* [gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/, sci-biology/samtools/files/
@ 2016-03-27 23:53 David Seifert
0 siblings, 0 replies; 3+ messages in thread
From: David Seifert @ 2016-03-27 23:53 UTC (permalink / raw
To: gentoo-commits
commit: deaa21ff2b928318d0e1b8fe45aa404411f08086
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Mar 27 23:52:51 2016 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Mar 27 23:52:51 2016 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=deaa21ff
sci-biology/samtools: Move to SLOT="0.1-legacy" for future legacy versions
Package-Manager: portage-2.2.28
.../samtools/files/samtools-0.1.20-buildsystem.patch | 20 ++++++++++----------
...tools-0.1.20.ebuild => samtools-0.1.20-r1.ebuild} | 2 +-
2 files changed, 11 insertions(+), 11 deletions(-)
diff --git a/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch b/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch
index dfdd890..eb9f693 100644
--- a/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch
+++ b/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch
@@ -75,15 +75,15 @@
.PHONY:all-recur lib-recur clean-recur cleanlocal-recur install-recur
-lib:libbam.a
-+lib:libbam-legacy.a
++lib:libbam-0.1-legacy.a
-libbam.a:$(LOBJS)
-+libbam-legacy.a:$(LOBJS)
++libbam-0.1-legacy.a:$(LOBJS)
$(AR) -csru $@ $(LOBJS)
samtools:lib-recur $(AOBJS)
- $(CC) $(CFLAGS) -o $@ $(AOBJS) $(LDFLAGS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) libbam-legacy.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) -L. -lbam-0.1-legacy -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread
razip:razip.o razf.o $(KNETFILE_O)
- $(CC) $(CFLAGS) -o $@ $^ -lz
@@ -105,21 +105,21 @@
-libbam.1.dylib-local:$(LOBJS)
- libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz
-+libbam-legacy.1.dylib-local:$(LOBJS)
-+ libtool -dynamic $(LOBJS) -o libbam-legacy.1.dylib -lc -lz
++libbam-0.1-legacy.1.dylib-local:$(LOBJS)
++ libtool -dynamic $(LOBJS) -o libbam-0.1-legacy.1.dylib -lc -lz
-libbam.so.1-local:$(LOBJS)
- $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz
-+libbam-legacy.so.1-local:$(LOBJS)
-+ $(CC) $(LDFLAGS) -shared -Wl,-soname,libbam-legacy.so -o libbam-legacy.so.1 $(LOBJS) -lc -lz -lm -lpthread
++libbam-0.1-legacy.so.1-local:$(LOBJS)
++ $(CC) $(LDFLAGS) -shared -Wl,-soname,libbam-0.1-legacy.so -o libbam-0.1-legacy.so.1 $(LOBJS) -lc -lz -lm -lpthread
dylib:
@$(MAKE) cleanlocal; \
case `uname` in \
- Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.so.1-local;; \
- Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.1.dylib-local;; \
-+ Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam-legacy.so.1-local;; \
-+ Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam-legacy.1.dylib-local;; \
++ Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam-0.1-legacy.so.1-local;; \
++ Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam-0.1-legacy.1.dylib-local;; \
*) echo 'Unknown OS';; \
esac
@@ -162,7 +162,7 @@
bamcheck:bamcheck.o
- $(CC) $(CFLAGS) -o $@ bamcheck.o -L.. -lm -lbam -lpthread -lz
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ bamcheck.o -L.. -lm -lbam-legacy -lpthread -lz
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ bamcheck.o -L.. -lm -lbam-0.1-legacy -lpthread -lz
bamcheck.o:bamcheck.c ../faidx.h ../khash.h ../sam.h ../razf.h
$(CC) $(CFLAGS) -c -I.. -o $@ bamcheck.c
diff --git a/sci-biology/samtools/samtools-0.1.20.ebuild b/sci-biology/samtools/samtools-0.1.20-r1.ebuild
similarity index 99%
rename from sci-biology/samtools/samtools-0.1.20.ebuild
rename to sci-biology/samtools/samtools-0.1.20-r1.ebuild
index 3ee9956..744d15f 100644
--- a/sci-biology/samtools/samtools-0.1.20.ebuild
+++ b/sci-biology/samtools/samtools-0.1.20-r1.ebuild
@@ -13,7 +13,7 @@ HOMEPAGE="http://samtools.sourceforge.net/"
SRC_URI="https://github.com/samtools/samtools/archive/${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="MIT"
-SLOT="legacy"
+SLOT="0.1-legacy"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
IUSE="examples"
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/, sci-biology/samtools/files/
@ 2017-09-02 9:32 David Seifert
0 siblings, 0 replies; 3+ messages in thread
From: David Seifert @ 2017-09-02 9:32 UTC (permalink / raw
To: gentoo-commits
commit: d401db74e7e270ab7e38d955308cd8d2dbc20a48
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Sep 2 09:30:07 2017 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Sep 2 09:32:42 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d401db74
sci-biology/samtools: Version bump to 1.5
Package-Manager: Portage-2.3.8, Repoman-2.3.3
sci-biology/samtools/Manifest | 1 +
.../samtools/files/samtools-1.5-buildsystem.patch | 413 +++++++++++++++++++++
sci-biology/samtools/samtools-1.5.ebuild | 61 +++
3 files changed, 475 insertions(+)
diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index d25774fee86..791e2050ee7 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 00000000000..248089e09fc
--- /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 $@ misc/maq2sam.c
diff --git a/sci-biology/samtools/samtools-1.5.ebuild b/sci-biology/samtools/samtools-1.5.ebuild
new file mode 100644
index 00000000000..c2bc7ce89cf
--- /dev/null
+++ b/sci-biology/samtools/samtools-1.5.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit autotools python-r1 toolchain-funcs
+
+DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
+HOMEPAGE="http://www.htslib.org/"
+SRC_URI="mirror://sourceforge/${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
+}
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/, sci-biology/samtools/files/
@ 2020-08-03 21:11 David Seifert
0 siblings, 0 replies; 3+ messages in thread
From: David Seifert @ 2020-08-03 21:11 UTC (permalink / raw
To: gentoo-commits
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
-}
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