diff options
| -rw-r--r-- | sci-biology/samtools/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/samtools/files/samtools-1.5-buildsystem.patch | 413 | ||||
| -rw-r--r-- | sci-biology/samtools/samtools-1.5.ebuild | 61 |
3 files changed, 475 insertions, 0 deletions
diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest index d25774fee86c..791e2050ee7f 100644 --- a/sci-biology/samtools/Manifest +++ b/sci-biology/samtools/Manifest @@ -5,3 +5,4 @@ DIST samtools-1.0.tar.bz2 4459669 SHA256 7340b843663c3f54a902a06f2f73c68198f3a62 DIST samtools-1.1.tar.bz2 4495373 SHA256 c24d26c303153d72b5bf3cc11f72c6c375a4ca1140cc485648c8c5473414b7f8 SHA512 a5552a6c8c4b0808b725b39ddb2fafa36c4f6623bfc7f84faadae7690223e4eec8d722af09c77145796ad9b3f01e04115dd0207207ccfafbb52ffc22d5fc09f0 WHIRLPOOL ed3131b2a8d8b4dab40b53d35a9b00b657670a949dc1597c91fbcd00392c1c1715a85a1d1e49bf0c73ae082738ccfb13d2c6809dbbeba17ff3028f6023ebc449 DIST samtools-1.2.tar.bz2 4547126 SHA256 420e7a4a107fe37619b9d300b6379452eb8eb04a4a9b65c3ec69de82ccc26daa SHA512 4849c3274e732267516b63799f5430c5415d575d46eddf6b704dac51053281094b03b90dd9f5367bcd14c22fb0fb1bd6a412f7d4225f7be5f5385437c5d2101d WHIRLPOOL 273185764a807365a20c381769f987ef02d14ae8e20a3a7fd5af4344769c5fab68d7155523e8c0c8c3cc86092898c2c8454cce8f1560d415bc2b41549cdf04f4 DIST samtools-1.3.tar.bz2 3978333 SHA256 beea4003c795a0a25224656815b4036f6864b8753053ed30c590bb052b70b60e SHA512 72920d4f0f10aa7b54ef448e03e6e769e1e07abd07388a2307d0e52548fa2909c03ca2c7eec5c63cf5b67724b2356833accb0079ce1486bb2ac66a45963a24ea WHIRLPOOL 3f798078100b4ed164f6c89d18cc8f62159437e2cfb2a228ac00f8d08313f7c39ef546214c0796c25a419c0a1065dc21d14b966fed769726b9b1975ec07e3b3e +DIST samtools-1.5.tar.bz2 4190142 SHA256 8542da26832ee08c1978713f5f6188ff750635b50d8ab126a0c7bb2ac1ae2df6 SHA512 ff3e39ba867ecbd88f3363b038508c1557e349ea4223483f8f4ecb17ff8864fb53cd193bc2059a147e30f07395bbf53c8518d0f70219e454375c8bffe56e3059 WHIRLPOOL 1a88c9617857f1f6d146df179aef5b5c6bb83de8c9d127c405e5756842ced84c194a3f09f69a4757a8adf6ca623c9fdc972f4bf609649d3e991dda8f616e3582 diff --git a/sci-biology/samtools/files/samtools-1.5-buildsystem.patch b/sci-biology/samtools/files/samtools-1.5-buildsystem.patch new file mode 100644 index 000000000000..248089e09fcf --- /dev/null +++ b/sci-biology/samtools/files/samtools-1.5-buildsystem.patch @@ -0,0 +1,413 @@ +--- a/config.mk.in ++++ b/config.mk.in +@@ -28,27 +28,26 @@ + # in the Makefile to reflect your configuration choices. If you don't run + # configure, the main Makefile contains suitable conservative defaults. + +-prefix = @prefix@ +-exec_prefix = @exec_prefix@ +-bindir = @bindir@ +-datarootdir = @datarootdir@ +-mandir = @mandir@ ++prefix = @prefix@ ++exec_prefix = @exec_prefix@ ++bindir = @bindir@ ++libdir = @libdir@ ++datarootdir = @datarootdir@ ++mandir = @mandir@ ++man1dir = $(mandir)/man1 + + CC = @CC@ ++AR = @AR@ + CPPFLAGS = @CPPFLAGS@ + CFLAGS = @CFLAGS@ + LDFLAGS = @LDFLAGS@ + LIBS = @LIBS@ + +-@Hsource@HTSDIR = @HTSDIR@ +-@Hsource@include $(HTSDIR)/htslib.mk +-@Hsource@include $(HTSDIR)/htslib_static.mk +-@Hsource@HTSLIB = $(HTSDIR)/libhts.a +-@Hsource@HTSLIB_LIB = $(HTSLIB) $(HTSLIB_static_LIBS) +-@Hsource@HTSLIB_LDFLAGS = $(HTSLIB_static_LDFLAGS) +-@Hsource@BGZIP = $(HTSDIR)/bgzip +-HTSLIB_CPPFLAGS = @HTSLIB_CPPFLAGS@ +-@Hinstall@HTSLIB_LDFLAGS = @HTSLIB_LDFLAGS@ +-@Hinstall@HTSLIB_LIB = -lhts ++HTSLIB_CFLAGS = @HTSLIB_CFLAGS@ ++HTSLIB_LIBS = @HTSLIB_LIBS@ + +-CURSES_LIB = @CURSES_LIB@ ++NCURSES_CFLAGS = @NCURSES_CFLAGS@ ++NCURSES_LIBS = @NCURSES_LIBS@ ++ ++ZLIB_CFLAGS = @ZLIB_CFLAGS@ ++ZLIB_LIBS = @ZLIB_LIBS@ +--- a/configure.ac ++++ b/configure.ac +@@ -29,9 +29,6 @@ + AC_CONFIG_SRCDIR([bamtk.c]) + AC_CONFIG_HEADERS([config.h]) + +-m4_include([m4/ax_with_curses.m4]) +-m4_include([m4/ax_with_htslib.m4]) +- + dnl Copyright notice to be copied into the generated configure script + AC_COPYRIGHT([Portions copyright (C) 2015 Genome Research Ltd. + +@@ -39,73 +36,27 @@ + redistribute it. There is NO WARRANTY, to the extent permitted by law.]) + + AC_PROG_CC ++AM_PROG_AR + + AC_SYS_LARGEFILE + +-AX_WITH_HTSLIB +-if test "$ax_cv_htslib" != yes; then +- AC_MSG_ERROR([HTSlib development files not found +- +-Samtools uses HTSlib to parse bioinformatics file formats etc. Building it +-requires an unpacked HTSlib source tree (which will be built in conjunction +-with samtools) or a previously-installed HTSlib. In either case you may +-need to configure --with-htslib=DIR to locate the appropriate HTSlib. +- +-FAILED. You must supply an HTSlib in order to build samtools successfully.]) +-fi +- +-if test "$ax_cv_htslib_which" = source; then +- Hsource= +- Hinstall='#' +-else +- Hsource='#' +- Hinstall= +-fi +-AC_SUBST([Hsource]) +-AC_SUBST([Hinstall]) ++dnl htslib ++PKG_CHECK_MODULES([HTSLIB], [htslib]) + ++dnl ncurses + AC_ARG_WITH([curses], + [AS_HELP_STRING([--without-curses], + [omit curses support, so no curses library needed])]) + +-if test "$with_curses" != no; then +- AX_WITH_CURSES +- if test "$ax_cv_curses" != yes; then +- AC_MSG_ERROR([curses development files not found +- +-The 'samtools tview' command uses the curses text user interface library. +-Building samtools with tview requires curses/ncurses/etc development files +-to be installed on the build machine; you may need to ensure a package such +-as libncurses5-dev (on Debian or Ubuntu Linux) or ncurses-devel (on RPM-based +-Linux distributions) is installed. +- +-FAILED. Either configure --without-curses or resolve this error to build +-samtools successfully.]) +- fi +-else +- CURSES_LIB= +- CURSES_CPPFLAGS= +- AC_SUBST([CURSES_LIB]) +- AC_SUBST([CURSES_CPPFLAGS]) +-fi +- +-save_LIBS=$LIBS +-zlib_devel=ok +-dnl Set a trivial non-empty INCLUDES to avoid excess default includes tests +-AC_CHECK_HEADER([zlib.h], [], [zlib_devel=missing], [;]) +-AC_CHECK_LIB(z, inflate, [], [zlib_devel=missing]) +-LIBS=$save_LIBS +- +-if test $zlib_devel != ok; then +- AC_MSG_ERROR([zlib development files not found +- +-Samtools uses compression routines from the zlib library <http://zlib.net>. +-Building samtools requires zlib development files to be installed on the build +-machine; you may need to ensure a package such as zlib1g-dev (on Debian or +-Ubuntu Linux) or zlib-devel (on RPM-based Linux distributions) is installed. ++AS_IF([test "x$with_curses" != "xno"], [ ++ PKG_CHECK_MODULES([NCURSES], [ncurses]) ++ ++ AC_DEFINE([HAVE_CURSES], [1]) ++ AC_DEFINE([HAVE_NCURSES_H], [1]) ++]) + +-FAILED. This error must be resolved in order to build samtools successfully.]) +-fi ++dnl zlib ++PKG_CHECK_MODULES([ZLIB], [zlib]) + + AC_CONFIG_FILES([config.mk]) + AC_OUTPUT +--- a/Makefile ++++ b/Makefile +@@ -21,14 +21,6 @@ + # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + # DEALINGS IN THE SOFTWARE. + +-CC = gcc +-AR = ar +-CPPFLAGS = +-#CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 +-CFLAGS = -g -Wall -O2 +-LDFLAGS = +-LIBS = +- + LOBJS= bam_aux.o bam.o bam_import.o sam.o \ + sam_header.o bam_plbuf.o + AOBJS= bam_index.o bam_plcmd.o sam_view.o \ +@@ -40,13 +32,6 @@ + bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o \ + bam_quickcheck.o bam_addrprg.o + +-prefix = /usr/local +-exec_prefix = $(prefix) +-bindir = $(exec_prefix)/bin +-datarootdir = $(prefix)/share +-mandir = $(datarootdir)/man +-man1dir = $(mandir)/man1 +- + # Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS) + misc_bindir = $(bindir) + +@@ -85,15 +70,14 @@ + + all: $(PROGRAMS) $(MISC_PROGRAMS) $(TEST_PROGRAMS) + +-ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) +-ALL_LDFLAGS = $(HTSLIB_LDFLAGS) $(LDFLAGS) +-ALL_LIBS = -lz $(LIBS) ++ALL_CPPFLAGS = -I. $(HTSLIB_CFLAGS) $(CPPFLAGS) ++ALL_LIBS = $(ZLIB_LIBS) $(LIBS) + + # Usually config.mk and config.h are generated by running configure + # or config.status, but if those aren't used create defaults here. + + config.mk: +- @sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.5#g;s/@HTSLIB_CPPFLAGS@/-I$$(HTSDIR)/g;s/@CURSES_LIB@/-lcurses/g' config.mk.in > $@ ++ @sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.5#g;s/@HTSLIB_CFLAGS@/-I$$(HTSDIR)/g;s/@NCURSES_LIBS@/-lcurses/g' config.mk.in > $@ + + config.h: + echo '/* Basic config.h generated by Makefile */' > $@ +@@ -133,17 +117,22 @@ + .c.o: + $(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ $< + ++$(LOBJS): ++ $(CC) $(CFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $< ++ + + LIBST_OBJS = sam_opts.o sam_utils.o + + +-lib:libbam.a ++lib: libbam.so.1.0 + +-libbam.a:$(LOBJS) +- $(AR) -csru $@ $(LOBJS) ++libbam.so.1.0:$(LOBJS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB) ++ ln -sf $@ libbam.so.1 ++ ln -sf $@ libbam.so + +-samtools: $(AOBJS) libbam.a libst.a $(HTSLIB) +- $(CC) $(ALL_LDFLAGS) -o $@ $(AOBJS) libbam.a libst.a $(HTSLIB_LIB) $(CURSES_LIB) -lm $(ALL_LIBS) -lpthread ++samtools: $(AOBJS) libbam.so.1.0 libst.a ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) libbam.so.1.0 libst.a $(HTSLIB_LIBS) $(NCURSES_LIBS) -lm $(ALL_LIBS) -lpthread + + # For building samtools and its test suite only: NOT to be installed. + libst.a: $(LIBST_OBJS) +@@ -151,58 +140,58 @@ + $(AR) -rcs $@ $(LIBST_OBJS) + + +-bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h) +-bam2bcf_h = bam2bcf.h $(htslib_hts_h) $(htslib_vcf_h) +-bam_lpileup_h = bam_lpileup.h $(htslib_sam_h) +-bam_plbuf_h = bam_plbuf.h $(htslib_sam_h) +-bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(htslib_khash_h) $(bam_lpileup_h) +-sam_h = sam.h $(htslib_sam_h) $(bam_h) +-sam_opts_h = sam_opts.h $(htslib_hts_h) +-sample_h = sample.h $(htslib_kstring_h) +- +-bam.o: bam.c config.h $(bam_h) $(htslib_kstring_h) sam_header.h +-bam2bcf.o: bam2bcf.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_kstring_h) $(htslib_kfunc_h) $(bam2bcf_h) +-bam2bcf_indel.o: bam2bcf_indel.c config.h $(htslib_hts_h) $(htslib_sam_h) $(bam2bcf_h) $(htslib_khash_h) $(htslib_ksort_h) +-bam2depth.o: bam2depth.c config.h $(htslib_sam_h) samtools.h $(sam_opts_h) +-bam_addrprg.o: bam_addrprg.c config.h $(htslib_sam_h) $(htslib_kstring_h) samtools.h $(sam_opts_h) ++bam_h = bam.h ++bam2bcf_h = bam2bcf.h ++bam_lpileup_h = bam_lpileup.h ++bam_plbuf_h = bam_plbuf.h ++bam_tview_h = bam_tview.h $(bam2bcf_h) $(bam_lpileup_h) ++sam_h = sam.h $(bam_h) ++sam_opts_h = sam_opts.h ++sample_h = sample.h ++ ++bam.o: bam.c config.h $(bam_h) sam_header.h ++bam2bcf.o: bam2bcf.c config.h $(bam2bcf_h) ++bam2bcf_indel.o: bam2bcf_indel.c config.h $(bam2bcf_h) ++bam2depth.o: bam2depth.c config.h samtools.h $(sam_opts_h) ++bam_addrprg.o: bam_addrprg.c config.h samtools.h $(sam_opts_h) + bam_aux.o: bam_aux.c config.h $(bam_h) +-bam_cat.o: bam_cat.c config.h $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_cram_h) $(htslib_khash_h) samtools.h ++bam_cat.o: bam_cat.c config.h samtools.h + bam_color.o: bam_color.c config.h $(bam_h) +-bam_import.o: bam_import.c config.h $(htslib_kstring_h) $(bam_h) $(htslib_kseq_h) +-bam_index.o: bam_index.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_h) samtools.h +-bam_lpileup.o: bam_lpileup.c config.h $(bam_plbuf_h) $(bam_lpileup_h) $(htslib_ksort_h) +-bam_mate.o: bam_mate.c config.h $(sam_opts_h) $(htslib_kstring_h) $(htslib_sam_h) samtools.h +-bam_md.o: bam_md.c config.h $(htslib_faidx_h) $(htslib_sam_h) $(htslib_kstring_h) $(sam_opts_h) samtools.h +-bam_plbuf.o: bam_plbuf.c config.h $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h) +-bam_plcmd.o: bam_plcmd.c config.h $(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) +-bam_quickcheck.o: bam_quickcheck.c config.h $(htslib_hts_h) $(htslib_sam_h) +-bam_reheader.o: bam_reheader.c config.h $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_hfile_h) $(htslib_cram_h) samtools.h +-bam_rmdup.o: bam_rmdup.c config.h $(htslib_sam_h) $(sam_opts_h) samtools.h $(bam_h) $(htslib_khash_h) +-bam_rmdupse.o: bam_rmdupse.c config.h $(bam_h) $(htslib_sam_h) $(htslib_khash_h) $(htslib_klist_h) samtools.h +-bam_sort.o: bam_sort.c config.h $(htslib_ksort_h) $(htslib_khash_h) $(htslib_klist_h) $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) samtools.h +-bam_split.o: bam_split.c config.h $(htslib_sam_h) $(htslib_khash_h) $(htslib_kstring_h) $(htslib_cram_h) $(sam_opts_h) samtools.h +-bam_stat.o: bam_stat.c config.h $(htslib_sam_h) samtools.h +-bam_tview.o: bam_tview.c config.h $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h) samtools.h $(sam_opts_h) ++bam_import.o: bam_import.c config.h $(bam_h) ++bam_index.o: bam_index.c config.h samtools.h ++bam_lpileup.o: bam_lpileup.c config.h $(bam_plbuf_h) $(bam_lpileup_h) ++bam_mate.o: bam_mate.c config.h $(sam_opts_h) samtools.h ++bam_md.o: bam_md.c config.h $(sam_opts_h) samtools.h ++bam_plbuf.o: bam_plbuf.c config.h $(bam_plbuf_h) ++bam_plcmd.o: bam_plcmd.c config.h sam_header.h samtools.h $(sam_opts_h) $(bam2bcf_h) $(sample_h) ++bam_quickcheck.o: bam_quickcheck.c config.h ++bam_reheader.o: bam_reheader.c config.h samtools.h ++bam_rmdup.o: bam_rmdup.c config.h $(sam_opts_h) samtools.h $(bam_h) ++bam_rmdupse.o: bam_rmdupse.c config.h $(bam_h) samtools.h ++bam_sort.o: bam_sort.c config.h $(sam_opts_h) samtools.h ++bam_split.o: bam_split.c config.h $(sam_opts_h) samtools.h ++bam_stat.o: bam_stat.c config.h samtools.h ++bam_tview.o: bam_tview.c config.h $(bam_tview_h) samtools.h $(sam_opts_h) + bam_tview_curses.o: bam_tview_curses.c config.h $(bam_tview_h) + bam_tview_html.o: bam_tview_html.c config.h $(bam_tview_h) +-bam_flags.o: bam_flags.c config.h $(htslib_sam_h) +-bamshuf.o: bamshuf.c config.h $(htslib_sam_h) $(htslib_hts_h) $(htslib_ksort_h) samtools.h $(sam_opts_h) +-bamtk.o: bamtk.c config.h $(htslib_hts_h) samtools.h version.h +-bedcov.o: bedcov.c config.h $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) $(htslib_kseq_h) +-bedidx.o: bedidx.c config.h $(htslib_ksort_h) $(htslib_kseq_h) $(htslib_khash_h) +-cut_target.o: cut_target.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) samtools.h $(sam_opts_h) +-dict.o: dict.c config.h $(htslib_kseq_h) $(htslib_hts_h) +-faidx.o: faidx.c config.h $(htslib_faidx_h) samtools.h +-padding.o: padding.c config.h $(htslib_kstring_h) $(htslib_sam_h) $(htslib_faidx_h) sam_header.h $(sam_opts_h) samtools.h +-phase.o: phase.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_kstring_h) $(sam_opts_h) samtools.h $(htslib_kseq_h) $(htslib_khash_h) $(htslib_ksort_h) +-sam.o: sam.c config.h $(htslib_faidx_h) $(sam_h) +-sam_header.o: sam_header.c config.h sam_header.h $(htslib_khash_h) ++bam_flags.o: bam_flags.c config.h ++bamshuf.o: bamshuf.c config.h samtools.h $(sam_opts_h) ++bamtk.o: bamtk.c config.h samtools.h version.h ++bedcov.o: bedcov.c config.h $(sam_opts_h) ++bedidx.o: bedidx.c config.h ++cut_target.o: cut_target.c config.h samtools.h $(sam_opts_h) ++dict.o: dict.c config.h ++faidx.o: faidx.c config.h samtools.h ++padding.o: padding.c config.h sam_header.h $(sam_opts_h) samtools.h ++phase.o: phase.c config.h $(sam_opts_h) samtools.h ++sam.o: sam.c config.h $(sam_h) ++sam_header.o: sam_header.c config.h sam_header.h + sam_opts.o: sam_opts.c config.h $(sam_opts_h) + sam_utils.o: sam_utils.c config.h samtools.h +-sam_view.o: sam_view.c config.h $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_h) samtools.h $(sam_opts_h) +-sample.o: sample.c config.h $(sample_h) $(htslib_khash_h) +-stats_isize.o: stats_isize.c config.h stats_isize.h $(htslib_khash_h) +-stats.o: stats.c config.h $(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) ++sam_view.o: sam_view.c config.h samtools.h $(sam_opts_h) ++sample.o: sample.c config.h $(sample_h) ++stats_isize.o: stats_isize.c config.h stats_isize.h ++stats.o: stats.c config.h sam_header.h samtools.h stats_isize.h $(sam_opts_h) + + + # test programs +@@ -224,30 +213,30 @@ + + + test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o libst.a $(HTSLIB) +- $(CC) $(ALL_LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread + + test/merge/test_rtrans_build: test/merge/test_rtrans_build.o libst.a $(HTSLIB) +- $(CC) $(ALL_LDFLAGS) -o $@ test/merge/test_rtrans_build.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/merge/test_rtrans_build.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread + + test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o libst.a $(HTSLIB) +- $(CC) $(ALL_LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread + + test/split/test_count_rg: test/split/test_count_rg.o test/test.o libst.a $(HTSLIB) +- $(CC) $(ALL_LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread + + test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o libst.a $(HTSLIB) +- $(CC) $(ALL_LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread + + test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o libst.a $(HTSLIB) +- $(CC) $(ALL_LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread + + test/split/test_parse_args: test/split/test_parse_args.o test/test.o libst.a $(HTSLIB) +- $(CC) $(ALL_LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread + + test/vcf-miniview: test/vcf-miniview.o $(HTSLIB) +- $(CC) $(ALL_LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB_LIB) $(ALL_LIBS) -lpthread ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread + +-test_test_h = test/test.h $(htslib_sam_h) ++test_test_h = test/test.h + + test/merge/test_bam_translate.o: test/merge/test_bam_translate.c config.h bam_sort.o $(test_test_h) + test/merge/test_rtrans_build.o: test/merge/test_rtrans_build.c config.h bam_sort.o +@@ -256,34 +245,34 @@ + test/split/test_expand_format_string.o: test/split/test_expand_format_string.c config.h bam_split.o $(test_test_h) + test/split/test_filter_header_rg.o: test/split/test_filter_header_rg.c config.h bam_split.o $(test_test_h) + test/split/test_parse_args.o: test/split/test_parse_args.c config.h bam_split.o $(test_test_h) +-test/test.o: test/test.c config.h $(htslib_sam_h) $(test_test_h) +-test/vcf-miniview.o: test/vcf-miniview.c config.h $(htslib_vcf_h) ++test/test.o: test/test.c config.h $(test_test_h) ++test/vcf-miniview.o: test/vcf-miniview.c config.h + + + # misc programs + + misc/ace2sam: misc/ace2sam.o +- $(CC) $(LDFLAGS) -o $@ misc/ace2sam.o $(ALL_LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/ace2sam.o $(ALL_LIBS) + + misc/maq2sam-short: misc/maq2sam-short.o +- $(CC) $(LDFLAGS) -o $@ misc/maq2sam-short.o $(ALL_LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/maq2sam-short.o $(ALL_LIBS) + + misc/maq2sam-long: misc/maq2sam-long.o +- $(CC) $(LDFLAGS) -o $@ misc/maq2sam-long.o $(ALL_LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/maq2sam-long.o $(ALL_LIBS) + + misc/md5fa: misc/md5fa.o $(HTSLIB) +- $(CC) $(ALL_LDFLAGS) -o $@ misc/md5fa.o $(HTSLIB_LIB) $(ALL_LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/md5fa.o $(HTSLIB_LIBS) $(ALL_LIBS) + + misc/md5sum-lite: misc/md5sum-lite.o $(HTSLIB) +- $(CC) $(ALL_LDFLAGS) -o $@ misc/md5sum-lite.o $(HTSLIB_LIB) $(ALL_LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/md5sum-lite.o $(HTSLIB_LIBS) $(ALL_LIBS) + + misc/wgsim: misc/wgsim.o +- $(CC) $(LDFLAGS) -o $@ misc/wgsim.o -lm $(ALL_LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/wgsim.o -lm $(ALL_LIBS) + +-misc/ace2sam.o: misc/ace2sam.c config.h $(htslib_kstring_h) $(htslib_kseq_h) +-misc/md5fa.o: misc/md5fa.c config.h $(htslib_kseq_h) $(htslib_hts_h) +-misc/md5sum-lite.o: misc/md5sum-lite.c config.h $(htslib_hts_h) +-misc/wgsim.o: misc/wgsim.c config.h $(htslib_kseq_h) ++misc/ace2sam.o: misc/ace2sam.c config.h ++misc/md5fa.o: misc/md5fa.c config.h ++misc/md5sum-lite.o: misc/md5sum-lite.c config.h ++misc/wgsim.o: misc/wgsim.c config.h + + misc/maq2sam-short.o: misc/maq2sam.c config.h + $(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ misc/maq2sam.c diff --git a/sci-biology/samtools/samtools-1.5.ebuild b/sci-biology/samtools/samtools-1.5.ebuild new file mode 100644 index 000000000000..c2bc7ce89cf6 --- /dev/null +++ b/sci-biology/samtools/samtools-1.5.ebuild @@ -0,0 +1,61 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 ) + +inherit autotools python-r1 toolchain-funcs + +DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats" +HOMEPAGE="http://www.htslib.org/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" +IUSE="examples" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + dev-lang/perl + =sci-libs/htslib-${PV}* + sys-libs/ncurses:0= + sys-libs/zlib + ${PYTHON_DEPS}" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +PATCHES=( "${FILESDIR}/${PN}-1.5-buildsystem.patch" ) + +src_prepare() { + default + + python_setup + python_fix_shebang misc/varfilter.py + + # remove bundled htslib + rm -r htslib-* || die + + eautoreconf +} + +src_test() { + local -x LD_LIBRARY_PATH="${S}" + default +} + +src_install() { + default + + # install libbam and headers + dolib.so libbam.so* + + insinto /usr/include/bam + doins *.h + + if use examples; then + dodoc -r examples + docompress -x /usr/share/doc/${PF}/examples + fi +} |