wattr_set(stdscr, d, 0, NULL); |
| 561 |
++ wget_wch(stdscr, &f); |
| 562 |
++ ]])], |
| 563 |
++ [ax_cv_header_ncursesw_h=yes], |
| 564 |
++ [ax_cv_header_ncursesw_h=no]) |
| 565 |
++ ]) |
| 566 |
++ AS_IF([test "x$ax_cv_header_ncursesw_h" = xyes], [ |
| 567 |
++ ax_cv_curses_enhanced=yes |
| 568 |
++ ax_cv_curses_color=yes |
| 569 |
++ ax_cv_curses_obsolete=yes |
| 570 |
++ AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions]) |
| 571 |
++ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) |
| 572 |
++ AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features]) |
| 573 |
++ AC_DEFINE([HAVE_NCURSESW_H], [1], [Define to 1 if <ncursesw.h> is present]) |
| 574 |
++ ]) |
| 575 |
++ |
| 576 |
++ AC_CACHE_CHECK([for working ncurses.h], [ax_cv_header_ncurses_h_with_ncursesw], [ |
| 577 |
++ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ |
| 578 |
++ @%:@define _XOPEN_SOURCE_EXTENDED 1 |
| 579 |
++ @%:@include <ncurses.h> |
| 580 |
++ ]], [[ |
| 581 |
++ chtype a = A_BOLD; |
| 582 |
++ int b = KEY_LEFT; |
| 583 |
++ chtype c = COLOR_PAIR(1) & A_COLOR; |
| 584 |
++ attr_t d = WA_NORMAL; |
| 585 |
++ cchar_t e; |
| 586 |
++ wint_t f; |
| 587 |
++ int g = getattrs(stdscr); |
| 588 |
++ int h = getcurx(stdscr) + getmaxx(stdscr); |
| 589 |
++ initscr(); |
| 590 |
++ init_pair(1, COLOR_WHITE, COLOR_RED); |
| 591 |
++ wattr_set(stdscr, d, 0, NULL); |
| 592 |
++ wget_wch(stdscr, &f); |
| 593 |
++ ]])], |
| 594 |
++ [ax_cv_header_ncurses_h_with_ncursesw=yes], |
| 595 |
++ [ax_cv_header_ncurses_h_with_ncursesw=no]) |
| 596 |
++ ]) |
| 597 |
++ AS_IF([test "x$ax_cv_header_ncurses_h_with_ncursesw" = xyes], [ |
| 598 |
++ ax_cv_curses_enhanced=yes |
| 599 |
++ ax_cv_curses_color=yes |
| 600 |
++ ax_cv_curses_obsolete=yes |
| 601 |
++ AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions]) |
| 602 |
++ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) |
| 603 |
++ AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features]) |
| 604 |
++ AC_DEFINE([HAVE_NCURSES_H], [1], [Define to 1 if <ncurses.h> is present]) |
| 605 |
++ ]) |
| 606 |
++ |
| 607 |
++ AS_IF([test "x$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], [ |
| 608 |
++ AC_MSG_WARN([could not find a working ncursesw/curses.h, ncursesw.h or ncurses.h]) |
| 609 |
++ ]) |
| 610 |
++ ]) |
| 611 |
++ ]) |
| 612 |
++ unset pkg_cv__ax_cv_ncursesw_lib |
| 613 |
++ unset pkg_cv__ax_cv_ncursesw_cppflags |
| 614 |
++ |
| 615 |
++ # Test for Ncurses |
| 616 |
++ AS_IF([test "x$CURSES_LIB" = x && test "x$with_ncurses" != xno && test "x$ax_cv_curses_which" = xno], [ |
| 617 |
++ _FIND_CURSES_FLAGS([ncurses]) |
| 618 |
++ |
| 619 |
++ AS_IF([test "x$ax_cv_ncurses" = xno && test "x$with_ncurses" = xyes], [ |
| 620 |
++ AC_MSG_ERROR([--with-ncurses specified but could not find Ncurses library]) |
| 621 |
++ ]) |
| 622 |
++ |
| 623 |
++ AS_IF([test "x$ax_cv_ncurses" = xyes], [ |
| 624 |
++ ax_cv_curses=yes |
| 625 |
++ ax_cv_curses_which=ncurses |
| 626 |
++ CURSES_LIB="$pkg_cv__ax_cv_ncurses_lib" |
| 627 |
++ CURSES_CPPFLAGS="$pkg_cv__ax_cv_ncurses_cppflags" |
| 628 |
++ AC_DEFINE([HAVE_NCURSES], [1], [Define to 1 if the Ncurses library is present]) |
| 629 |
++ AC_DEFINE([HAVE_CURSES], [1], [Define to 1 if a SysV or X/Open compatible Curses library is present]) |
| 630 |
++ |
| 631 |
++ AC_CACHE_CHECK([for working ncurses/curses.h], [ax_cv_header_ncurses_curses_h], [ |
| 632 |
++ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ |
| 633 |
++ @%:@include <ncurses/curses.h> |
| 634 |
++ ]], [[ |
| 635 |
++ chtype a = A_BOLD; |
| 636 |
++ int b = KEY_LEFT; |
| 637 |
++ chtype c = COLOR_PAIR(1) & A_COLOR; |
| 638 |
++ int g = getattrs(stdscr); |
| 639 |
++ int h = getcurx(stdscr) + getmaxx(stdscr); |
| 640 |
++ initscr(); |
| 641 |
++ init_pair(1, COLOR_WHITE, COLOR_RED); |
| 642 |
++ ]])], |
| 643 |
++ [ax_cv_header_ncurses_curses_h=yes], |
| 644 |
++ [ax_cv_header_ncurses_curses_h=no]) |
| 645 |
++ ]) |
| 646 |
++ AS_IF([test "x$ax_cv_header_ncurses_curses_h" = xyes], [ |
| 647 |
++ ax_cv_curses_color=yes |
| 648 |
++ ax_cv_curses_obsolete=yes |
| 649 |
++ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) |
| 650 |
++ AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features]) |
| 651 |
++ AC_DEFINE([HAVE_NCURSES_CURSES_H], [1], [Define to 1 if <ncurses/curses.h> is present]) |
| 652 |
++ ]) |
| 653 |
++ |
| 654 |
++ AC_CACHE_CHECK([for working ncurses.h], [ax_cv_header_ncurses_h], [ |
| 655 |
++ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ |
| 656 |
++ @%:@include <ncurses.h> |
| 657 |
++ ]], [[ |
| 658 |
++ chtype a = A_BOLD; |
| 659 |
++ int b = KEY_LEFT; |
| 660 |
++ chtype c = COLOR_PAIR(1) & A_COLOR; |
| 661 |
++ int g = getattrs(stdscr); |
| 662 |
++ int h = getcurx(stdscr) + getmaxx(stdscr); |
| 663 |
++ initscr(); |
| 664 |
++ init_pair(1, COLOR_WHITE, COLOR_RED); |
| 665 |
++ ]])], |
| 666 |
++ [ax_cv_header_ncurses_h=yes], |
| 667 |
++ [ax_cv_header_ncurses_h=no]) |
| 668 |
++ ]) |
| 669 |
++ AS_IF([test "x$ax_cv_header_ncurses_h" = xyes], [ |
| 670 |
++ ax_cv_curses_color=yes |
| 671 |
++ ax_cv_curses_obsolete=yes |
| 672 |
++ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) |
| 673 |
++ AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features]) |
| 674 |
++ AC_DEFINE([HAVE_NCURSES_H], [1], [Define to 1 if <ncurses.h> is present]) |
| 675 |
++ ]) |
| 676 |
++ |
| 677 |
++ AS_IF([test "x$ax_cv_header_ncurses_curses_h" = xno && test "x$ax_cv_header_ncurses_h" = xno], [ |
| 678 |
++ AC_MSG_WARN([could not find a working ncurses/curses.h or ncurses.h]) |
| 679 |
++ ]) |
| 680 |
++ ]) |
| 681 |
++ ]) |
| 682 |
++ unset pkg_cv__ax_cv_ncurses_lib |
| 683 |
++ unset pkg_cv__ax_cv_ncurses_cppflags |
| 684 |
++ |
| 685 |
++ # Test for plain Curses (or if CURSES_LIB was set by user) |
| 686 |
++ AS_IF([test "x$with_plaincurses" != xno && test "x$ax_cv_curses_which" = xno], [ |
| 687 |
++ AS_IF([test "x$CURSES_LIB" != x], [ |
| 688 |
++ LIBS="$ax_saved_LIBS $CURSES_LIB" |
| 689 |
++ ], [ |
| 690 |
++ LIBS="$ax_saved_LIBS -lcurses" |
| 691 |
++ ]) |
| 692 |
++ |
| 693 |
++ AC_CACHE_CHECK([for Curses library], [ax_cv_plaincurses], [ |
| 694 |
++ AC_LINK_IFELSE([AC_LANG_CALL([], [initscr])], |
| 695 |
++ [ax_cv_plaincurses=yes], [ax_cv_plaincurses=no]) |
| 696 |
++ ]) |
| 697 |
++ |
| 698 |
++ AS_IF([test "x$ax_cv_plaincurses" = xyes], [ |
| 699 |
++ ax_cv_curses=yes |
| 700 |
++ ax_cv_curses_which=plaincurses |
| 701 |
++ AS_IF([test "x$CURSES_LIB" = x], [ |
| 702 |
++ CURSES_LIB="-lcurses" |
| 703 |
++ ]) |
| 704 |
++ AC_DEFINE([HAVE_CURSES], [1], [Define to 1 if a SysV or X/Open compatible Curses library is present]) |
| 705 |
++ |
| 706 |
++ # Check for base conformance (and header file) |
| 707 |
++ |
| 708 |
++ AC_CACHE_CHECK([for working curses.h], [ax_cv_header_curses_h], [ |
| 709 |
++ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ |
| 710 |
++ @%:@include <curses.h> |
| 711 |
++ ]], [[ |
| 712 |
++ chtype a = A_BOLD; |
| 713 |
++ int b = KEY_LEFT; |
| 714 |
++ initscr(); |
| 715 |
++ ]])], |
| 716 |
++ [ax_cv_header_curses_h=yes], |
| 717 |
++ [ax_cv_header_curses_h=no]) |
| 718 |
++ ]) |
| 719 |
++ AS_IF([test "x$ax_cv_header_curses_h" = xyes], [ |
| 720 |
++ AC_DEFINE([HAVE_CURSES_H], [1], [Define to 1 if <curses.h> is present]) |
| 721 |
++ |
| 722 |
++ # Check for X/Open Enhanced conformance |
| 723 |
++ |
| 724 |
++ AC_CACHE_CHECK([for X/Open Enhanced Curses conformance], [ax_cv_plaincurses_enhanced], [ |
| 725 |
++ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ |
| 726 |
++ @%:@define _XOPEN_SOURCE_EXTENDED 1 |
| 727 |
++ @%:@include <curses.h> |
| 728 |
++ @%:@ifndef _XOPEN_CURSES |
| 729 |
++ @%:@error "this Curses library is not enhanced" |
| 730 |
++ "this Curses library is not enhanced" |
| 731 |
++ @%:@endif |
| 732 |
++ ]], [[ |
| 733 |
++ chtype a = A_BOLD; |
| 734 |
++ int b = KEY_LEFT; |
| 735 |
++ chtype c = COLOR_PAIR(1) & A_COLOR; |
| 736 |
++ attr_t d = WA_NORMAL; |
| 737 |
++ cchar_t e; |
| 738 |
++ wint_t f; |
| 739 |
++ initscr(); |
| 740 |
++ init_pair(1, COLOR_WHITE, COLOR_RED); |
| 741 |
++ wattr_set(stdscr, d, 0, NULL); |
| 742 |
++ wget_wch(stdscr, &f); |
| 743 |
++ ]])], |
| 744 |
++ [ax_cv_plaincurses_enhanced=yes], |
| 745 |
++ [ax_cv_plaincurses_enhanced=no]) |
| 746 |
++ ]) |
| 747 |
++ AS_IF([test "x$ax_cv_plaincurses_enhanced" = xyes], [ |
| 748 |
++ ax_cv_curses_enhanced=yes |
| 749 |
++ ax_cv_curses_color=yes |
| 750 |
++ AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions]) |
| 751 |
++ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) |
| 752 |
++ ]) |
| 753 |
++ |
| 754 |
++ # Check for color functions |
| 755 |
++ |
| 756 |
++ AC_CACHE_CHECK([for Curses color functions], [ax_cv_plaincurses_color], [ |
| 757 |
++ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ |
| 758 |
++ @%:@define _XOPEN_SOURCE_EXTENDED 1 |
| 759 |
++ @%:@include <curses.h> |
| 760 |
++ ]], [[ |
| 761 |
++ chtype a = A_BOLD; |
| 762 |
++ int b = KEY_LEFT; |
| 763 |
++ chtype c = COLOR_PAIR(1) & A_COLOR; |
| 764 |
++ initscr(); |
| 765 |
++ init_pair(1, COLOR_WHITE, COLOR_RED); |
| 766 |
++ ]])], |
| 767 |
++ [ax_cv_plaincurses_color=yes], |
| 768 |
++ [ax_cv_plaincurses_color=no]) |
| 769 |
++ ]) |
| 770 |
++ AS_IF([test "x$ax_cv_plaincurses_color" = xyes], [ |
| 771 |
++ ax_cv_curses_color=yes |
| 772 |
++ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) |
| 773 |
++ ]) |
| 774 |
++ |
| 775 |
++ # Check for obsolete functions |
| 776 |
++ |
| 777 |
++ AC_CACHE_CHECK([for obsolete Curses functions], [ax_cv_plaincurses_obsolete], [ |
| 778 |
++ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ |
| 779 |
++ @%:@include <curses.h> |
| 780 |
++ ]], [[ |
| 781 |
++ chtype a = A_BOLD; |
| 782 |
++ int b = KEY_LEFT; |
| 783 |
++ int g = getattrs(stdscr); |
| 784 |
++ int h = getcurx(stdscr) + getmaxx(stdscr); |
| 785 |
++ initscr(); |
| 786 |
++ ]])], |
| 787 |
++ [ax_cv_plaincurses_obsolete=yes], |
| 788 |
++ [ax_cv_plaincurses_obsolete=no]) |
| 789 |
++ ]) |
| 790 |
++ AS_IF([test "x$ax_cv_plaincurses_obsolete" = xyes], [ |
| 791 |
++ ax_cv_curses_obsolete=yes |
| 792 |
++ AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features]) |
| 793 |
++ ]) |
| 794 |
++ ]) |
| 795 |
++ |
| 796 |
++ AS_IF([test "x$ax_cv_header_curses_h" = xno], [ |
| 797 |
++ AC_MSG_WARN([could not find a working curses.h]) |
| 798 |
++ ]) |
| 799 |
++ ]) |
| 800 |
++ ]) |
| 801 |
++ |
| 802 |
++ AS_IF([test "x$ax_cv_curses" != xyes], [ax_cv_curses=no]) |
| 803 |
++ AS_IF([test "x$ax_cv_curses_enhanced" != xyes], [ax_cv_curses_enhanced=no]) |
| 804 |
++ AS_IF([test "x$ax_cv_curses_color" != xyes], [ax_cv_curses_color=no]) |
| 805 |
++ AS_IF([test "x$ax_cv_curses_obsolete" != xyes], [ax_cv_curses_obsolete=no]) |
| 806 |
++ |
| 807 |
++ LIBS=$ax_saved_LIBS |
| 808 |
++ CPPFLAGS=$ax_saved_CPPFLAGS |
| 809 |
++ |
| 810 |
++ unset ax_saved_LIBS |
| 811 |
++ unset ax_saved_CPPFLAGS |
| 812 |
++])dnl |
| 813 |
+--- samtools-1.3/m4/ax_with_htslib.m4 |
| 814 |
++++ samtools-1.3/m4/ax_with_htslib.m4 |
| 815 |
+@@ -0,0 +1,140 @@ |
| 816 |
++# =========================================================================== |
| 817 |
++# http://www.gnu.org/software/autoconf-archive/ax_with_htslib.html |
| 818 |
++# =========================================================================== |
| 819 |
++# |
| 820 |
++# SYNOPSIS |
| 821 |
++# |
| 822 |
++# AX_WITH_HTSLIB |
| 823 |
++# |
| 824 |
++# DESCRIPTION |
| 825 |
++# |
| 826 |
++# This macro checks whether HTSlib <http://www.htslib.org/> is installed |
| 827 |
++# or nearby, and adds a --with-htslib=DIR option to the configure script |
| 828 |
++# for specifying the location. It locates either an installation prefix |
| 829 |
++# (with 'include' and 'lib' subdirectories) or an HTSlib source tree, as |
| 830 |
++# HTSlib is fast-moving and users may wish to use an in-development tree. |
| 831 |
++# |
| 832 |
++# Different checks occur depending on the --with-htslib argument given: |
| 833 |
++# |
| 834 |
++# With --with-htslib=DIR, checks whether DIR is a source tree or contains |
| 835 |
++# a working installation. |
| 836 |
++# By default, searches for a source tree (with a name matching htslib*) |
| 837 |
++# within or alongside $srcdir. Produces AC_MSG_ERROR if there are |
| 838 |
++# several equally-likely candidates. If there are none, checks for |
| 839 |
++# a working default installation. |
| 840 |
++# With --with-htslib=system, checks for a working default installation. |
| 841 |
++# |
| 842 |
++# If a source tree is found or specified, it is added to AC_CONFIG_SUBDIRS |
| 843 |
++# (which unfortunately may cause a "you should use literals" warning when |
| 844 |
++# autoconf is run). |
| 845 |
++# |
| 846 |
++# The following output variables are set by this macro: |
| 847 |
++# |
| 848 |
++# HTSDIR Directory containing HTSlib source tree |
| 849 |
++# HTSLIB_CPPFLAGS Preprocessor flags for compiling with HTSlib |
| 850 |
++# HTSLIB_LDFLAGS Linker flags for linking with HTSlib |
| 851 |
++# |
| 852 |
++# The following shell variables may be defined: |
| 853 |
++# |
| 854 |
++# ax_cv_htslib Set to "yes" if HTSlib was found |
| 855 |
++# ax_cv_htslib_which Set to "source", "install", or "none" |
| 856 |
++# |
| 857 |
++# LICENSE |
| 858 |
++# |
| 859 |
++# Copyright (C) 2015 Genome Research Ltd |
| 860 |
++# |
| 861 |
++# Copying and distribution of this file, with or without modification, are |
| 862 |
++# permitted in any medium without royalty provided the copyright notice |
| 863 |
++# and this notice are preserved. This file is offered as-is, without any |
| 864 |
++# warranty. |
| 865 |
++ |
| 866 |
++#serial 1 |
| 867 |
++ |
| 868 |
++AC_DEFUN([AX_WITH_HTSLIB], |
| 869 |
++[AC_ARG_WITH([htslib], |
| 870 |
++ [AS_HELP_STRING([--with-htslib=DIR], |
| 871 |
++ [use the HTSlib source tree or installation in DIR]) |
| 872 |
++dnl Not indented, to avoid extra whitespace outwith AS_HELP_STRING() |
| 873 |
++AS_HELP_STRING([--with-htslib=system], |
| 874 |
++ [use only a system HTSlib installation])], |
| 875 |
++ [], [with_htslib=search]) |
| 876 |
++ |
| 877 |
++case $with_htslib in |
| 878 |
++yes|search) |
| 879 |
++ AC_MSG_CHECKING([location of HTSlib source tree]) |
| 880 |
++ case $srcdir in |
| 881 |
++ .) srcp= ;; |
| 882 |
++ *) srcp=$srcdir/ ;; |
| 883 |
++ esac |
| 884 |
++ found= |
| 885 |
++ for dir in ${srcp}htslib* -- ${srcp}../htslib -- ${srcp}../htslib* |
| 886 |
++ do |
| 887 |
++ if test "$dir" = "--"; then |
| 888 |
++ test -n "$found" && break |
| 889 |
++ elif test -f "$dir/hts.c" && test -f "$dir/htslib/hts.h"; then |
| 890 |
++ found="${found}1" |
| 891 |
++ HTSDIR=$dir |
| 892 |
++ fi |
| 893 |
++ done |
| 894 |
++ if test -z "$found"; then |
| 895 |
++ AC_MSG_RESULT([none found]) |
| 896 |
++ ax_cv_htslib_which=system |
| 897 |
++ elif test "$found" = 1; then |
| 898 |
++ AC_MSG_RESULT([$HTSDIR]) |
| 899 |
++ ax_cv_htslib_which=source |
| 900 |
++ else |
| 901 |
++ AC_MSG_RESULT([several directories found]) |
| 902 |
++ AC_MSG_ERROR([use --with-htslib=DIR to select which HTSlib to use]) |
| 903 |
++ fi |
| 904 |
++ ;; |
| 905 |
++no) ax_cv_htslib_which=none ;; |
| 906 |
++system) ax_cv_htslib_which=system ;; |
| 907 |
++*) |
| 908 |
++ HTSDIR=$with_htslib |
| 909 |
++ if test -f "$HTSDIR/hts.c" && test -f "$HTSDIR/htslib/hts.h"; then |
| 910 |
++ ax_cv_htslib_which=source |
| 911 |
++ else |
| 912 |
++ ax_cv_htslib_which=install |
| 913 |
++ fi |
| 914 |
++ ;; |
| 915 |
++esac |
| 916 |
++ |
| 917 |
++case $ax_cv_htslib_which in |
| 918 |
++source) |
| 919 |
++ ax_cv_htslib=yes |
| 920 |
++ HTSLIB_CPPFLAGS="-I$HTSDIR" |
| 921 |
++ HTSLIB_LDFLAGS="-L$HTSDIR" |
| 922 |
++ # We can't use a literal, because $HTSDIR is user-provided and variable |
| 923 |
++ AC_CONFIG_SUBDIRS($HTSDIR) |
| 924 |
++ ;; |
| 925 |
++system) |
| 926 |
++ AC_CHECK_HEADER([htslib/sam.h], |
| 927 |
++ [AC_CHECK_LIB(hts, hts_version, [ax_cv_htslib=yes], [ax_cv_htslib=no])], |
| 928 |
++ [ax_cv_htslib=no], [;]) |
| 929 |
++ ax_cv_htslib_which=install |
| 930 |
++ HTSDIR= |
| 931 |
++ HTSLIB_CPPFLAGS= |
| 932 |
++ HTSLIB_LDFLAGS= |
| 933 |
++ ;; |
| 934 |
++install) |
| 935 |
++ ax_saved_CPPFLAGS=$CPPFLAGS |
| 936 |
++ ax_saved_LDFLAGS=$LDFLAGS |
| 937 |
++ HTSLIB_CPPFLAGS="-I$HTSDIR/include" |
| 938 |
++ HTSLIB_LDFLAGS="-L$HTSDIR/lib" |
| 939 |
++ CPPFLAGS="$CPPFLAGS $HTSLIB_CPPFLAGS" |
| 940 |
++ LDFLAGS="$LDFLAGS $HTSLIB_LDFLAGS" |
| 941 |
++ AC_CHECK_HEADER([htslib/sam.h], |
| 942 |
++ [AC_CHECK_LIB(hts, hts_version, [ax_cv_htslib=yes], [ax_cv_htslib=no])], |
| 943 |
++ [ax_cv_htslib=no], [;]) |
| 944 |
++ HTSDIR= |
| 945 |
++ CPPFLAGS=$ax_saved_CPPFLAGS |
| 946 |
++ LDFLAGS=$ax_saved_LDFLAGS |
| 947 |
++ ;; |
| 948 |
++none) |
| 949 |
++ ax_cv_htslib=no |
| 950 |
++ ;; |
| 951 |
++esac |
| 952 |
++ |
| 953 |
++AC_SUBST([HTSDIR]) |
| 954 |
++AC_SUBST([HTSLIB_CPPFLAGS]) |
| 955 |
++AC_SUBST([HTSLIB_LDFLAGS])]) |
| 956 |
|
| 957 |
diff --git a/sci-biology/samtools/samtools-1.3.ebuild b/sci-biology/samtools/samtools-1.3.ebuild |
| 958 |
new file mode 100644 |
| 959 |
index 0000000..ec510ec |
| 960 |
--- /dev/null |
| 961 |
+++ b/sci-biology/samtools/samtools-1.3.ebuild |
| 962 |
@@ -0,0 +1,86 @@ |
| 963 |
+# Copyright 1999-2016 Gentoo Foundation |
| 964 |
+# Distributed under the terms of the GNU General Public License v2 |
| 965 |
+# $Id$ |
| 966 |
+ |
| 967 |
+EAPI=6 |
| 968 |
+ |
| 969 |
+PYTHON_COMPAT=( python2_7 ) |
| 970 |
+ |
| 971 |
+inherit autotools python-r1 toolchain-funcs |
| 972 |
+ |
| 973 |
+DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats" |
| 974 |
+HOMEPAGE="http://www.htslib.org/" |
| 975 |
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" |
| 976 |
+ |
| 977 |
+LICENSE="MIT" |
| 978 |
+SLOT="0" |
| 979 |
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" |
| 980 |
+IUSE="examples" |
| 981 |
+ |
| 982 |
+REQUIRED_USE="${PYTHON_REQUIRED_USE}" |
| 983 |
+ |
| 984 |
+RDEPEND="sys-libs/ncurses:0= |
| 985 |
+ >=sci-libs/htslib-${PV} |
| 986 |
+ dev-lang/lua:0 |
| 987 |
+ dev-lang/perl" |
| 988 |
+DEPEND="${RDEPEND} |
| 989 |
+ virtual/pkgconfig" |
| 990 |
+ |
| 991 |
+PATCHES=( |
| 992 |
+ "${FILESDIR}/${P}-buildsystem.patch" |
| 993 |
+ "${FILESDIR}/${P}-ncurses.patch" |
| 994 |
+) |
| 995 |
+ |
| 996 |
+src_prepare() { |
| 997 |
+ default |
| 998 |
+ |
| 999 |
+ # unbundle libs |
| 1000 |
+ find htslib-* -delete || die |
| 1001 |
+ |
| 1002 |
+ sed -i -e 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die |
| 1003 |
+ sed -i -e '/htslib.mk/d' -i Makefile || die |
| 1004 |
+ |
| 1005 |
+ tc-export CC AR |
| 1006 |
+ |
| 1007 |
+ rm -f aclocal.m4 || die |
| 1008 |
+ eautoreconf |
| 1009 |
+} |
| 1010 |
+ |
| 1011 |
+src_compile() { |
| 1012 |
+ local mymakeargs=( |
| 1013 |
+ LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" |
| 1014 |
+ HTSDIR="${EPREFIX}/usr/include" |
| 1015 |
+ HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) |
| 1016 |
+ BAMLIB="libbam.so" |
| 1017 |
+ libdir=/usr/$(get_libdir) |
| 1018 |
+ ) |
| 1019 |
+ emake "${mymakeargs[@]}" |
| 1020 |
+} |
| 1021 |
+ |
| 1022 |
+src_test() { |
| 1023 |
+ local mymakeargs=( |
| 1024 |
+ LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" |
| 1025 |
+ HTSDIR="${EPREFIX}/usr/include" |
| 1026 |
+ HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) |
| 1027 |
+ BAMLIB="libbam.so" |
| 1028 |
+ ) |
| 1029 |
+ LD_LIBRARY_PATH="${S}" emake "${mymakeargs[@]}" test |
| 1030 |
+} |
| 1031 |
+ |
| 1032 |
+src_install() { |
| 1033 |
+ dobin samtools $(find misc -type f -executable) |
| 1034 |
+ |
| 1035 |
+ python_replicate_script "${ED}"/usr/bin/varfilter.py |
| 1036 |
+ dolib.so libbam.so* |
| 1037 |
+ |
| 1038 |
+ insinto /usr/include/bam |
| 1039 |
+ doins *.h |
| 1040 |
+ |
| 1041 |
+ doman ${PN}.1 |
| 1042 |
+ dodoc AUTHORS NEWS README |
| 1043 |
+ |
| 1044 |
+ if use examples; then |
| 1045 |
+ insinto /usr/share/${PN} |
| 1046 |
+ doins -r examples |
| 1047 |
+ fi |
| 1048 |
+} |
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