summaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorDavid Seifert <soap@gentoo.org>2020-08-03 23:11:18 +0200
committerDavid Seifert <soap@gentoo.org>2020-08-03 23:11:18 +0200
commitb6948f3ed9612bc6f11b4ccab40ac4d80f73e397 (patch)
tree5803c6b4bfc33e4b3491ee8ed24ce230b4280139
parentsci-biology/bcftools: Remove old (diff)
downloadgentoo-b6948f3ed9612bc6f11b4ccab40ac4d80f73e397.tar.gz
gentoo-b6948f3ed9612bc6f11b4ccab40ac4d80f73e397.tar.bz2
gentoo-b6948f3ed9612bc6f11b4ccab40ac4d80f73e397.zip
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@gentoo.org>
-rw-r--r--sci-biology/samtools/Manifest2
-rw-r--r--sci-biology/samtools/files/samtools-1.5-buildsystem.patch413
-rw-r--r--sci-biology/samtools/samtools-1.5.ebuild61
-rw-r--r--sci-biology/samtools/samtools-1.9-r1.ebuild49
4 files changed, 0 insertions, 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
-}