commit: b6948f3ed9612bc6f11b4ccab40ac4d80f73e397 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Mon Aug 3 21:11:18 2020 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Mon Aug 3 21:11:18 2020 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b6948f3e
sci-biology/samtools: Remove old Closes: https://bugs.gentoo.org/728018 Package-Manager: Portage-3.0.1, Repoman-2.3.23 Signed-off-by: David Seifert <soap <AT> gentoo.org> sci-biology/samtools/Manifest | 2 - .../samtools/files/samtools-1.5-buildsystem.patch | 413 --------------------- sci-biology/samtools/samtools-1.5.ebuild | 61 --- sci-biology/samtools/samtools-1.9-r1.ebuild | 49 --- 4 files changed, 525 deletions(-) diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest index b06f63a40e7..622e57502c3 100644 --- a/sci-biology/samtools/Manifest +++ b/sci-biology/samtools/Manifest @@ -1,4 +1,2 @@ DIST samtools-0.1.20.tar.gz 566387 BLAKE2B a62d74c408877754af50f5e5fea0e2289ec1e0c9f25013ed0d039bfe8ef61108600d917f8c9d356e98aca632795b4eb0f01ea1b54526a652577fb74a38a433c2 SHA512 15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5 DIST samtools-1.10.tar.bz2 4721173 BLAKE2B 103c71ec5740eac151a4fc40d67286ee00123c7befd5f654cf5c89812bda44f82b38ab662a4a3216ac84434cabab49500b903612137f97f89a7ea38063e8fc08 SHA512 828ec2638592b440e06b81eafc57634416ab54dac6caaecb06f22a90e9bf99da1fd8bb54509cb98591899c4e097ac9038ee5d57ea7bfe1a18967cde4018d840a -DIST samtools-1.5.tar.bz2 4190142 BLAKE2B 1d3478f9adf76925a3721e145795ce4a4caf580244f5ba5bc1ddd14d1b13c723c6fddc24cdadf0a23ca5dcd7007a9985f54e7532cb15d5d9433b1164f5a22023 SHA512 ff3e39ba867ecbd88f3363b038508c1557e349ea4223483f8f4ecb17ff8864fb53cd193bc2059a147e30f07395bbf53c8518d0f70219e454375c8bffe56e3059 -DIST samtools-1.9.tar.bz2 4440405 BLAKE2B 409265fed9ff3fcd09096c968224499750da69324eeded754e367430c0f53f9246ccc9a31e166f13ea7bc767fefab499bcfda4d008d5ac82971984c67b533aff SHA512 6c8207754615ae8dad84b278f93e7d57eb40b818efb80f6aff6aba22fde5772247724e86596e765791e3175ffbb683393dd3ddfe7681c73eef4eb4f2342bf68f diff --git a/sci-biology/samtools/files/samtools-1.5-buildsystem.patch b/sci-biology/samtools/files/samtools-1.5-buildsystem.patch deleted file mode 100644 index c466e66a9d1..00000000000 --- a/sci-biology/samtools/files/samtools-1.5-buildsystem.patch +++ /dev/null @@ -1,413 +0,0 @@ ---- 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) $(ALL_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 $@ misc/maq2sam.c diff --git a/sci-biology/samtools/samtools-1.5.ebuild b/sci-biology/samtools/samtools-1.5.ebuild deleted file mode 100644 index c2bc7ce89cf..00000000000 --- a/sci-biology/samtools/samtools-1.5.ebuild +++ /dev/null @@ -1,61 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit autotools python-r1 toolchain-funcs - -DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats" -HOMEPAGE="http://www.htslib.org/"; -SRC_URI="mirror://sourceforge/${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 -} diff --git a/sci-biology/samtools/samtools-1.9-r1.ebuild b/sci-biology/samtools/samtools-1.9-r1.ebuild deleted file mode 100644 index 0d0f993895f..00000000000 --- a/sci-biology/samtools/samtools-1.9-r1.ebuild +++ /dev/null @@ -1,49 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit autotools 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" - -RDEPEND=" - dev-lang/perl - =sci-libs/htslib-${PV}* - sys-libs/ncurses:0= - sys-libs/zlib:=" -DEPEND="${RDEPEND}" -BDEPEND="virtual/pkgconfig" - -src_prepare() { - default - - # remove bundled htslib - rm -r htslib-* || die - - eautoreconf -} - -src_test() { - local -x LD_LIBRARY_PATH="${S}" - default -} - -src_install() { - default - - # varfilter.py has been retired upstream for being py2 only - rm "${ED}"/usr/bin/varfilter.py || die - - if use examples; then - dodoc -r examples - docompress -x /usr/share/doc/${PF}/examples - fi -}
