commit: 70386b8c804f2bf2fb7aca4be74d511d765ad1e4 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sat Sep 2 11:07:41 2017 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sat Sep 2 12:37:02 2017 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=70386b8c
sci-biology/samtools: Remove old Bug: https://bugs.gentoo.org/show_bug.cgi?id=548170 Bug: https://bugs.gentoo.org/show_bug.cgi?id=620618 Bug: https://bugs.gentoo.org/show_bug.cgi?id=625504 Package-Manager: Portage-2.3.8, Repoman-2.3.3 Closes: https://github.com/gentoo/gentoo/pull/5593 sci-biology/samtools/Manifest | 6 - .../files/samtools-0.1.19-buildsystem.patch | 183 ----- .../samtools/files/samtools-1.0-buildsystem.patch | 59 -- .../samtools/files/samtools-1.1-buildsystem.patch | 153 ----- .../samtools/files/samtools-1.2-buildsystem.patch | 193 ------ .../samtools/files/samtools-1.3-buildsystem.patch | 174 ----- .../samtools/files/samtools-1.3-ncurses.patch | 737 --------------------- sci-biology/samtools/samtools-0.1.12.ebuild | 30 - sci-biology/samtools/samtools-0.1.19-r2.ebuild | 60 -- sci-biology/samtools/samtools-1.0-r1.ebuild | 72 -- sci-biology/samtools/samtools-1.0.ebuild | 68 -- sci-biology/samtools/samtools-1.1.ebuild | 82 --- sci-biology/samtools/samtools-1.2.ebuild | 82 --- sci-biology/samtools/samtools-1.3-r1.ebuild | 96 --- 14 files changed, 1995 deletions(-) diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest index 791e2050ee7..a1c0aa6b427 100644 --- a/sci-biology/samtools/Manifest +++ b/sci-biology/samtools/Manifest @@ -1,8 +1,2 @@ -DIST samtools-0.1.12a.tar.bz2 355633 SHA256 377ed5cd2a4bb2b1ad572ca6fcafdd8ed644b67f01ab00fa020618fac11e59ac SHA512 8a3273c174fb478772f31a9c73183b5f7c6841ba4e20586aafc2cd3e966830d3a4ca8c7485ce5981fe85d7cd820170e2ac2e124d8cf077e35218a7381f305012 WHIRLPOOL da61692666dffbb32e172f87e77287e145a0c0f6d62d47e5d04d153ce478db5df1d4694bd93d654af11643f9b656551232b5cc085b619bb8d8536720de36984c -DIST samtools-0.1.19.tar.bz2 514507 SHA256 d080c9d356e5f0ad334007e4461cbcee3c4ca97b8a7a5a48c44883cf9dee63d4 SHA512 d145f1d65eefefbdfb781945684b8b591419fb109ac7401a62cae65b9ca1e1271f001496e1038334ff9ab1c0e5bf9bcc059f70aaa273551193fbd68101fd188d WHIRLPOOL 7811388ae8b24c5d7a328d2da252b8d3afaefdab508bd97684d556d2d4ee60d9c8846ffa562beaa9d0c6a5e6bfac24fcd9d211dfee20383cf452609badc8ecd5 DIST samtools-0.1.20.tar.gz 566387 SHA256 500019b4d1886ad995513d5ce8b413b14b51f16f251ce76bc0b35a446b182a47 SHA512 15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5 WHIRLPOOL 3ea05df172ea6afe31bd3880f918e0b286f65839f78ed846a0d3aef84ec70df1e3741ff6dcad5f70d62a06687f07b35609829aabd33c6688fac0d59effd979e0 -DIST samtools-1.0.tar.bz2 4459669 SHA256 7340b843663c3f54a902a06f2f73c68198f3a62d29a2ed20671139957f7fd7c0 SHA512 5b80995c522d08b06a4c559f60a5e200d9085be7f44c3c9618db91e3de85e36c1473e42715eae8175520d7da3df8245bafa82e625d2fc08e0197adb395851693 WHIRLPOOL 2aa0f8639da9b0b828ca7296969e5c600b0e5452ad3231b914e4a7be418700906a4d695c928eaf837b643255567ec82cfadf0b53007e0f1e3a956856f6c4c832 -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-0.1.19-buildsystem.patch b/sci-biology/samtools/files/samtools-0.1.19-buildsystem.patch deleted file mode 100644 index d5ff3bd45da..00000000000 --- a/sci-biology/samtools/files/samtools-0.1.19-buildsystem.patch +++ /dev/null @@ -1,183 +0,0 @@ - Makefile | 22 +++++++++++----------- - bcftools/Makefile | 12 ++++++------ - misc/Makefile | 28 ++++++++++++++-------------- - 3 files changed, 31 insertions(+), 31 deletions(-) - -diff --git a/Makefile b/Makefile -index 2f51bfc..4dda5a4 100644 ---- a/Makefile -+++ b/Makefile -@@ -1,7 +1,7 @@ --CC= gcc --CFLAGS= -g -Wall -O2 --#LDFLAGS= -Wl,-rpath,\$$ORIGIN/../lib --DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -+CC?= gcc -+CFLAGS?= -g -Wall -O2 -+#LDFLAGS+= -Wl,-rpath,\$$ORIGIN/../lib -+CPPFLAGS+= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 - KNETFILE_O= knetfile.o - LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \ - bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o \ -@@ -21,14 +21,14 @@ LIBCURSES= -lcurses # -lXCurses - .PHONY: all lib - - .c.o: -- $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@ -+ $(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@ - - all-recur lib-recur clean-recur cleanlocal-recur install-recur: - @target=`echo $@ | sed s/-recur//`; \ - wdir=`pwd`; \ - list='$(SUBDIRS)'; for subdir in $$list; do \ - cd $$subdir; \ -- $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \ -+ $(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \ - INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \ - cd $$wdir; \ - done; -@@ -44,16 +44,16 @@ libbam.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.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread - - razip:razip.o razf.o $(KNETFILE_O) -- $(CC) $(CFLAGS) -o $@ $^ -lz -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ -lz - - bgzip:bgzip.o bgzf.o $(KNETFILE_O) -- $(CC) $(CFLAGS) -o $@ $^ -lz -lpthread -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ -lz -lpthread - - bgzf.o:bgzf.c bgzf.h -- $(CC) -c $(CFLAGS) $(DFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@ -+ $(CC) -c $(CFLAGS) $(CPPFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@ - - razip.o:razf.h - bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h -@@ -84,7 +84,7 @@ libbam.1.dylib-local:$(LOBJS) - libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz - - libbam.so.1-local:$(LOBJS) -- $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz -+ $(CC) $(LDFLAGS) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz -lm -lpthread - - dylib: - @$(MAKE) cleanlocal; \ -diff --git a/bcftools/Makefile b/bcftools/Makefile -index be831de..7ef796c 100644 ---- a/bcftools/Makefile -+++ b/bcftools/Makefile -@@ -1,6 +1,6 @@ --CC= gcc --CFLAGS= -g -Wall -O2 #-m64 #-arch ppc --DFLAGS= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -+CC?= gcc -+CFLAGS?= -g -Wall -O2 #-m64 #-arch ppc -+CPPFLAGS+= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE - LOBJS= bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o - OMISC= .. - AOBJS= call1.o main.o $(OMISC)/kstring.o $(OMISC)/bgzf.o $(OMISC)/knetfile.o $(OMISC)/bedidx.o -@@ -11,14 +11,14 @@ SUBDIRS= . - .SUFFIXES:.c .o - - .c.o: -- $(CC) -c $(CFLAGS) $(DFLAGS) -I.. $(INCLUDES) $< -o $@ -+ $(CC) -c $(CFLAGS) $(CPPFLAGS) -I.. $(INCLUDES) $< -o $@ - - all-recur lib-recur clean-recur cleanlocal-recur install-recur: - @target=`echo $@ | sed s/-recur//`; \ - wdir=`pwd`; \ - list='$(SUBDIRS)'; for subdir in $$list; do \ - cd $$subdir; \ -- $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \ -+ $(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \ - INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \ - cd $$wdir; \ - done; -@@ -31,7 +31,7 @@ libbcf.a:$(LOBJS) - $(AR) -csru $@ $(LOBJS) - - bcftools:lib $(AOBJS) -- $(CC) $(CFLAGS) -o $@ $(AOBJS) -L. $(LIBPATH) -lbcf -lm -lz -lpthread -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) -L. $(LIBPATH) -lbcf -lm -lz -lpthread - - bcf.o:bcf.h - vcf.o:bcf.h -diff --git a/misc/Makefile b/misc/Makefile -index d36e7ac..7ae1dc3 100644 ---- a/misc/Makefile -+++ b/misc/Makefile -@@ -1,8 +1,8 @@ --CC= gcc --CXX= g++ --CFLAGS= -g -Wall -O2 #-m64 #-arch ppc --CXXFLAGS= $(CFLAGS) --DFLAGS= -D_FILE_OFFSET_BITS=64 -+CC?= gcc -+CXX?= g++ -+CFLAGS?= -g -Wall -O2 #-m64 #-arch ppc -+CXXFLAGS?= $(CFLAGS) -+CPPFLAGS+= -D_FILE_OFFSET_BITS=64 - OBJS= - PROG= md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck - INCLUDES= -I.. -@@ -11,7 +11,7 @@ SUBDIRS= . - .SUFFIXES:.c .o - - .c.o: -- $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@ -+ $(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@ - - all:$(PROG) - -@@ -20,7 +20,7 @@ lib-recur all-recur clean-recur cleanlocal-recur install-recur: - wdir=`pwd`; \ - list='$(SUBDIRS)'; for subdir in $$list; do \ - cd $$subdir; \ -- $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \ -+ $(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \ - INCLUDES="$(INCLUDES)" $$target || exit 1; \ - cd $$wdir; \ - done; -@@ -28,31 +28,31 @@ lib-recur all-recur clean-recur cleanlocal-recur install-recur: - lib: - - bamcheck:bamcheck.o -- $(CC) $(CFLAGS) -o $@ bamcheck.o -L.. -lm -lbam -lpthread -lz -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ bamcheck.o -L.. -lm -lbam -lpthread -lz - - bamcheck.o:bamcheck.c ../faidx.h ../khash.h ../sam.h ../razf.h - $(CC) $(CFLAGS) -c -I.. -o $@ bamcheck.c - - ace2sam:ace2sam.o -- $(CC) $(CFLAGS) -o $@ ace2sam.o -lz -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ ace2sam.o -lz - - wgsim:wgsim.o -- $(CC) $(CFLAGS) -o $@ wgsim.o -lm -lz -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ wgsim.o -lm -lz - - md5fa:md5.o md5fa.o md5.h ../kseq.h -- $(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ md5.o md5fa.o -lz - - md5sum-lite:md5sum-lite.o -- $(CC) $(CFLAGS) -o $@ md5sum-lite.o -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ md5sum-lite.o - - md5sum-lite.o:md5.c md5.h - $(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c - - maq2sam-short:maq2sam.c -- $(CC) $(CFLAGS) -o $@ maq2sam.c -lz -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ maq2sam.c -lz - - maq2sam-long:maq2sam.c -- $(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -lz -+ $(CC) $(CFLAGS) -DMAQ_LONGREADS $(LDFLAGS) -o $@ maq2sam.c -lz - - md5fa.o:md5.h md5fa.c - $(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c diff --git a/sci-biology/samtools/files/samtools-1.0-buildsystem.patch b/sci-biology/samtools/files/samtools-1.0-buildsystem.patch deleted file mode 100644 index 53a8b66f918..00000000000 --- a/sci-biology/samtools/files/samtools-1.0-buildsystem.patch +++ /dev/null @@ -1,59 +0,0 @@ - Makefile | 26 ++++++++++++++++++-------- - 1 file changed, 18 insertions(+), 8 deletions(-) - -diff --git a/Makefile b/Makefile -index ae59abf..0d2788c 100644 ---- a/Makefile -+++ b/Makefile -@@ -21,11 +21,12 @@ - # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER - # DEALINGS IN THE SOFTWARE. - --CC = gcc --CPPFLAGS = $(DFLAGS) $(INCLUDES) --CFLAGS = -g -Wall -O2 --LDFLAGS = --LDLIBS = -+CC ?= gcc -+CPPFLAGS += $(DFLAGS) $(INCLUDES) -+CFLAGS ?= -g -Wall -O2 -+LDFLAGS += -+LDLIBS += -+BAMLIB ?= libbam.a - DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 - LOBJS= bam_aux.o bam.o bam_import.o sam.o \ - sam_header.o bam_plbuf.o -@@ -42,6 +43,7 @@ LIBCURSES= -lcurses # -lXCurses - prefix = /usr/local - exec_prefix = $(prefix) - bindir = $(exec_prefix)/bin -+bindir = $(exec_prefix)/lib - mandir = $(prefix)/share/man - man1dir = $(mandir)/man1 - -@@ -115,14 +117,22 @@ version.h: - .c.o: - $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ $< - -+$(LOBJS): -+ $(CC) $(CFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $< - --lib:libbam.a -+ -+lib:libbam.a libbam.so.1.0 - - libbam.a:$(LOBJS) - $(AR) -csru $@ $(LOBJS) - --samtools: $(AOBJS) libbam.a $(HTSLIB) -- $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz -+libbam.so.1.0:$(LOBJS) -+ $(CC) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB) -lz -+ ln -sf $@ libbam.so.0 -+ ln -sf $@ libbam.so -+ -+samtools: $(AOBJS) $(HTSLIB) lib -+ $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) $(BAMLIB) $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz - - bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h) - bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.h diff --git a/sci-biology/samtools/files/samtools-1.1-buildsystem.patch b/sci-biology/samtools/files/samtools-1.1-buildsystem.patch deleted file mode 100644 index b9ae77de67d..00000000000 --- a/sci-biology/samtools/files/samtools-1.1-buildsystem.patch +++ /dev/null @@ -1,153 +0,0 @@ - Makefile | 76 ++++++++++++++++++++++++++++++++++++---------------------------- - 1 file changed, 43 insertions(+), 33 deletions(-) - -diff --git a/Makefile b/Makefile -index 43cefc3..743dd07 100644 ---- a/Makefile -+++ b/Makefile -@@ -21,11 +21,12 @@ - # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER - # DEALINGS IN THE SOFTWARE. - --CC = gcc --CPPFLAGS = $(DFLAGS) $(INCLUDES) --CFLAGS = -g -Wall -O2 --LDFLAGS = --LDLIBS = -+CC ?= gcc -+CPPFLAGS += $(DFLAGS) $(INCLUDES) -+CFLAGS ?= -g -Wall -O2 -+LDFLAGS += -+LDLIBS += -+BAMLIB ?= libbam.a - DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 - LOBJS= bam_aux.o bam.o bam_import.o sam.o \ - sam_header.o bam_plbuf.o -@@ -42,6 +43,7 @@ LIBCURSES= -lcurses # -lXCurses - prefix = /usr/local - exec_prefix = $(prefix) - bindir = $(exec_prefix)/bin -+libdir = $(exec_prefix)/lib - mandir = $(prefix)/share/man - man1dir = $(mandir)/man1 - -@@ -115,63 +117,71 @@ version.h: - .c.o: - $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ $< - -+$(LOBJS): -+ $(CC) $(CFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $< - --lib:libbam.a -+ -+lib:libbam.a libbam.so.1.0 - - libbam.a:$(LOBJS) - $(AR) -csru $@ $(LOBJS) - --samtools: $(AOBJS) libbam.a $(HTSLIB) -- $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz -+libbam.so.1.0:$(LOBJS) -+ $(CC) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB) -lz -+ ln -sf $@ libbam.so.0 -+ ln -sf $@ libbam.so -+ -+samtools: $(AOBJS) lib -+ $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) $(BAMLIB) $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz - - bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h) - bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.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) $(HTSDIR)/htslib/khash.h $(bam_lpileup_h) -+bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(bam_lpileup_h) - sam_h = sam.h $(htslib_sam_h) $(bam_h) --sample_h = sample.h $(HTSDIR)/htslib/kstring.h -+sample_h = sample.h - - bam.o: bam.c $(bam_h) sam_header.h --bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kfunc.h $(bam2bcf_h) errmod.h -+bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(bam2bcf_h) errmod.h - bam2bcf_indel.o: bam2bcf_indel.c bam2bcf.h - bam2depth.o: bam2depth.c $(htslib_sam_h) samtools.h - bam_aux.o: bam_aux.c - bam_cat.o: bam_cat.c $(htslib_bgzf_h) $(bam_h) - bam_color.o: bam_color.c $(bam_h) --bam_import.o: bam_import.c $(HTSDIR)/htslib/kstring.h $(bam_h) $(HTSDIR)/htslib/kseq.h --bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) $(HTSDIR)/htslib/khash.h --bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) $(HTSDIR)/htslib/ksort.h -+bam_import.o: bam_import.c $(bam_h) -+bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) -+bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) - bam_mate.o: bam_mate.c $(bam_h) - bam_md.o: bam_md.c $(htslib_faidx_h) $(sam_h) kaln.h kprobaln.h - bam_pileup.o: bam_pileup.c $(sam_h) - bam_plbuf.o: bam_plbuf.c $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h) --bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/khash_str2int.h sam_header.h samtools.h $(bam2bcf_h) $(sample_h) -+bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) sam_header.h samtools.h $(bam2bcf_h) $(sample_h) - bam_reheader.o: bam_reheader.c $(htslib_bgzf_h) $(bam_h) --bam_rmdup.o: bam_rmdup.c $(sam_h) $(HTSDIR)/htslib/khash.h --bam_rmdupse.o: bam_rmdupse.c $(sam_h) $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/klist.h --bam_sort.o: bam_sort.c $(HTSDIR)/htslib/ksort.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/klist.h $(HTSDIR)/htslib/kstring.h $(htslib_sam_h) -+bam_rmdup.o: bam_rmdup.c $(sam_h) -+bam_rmdupse.o: bam_rmdupse.c $(sam_h) -+bam_sort.o: bam_sort.c $(htslib_sam_h) - bam_stat.o: bam_stat.c $(bam_h) samtools.h - bam_tview.o: bam_tview.c $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h) - bam_tview_curses.o: bam_tview_curses.c $(bam_tview_h) - bam_tview_html.o: bam_tview_html.c $(bam_tview_h) - bam_flags.o: bam_flags.c $(sam_h) --bamshuf.o: bamshuf.c $(htslib_sam_h) $(HTSDIR)/htslib/ksort.h samtools.h -+bamshuf.o: bamshuf.c $(htslib_sam_h) samtools.h - bamtk.o: bamtk.c $(bam_h) version.h samtools.h --bedcov.o: bedcov.c $(HTSDIR)/htslib/kstring.h $(htslib_sam_h) $(HTSDIR)/htslib/kseq.h --bedidx.o: bedidx.c $(HTSDIR)/htslib/ksort.h $(HTSDIR)/htslib/kseq.h $(HTSDIR)/htslib/khash.h -+bedcov.o: bedcov.c $(htslib_sam_h) -+bedidx.o: bedidx.c - cut_target.o: cut_target.c $(bam_h) errmod.h $(htslib_faidx_h) --errmod.o: errmod.c errmod.h $(HTSDIR)/htslib/ksort.h -+errmod.o: errmod.c errmod.h - kaln.o: kaln.c kaln.h - kprobaln.o: kprobaln.c kprobaln.h - padding.o: padding.c sam_header.h $(sam_h) $(bam_h) $(htslib_faidx_h) --phase.o: phase.c $(htslib_sam_h) errmod.h $(HTSDIR)/htslib/kseq.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/ksort.h -+phase.o: phase.c $(htslib_sam_h) errmod.h - sam.o: sam.c $(htslib_faidx_h) $(sam_h) --sam_header.o: sam_header.c sam_header.h $(HTSDIR)/htslib/khash.h --sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/khash.h samtools.h --sample.o: sample.c $(sample_h) $(HTSDIR)/htslib/khash.h --stats_isize.o: stats_isize.c stats_isize.h $(HTSDIR)/htslib/khash.h --stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/khash_str2int.h $(htslib_faidx_h) -+sam_header.o: sam_header.c sam_header.h -+sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) samtools.h -+sample.o: sample.c $(sample_h) -+stats_isize.o: stats_isize.c stats_isize.h -+stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(htslib_faidx_h) - - - # test programs -@@ -179,8 +189,8 @@ stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(HTSDIR)/htslib - # For tests that might use it, set $REF_PATH explicitly to use only reference - # areas within the test suite (or set it to ':' to use no reference areas). - # (regression.sh sets $REF_PATH to a subdirectory itself.) --check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS) -- REF_PATH=: test/test.pl --exec bgzip=$(BGZIP) -+check test: samtools $(BUILT_TEST_PROGRAMS) -+ REF_PATH=: test/test.pl --exec bgzip=bgzip - test/merge/test_bam_translate test/merge/test_bam_translate.tmp - test/merge/test_pretty_header - test/merge/test_rtrans_build -@@ -253,10 +263,10 @@ misc/md5sum-lite: misc/md5sum-lite.o - misc/wgsim: misc/wgsim.o - $(CC) $(LDFLAGS) -o $@ misc/wgsim.o $(LDLIBS) -lm -lz - --misc/ace2sam.o: misc/ace2sam.c $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kseq.h -+misc/ace2sam.o: misc/ace2sam.c - misc/md5.o: misc/md5.c misc/md5.h --misc/md5fa.o: misc/md5fa.c misc/md5.h $(HTSDIR)/htslib/kseq.h --misc/wgsim.o: misc/wgsim.c $(HTSDIR)/htslib/kseq.h -+misc/md5fa.o: misc/md5fa.c misc/md5.h -+misc/wgsim.o: misc/wgsim.c - - misc/maq2sam-short.o: misc/maq2sam.c - $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ misc/maq2sam.c diff --git a/sci-biology/samtools/files/samtools-1.2-buildsystem.patch b/sci-biology/samtools/files/samtools-1.2-buildsystem.patch deleted file mode 100644 index 2343b2245a2..00000000000 --- a/sci-biology/samtools/files/samtools-1.2-buildsystem.patch +++ /dev/null @@ -1,193 +0,0 @@ - Makefile | 94 +++++++++++++++++++++++++++++++++++----------------------------- - 1 file changed, 52 insertions(+), 42 deletions(-) - -diff --git a/Makefile b/Makefile -index e368cee..9054526 100644 ---- a/Makefile -+++ b/Makefile -@@ -21,11 +21,12 @@ - # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER - # DEALINGS IN THE SOFTWARE. - --CC = gcc --CPPFLAGS = $(DFLAGS) $(INCLUDES) --CFLAGS = -g -Wall -O2 --LDFLAGS = --LDLIBS = -+CC ?= gcc -+CPPFLAGS += $(DFLAGS) $(INCLUDES) -+CFLAGS ?= -g -Wall -O2 -+LDFLAGS += -+LDLIBS += -+BAMLIB ?= libbam.a - DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 - LOBJS= bam_aux.o bam.o bam_import.o sam.o \ - sam_header.o bam_plbuf.o -@@ -42,6 +43,7 @@ LIBCURSES= -lcurses # -lXCurses - prefix = /usr/local - exec_prefix = $(prefix) - bindir = $(exec_prefix)/bin -+libdir = $(exec_prefix)/lib - mandir = $(prefix)/share/man - man1dir = $(mandir)/man1 - -@@ -115,62 +117,70 @@ version.h: - .c.o: - $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ $< - -+$(LOBJS): -+ $(CC) $(CFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $< - --lib:libbam.a -+ -+lib:libbam.a libbam.so.1.0 - - libbam.a:$(LOBJS) - $(AR) -csru $@ $(LOBJS) - --samtools: $(AOBJS) libbam.a $(HTSLIB) -- $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz -+libbam.so.1.0:$(LOBJS) -+ $(CC) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB) -lz -+ ln -sf $@ libbam.so.0 -+ ln -sf $@ libbam.so -+ -+samtools: $(AOBJS) lib -+ $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) $(BAMLIB) $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz - - bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h) - bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.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) $(HTSDIR)/htslib/khash.h $(bam_lpileup_h) -+bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(bam_lpileup_h) - sam_h = sam.h $(htslib_sam_h) $(bam_h) --sample_h = sample.h $(HTSDIR)/htslib/kstring.h -+sample_h = sample.h - - bam.o: bam.c $(bam_h) sam_header.h --bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kfunc.h $(bam2bcf_h) errmod.h -+bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(bam2bcf_h) errmod.h - bam2bcf_indel.o: bam2bcf_indel.c $(htslib_sam_h) $(bam2bcf_h) kprobaln.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/ksort.h - bam2depth.o: bam2depth.c $(htslib_sam_h) samtools.h - bam_aux.o: bam_aux.c - bam_cat.o: bam_cat.c $(htslib_bgzf_h) $(bam_h) - bam_color.o: bam_color.c $(bam_h) --bam_import.o: bam_import.c $(HTSDIR)/htslib/kstring.h $(bam_h) $(HTSDIR)/htslib/kseq.h --bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) $(HTSDIR)/htslib/khash.h --bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) $(HTSDIR)/htslib/ksort.h -+bam_import.o: bam_import.c $(bam_h) -+bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) -+bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) - bam_mate.o: bam_mate.c $(bam_h) - bam_md.o: bam_md.c $(htslib_faidx_h) $(sam_h) kprobaln.h - bam_pileup.o: bam_pileup.c $(sam_h) - bam_plbuf.o: bam_plbuf.c $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h) --bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/khash_str2int.h sam_header.h samtools.h $(bam2bcf_h) $(sample_h) -+bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) sam_header.h samtools.h $(bam2bcf_h) $(sample_h) - bam_reheader.o: bam_reheader.c $(htslib_bgzf_h) $(bam_h) --bam_rmdup.o: bam_rmdup.c $(sam_h) $(HTSDIR)/htslib/khash.h --bam_rmdupse.o: bam_rmdupse.c $(sam_h) $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/klist.h --bam_sort.o: bam_sort.c $(HTSDIR)/htslib/ksort.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/klist.h $(HTSDIR)/htslib/kstring.h $(htslib_sam_h) -+bam_rmdup.o: bam_rmdup.c $(sam_h) -+bam_rmdupse.o: bam_rmdupse.c $(sam_h) -+bam_sort.o: bam_sort.c $(htslib_sam_h) - bam_stat.o: bam_stat.c $(bam_h) samtools.h - bam_tview.o: bam_tview.c $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h) - bam_tview_curses.o: bam_tview_curses.c $(bam_tview_h) - bam_tview_html.o: bam_tview_html.c $(bam_tview_h) - bam_flags.o: bam_flags.c $(sam_h) --bamshuf.o: bamshuf.c $(htslib_sam_h) $(HTSDIR)/htslib/ksort.h samtools.h -+bamshuf.o: bamshuf.c $(htslib_sam_h) samtools.h - bamtk.o: bamtk.c $(htslib_hts_h) version.h samtools.h --bedcov.o: bedcov.c $(HTSDIR)/htslib/kstring.h $(htslib_sam_h) $(HTSDIR)/htslib/kseq.h --bedidx.o: bedidx.c $(HTSDIR)/htslib/ksort.h $(HTSDIR)/htslib/kseq.h $(HTSDIR)/htslib/khash.h -+bedcov.o: bedcov.c $(htslib_sam_h) -+bedidx.o: bedidx.c - cut_target.o: cut_target.c $(bam_h) errmod.h $(htslib_faidx_h) --errmod.o: errmod.c errmod.h $(HTSDIR)/htslib/ksort.h -+errmod.o: errmod.c errmod.h - kprobaln.o: kprobaln.c kprobaln.h - padding.o: padding.c sam_header.h $(sam_h) $(bam_h) $(htslib_faidx_h) --phase.o: phase.c $(htslib_sam_h) errmod.h $(HTSDIR)/htslib/kseq.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/ksort.h -+phase.o: phase.c $(htslib_sam_h) errmod.h - sam.o: sam.c $(htslib_faidx_h) $(sam_h) --sam_header.o: sam_header.c sam_header.h $(HTSDIR)/htslib/khash.h --sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/khash.h samtools.h --sample.o: sample.c $(sample_h) $(HTSDIR)/htslib/khash.h --stats_isize.o: stats_isize.c stats_isize.h $(HTSDIR)/htslib/khash.h --stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/khash_str2int.h $(htslib_faidx_h) -+sam_header.o: sam_header.c sam_header.h -+sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) samtools.h -+sample.o: sample.c $(sample_h) -+stats_isize.o: stats_isize.c stats_isize.h -+stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(htslib_faidx_h) - - - # test programs -@@ -178,8 +188,8 @@ stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(HTSDIR)/htslib - # For tests that might use it, set $REF_PATH explicitly to use only reference - # areas within the test suite (or set it to ':' to use no reference areas). - # (regression.sh sets $REF_PATH to a subdirectory itself.) --check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS) -- REF_PATH=: test/test.pl --exec bgzip=$(BGZIP) -+check test: samtools $(BUILT_TEST_PROGRAMS) -+ REF_PATH=: test/test.pl --exec bgzip=bgzip - test/merge/test_bam_translate test/merge/test_bam_translate.tmp - test/merge/test_pretty_header - test/merge/test_rtrans_build -@@ -191,31 +201,31 @@ check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS) - test/split/test_parse_args - - --test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o $(HTSLIB) -+test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o - $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o $(HTSLIB) $(LDLIBS) -lz - --test/merge/test_pretty_header: test/merge/test_pretty_header.o $(HTSLIB) -+test/merge/test_pretty_header: test/merge/test_pretty_header.o - $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_pretty_header.o $(HTSLIB) $(LDLIBS) -lz - --test/merge/test_rtrans_build: test/merge/test_rtrans_build.o $(HTSLIB) -+test/merge/test_rtrans_build: test/merge/test_rtrans_build.o - $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_rtrans_build.o $(HTSLIB) $(LDLIBS) -lz - --test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o $(HTSLIB) -+test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o - $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o $(HTSLIB) $(LDLIBS) -lz - --test/split/test_count_rg: test/split/test_count_rg.o test/test.o $(HTSLIB) -+test/split/test_count_rg: test/split/test_count_rg.o test/test.o - $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o $(HTSLIB) $(LDLIBS) -lz - --test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o $(HTSLIB) -+test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o - $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o $(HTSLIB) $(LDLIBS) -lz - --test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o $(HTSLIB) -+test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o - $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o $(HTSLIB) $(LDLIBS) -lz - --test/split/test_parse_args: test/split/test_parse_args.o test/test.o $(HTSLIB) -+test/split/test_parse_args: test/split/test_parse_args.o test/test.o - $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o $(HTSLIB) $(LDLIBS) -lz - --test/vcf-miniview: test/vcf-miniview.o $(HTSLIB) -+test/vcf-miniview: test/vcf-miniview.o - $(CC) -pthread $(LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB) $(LDLIBS) -lz - - test_test_h = test/test.h $(htslib_sam_h) -@@ -252,10 +262,10 @@ misc/md5sum-lite: misc/md5sum-lite.o - misc/wgsim: misc/wgsim.o - $(CC) $(LDFLAGS) -o $@ misc/wgsim.o $(LDLIBS) -lm -lz - --misc/ace2sam.o: misc/ace2sam.c $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kseq.h -+misc/ace2sam.o: misc/ace2sam.c - misc/md5.o: misc/md5.c misc/md5.h --misc/md5fa.o: misc/md5fa.c misc/md5.h $(HTSDIR)/htslib/kseq.h --misc/wgsim.o: misc/wgsim.c $(HTSDIR)/htslib/kseq.h -+misc/md5fa.o: misc/md5fa.c misc/md5.h -+misc/wgsim.o: misc/wgsim.c - - misc/maq2sam-short.o: misc/maq2sam.c - $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ misc/maq2sam.c diff --git a/sci-biology/samtools/files/samtools-1.3-buildsystem.patch b/sci-biology/samtools/files/samtools-1.3-buildsystem.patch deleted file mode 100644 index 61f6b03bd8e..00000000000 --- a/sci-biology/samtools/files/samtools-1.3-buildsystem.patch +++ /dev/null @@ -1,174 +0,0 @@ ---- samtools-1.3/Makefile -+++ samtools-1.3/Makefile -@@ -21,11 +21,12 @@ - # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER - # DEALINGS IN THE SOFTWARE. - --CC = gcc --CPPFLAGS = --CFLAGS = -g -Wall -O2 --LDFLAGS = --LIBS = -+CC ?= gcc -+CPPFLAGS += -+CFLAGS ?= -g -Wall -O2 -+LDFLAGS += -+LIBS += -+BAMLIB ?= libbam.a - - DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE - LOBJS= bam_aux.o bam.o bam_import.o sam.o \ -@@ -42,6 +43,7 @@ - prefix = /usr/local - exec_prefix = $(prefix) - bindir = $(exec_prefix)/bin -+libdir ?= $(exec_prefix)/lib - datarootdir = $(prefix)/share - mandir = $(datarootdir)/man - man1dir = $(mandir)/man1 -@@ -129,67 +131,74 @@ - .c.o: - $(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ $< - -+$(LOBJS): -+ $(CC) $(CFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $< - --lib:libbam.a -+lib:libbam.a libbam.so.1.0 - - libbam.a:$(LOBJS) - $(AR) -csru $@ $(LOBJS) - --samtools: $(AOBJS) libbam.a $(HTSLIB) -- $(CC) -pthread $(ALL_LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB_LIB) $(CURSES_LIB) -lm $(ALL_LIBS) -+libbam.so.1.0:$(LOBJS) -+ $(CC) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB) -lz -+ ln -sf $@ libbam.so.1 -+ ln -sf $@ libbam.so -+ -+samtools: $(AOBJS) lib -+ $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) $(BAMLIB) $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz - - bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h) - bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.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) -+bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_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) -+sample_h = sample.h - - bam.o: bam.c $(bam_h) $(htslib_kstring_h) sam_header.h --bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(htslib_kstring_h) $(htslib_kfunc_h) $(bam2bcf_h) errmod.h -+bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(bam2bcf_h) errmod.h - bam2bcf_indel.o: bam2bcf_indel.c $(htslib_sam_h) $(bam2bcf_h) kprobaln.h $(htslib_khash_h) $(htslib_ksort_h) - bam2depth.o: bam2depth.c $(htslib_sam_h) samtools.h $(sam_opts_h) - bam_addrprg.o: bam_addrprg.c $(htslib_sam_h) $(htslib_kstring_h) samtools.h $(sam_opts_h) - bam_aux.o: bam_aux.c $(bam_h) - bam_cat.o: bam_cat.c $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_cram_h) $(htslib_khash_h) - bam_color.o: bam_color.c $(bam_h) --bam_import.o: bam_import.c $(htslib_kstring_h) $(bam_h) $(htslib_kseq_h) --bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_h) samtools.h --bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) $(htslib_ksort_h) -+bam_import.o: bam_import.c $(bam_h) -+bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) -+bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) - bam_mate.o: bam_mate.c $(sam_opts_h) $(htslib_kstring_h) $(htslib_sam_h) - bam_md.o: bam_md.c $(htslib_faidx_h) $(htslib_sam_h) $(htslib_kstring_h) kprobaln.h $(sam_opts_h) - bam_plbuf.o: bam_plbuf.c $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h) --bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) sam_header.h samtools.h $(sam_opts_h) $(bam2bcf_h) $(sample_h) -+bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) sam_header.h samtools.h $(bam2bcf_h) $(sample_h) - bam_quickcheck.o: bam_quickcheck.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_bgzf_h) - bam_reheader.o: bam_reheader.c $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_hfile_h) $(htslib_cram_h) samtools.h --bam_rmdup.o: bam_rmdup.c $(htslib_sam_h) $(sam_opts_h) $(bam_h) $(htslib_khash_h) --bam_rmdupse.o: bam_rmdupse.c $(bam_h) $(htslib_sam_h) $(htslib_khash_h) $(htslib_klist_h) --bam_sort.o: bam_sort.c $(htslib_ksort_h) $(htslib_khash_h) $(htslib_klist_h) $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) -+bam_rmdup.o: bam_rmdup.c $(sam_h) -+bam_rmdupse.o: bam_rmdupse.c $(sam_h) -+bam_sort.o: bam_sort.c $(htslib_sam_h) - bam_split.o: bam_split.c $(htslib_sam_h) $(htslib_khash_h) $(htslib_kstring_h) $(sam_opts_h) - bam_stat.o: bam_stat.c $(htslib_sam_h) samtools.h - bam_tview.o: bam_tview.c $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_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 $(bam_tview_h) - bam_flags.o: bam_flags.c $(htslib_sam_h) --bamshuf.o: bamshuf.c $(htslib_sam_h) $(htslib_hts_h) $(htslib_ksort_h) samtools.h $(sam_opts_h) -+bamshuf.o: bamshuf.c $(htslib_sam_h) samtools.h - bamtk.o: bamtk.c $(htslib_hts_h) samtools.h version.h --bedcov.o: bedcov.c $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) $(htslib_kseq_h) --bedidx.o: bedidx.c $(htslib_ksort_h) $(htslib_kseq_h) $(htslib_khash_h) -+bedcov.o: bedcov.c $(htslib_sam_h) -+bedidx.o: bedidx.c - cut_target.o: cut_target.c $(htslib_sam_h) errmod.h $(htslib_faidx_h) $(sam_opts_h) - dict.o: dict.c $(htslib_kseq_h) $(htslib_hts_h) --errmod.o: errmod.c errmod.h $(htslib_ksort_h) -+errmod.o: errmod.c errmod.h - kprobaln.o: kprobaln.c kprobaln.h - padding.o: padding.c $(htslib_kstring_h) $(htslib_sam_h) $(htslib_faidx_h) sam_header.h $(sam_opts_h) --phase.o: phase.c $(htslib_sam_h) errmod.h $(sam_opts_h) $(htslib_kseq_h) $(htslib_khash_h) $(htslib_ksort_h) -+phase.o: phase.c $(htslib_sam_h) errmod.h - sam.o: sam.c $(htslib_faidx_h) $(sam_h) --sam_header.o: sam_header.c sam_header.h $(htslib_khash_h) -+sam_header.o: sam_header.c sam_header.h - sam_opts.o: sam_opts.c $(sam_opts_h) --sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_h) samtools.h $(sam_opts_h) --sample.o: sample.c $(sample_h) $(htslib_khash_h) --stats_isize.o: stats_isize.c stats_isize.h $(htslib_khash_h) --stats.o: stats.c $(htslib_faidx_h) $(htslib_sam_h) $(htslib_hts_h) sam_header.h $(htslib_khash_str2int_h) samtools.h $(htslib_khash_h) $(htslib_kstring_h) stats_isize.h $(sam_opts_h) -+sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) samtools.h -+sample.o: sample.c $(sample_h) -+stats_isize.o: stats_isize.c stats_isize.h -+stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(htslib_faidx_h) - - - # test programs -@@ -197,8 +206,8 @@ - # For tests that might use it, set $REF_PATH explicitly to use only reference - # areas within the test suite (or set it to ':' to use no reference areas). - # (regression.sh sets $REF_PATH to a subdirectory itself.) --check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS) -- REF_PATH=: test/test.pl --exec bgzip=$(BGZIP) -+check test: samtools $(BUILT_TEST_PROGRAMS) -+ REF_PATH=: test/test.pl --exec bgzip=bgzip - test/merge/test_bam_translate test/merge/test_bam_translate.tmp - test/merge/test_rtrans_build - test/merge/test_trans_tbl_init -@@ -210,28 +219,28 @@ - test/split/test_parse_args - - --test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o sam_opts.o $(HTSLIB) -+test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o - $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) - --test/merge/test_rtrans_build: test/merge/test_rtrans_build.o sam_opts.o $(HTSLIB) -+test/merge/test_rtrans_build: test/merge/test_rtrans_build.o - $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_rtrans_build.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) - --test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o sam_opts.o $(HTSLIB) -+test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o - $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) - --test/split/test_count_rg: test/split/test_count_rg.o test/test.o sam_opts.o $(HTSLIB) -+test/split/test_count_rg: test/split/test_count_rg.o test/test.o - $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) - --test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o sam_opts.o $(HTSLIB) -+test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o - $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) - --test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o sam_opts.o $(HTSLIB) -+test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o - $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) - --test/split/test_parse_args: test/split/test_parse_args.o test/test.o sam_opts.o $(HTSLIB) -+test/split/test_parse_args: test/split/test_parse_args.o test/test.o - $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) - --test/vcf-miniview: test/vcf-miniview.o $(HTSLIB) -+test/vcf-miniview: test/vcf-miniview.o - $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB_LIB) $(ALL_LIBS) - - test_test_h = test/test.h $(htslib_sam_h) diff --git a/sci-biology/samtools/files/samtools-1.3-ncurses.patch b/sci-biology/samtools/files/samtools-1.3-ncurses.patch deleted file mode 100644 index baeb6701cd2..00000000000 --- a/sci-biology/samtools/files/samtools-1.3-ncurses.patch +++ /dev/null @@ -1,737 +0,0 @@ -* Add modern AX_WITH_CURSES that prefers using pkg-config for detecting ncurses -* Change macro structure by moving AX_WITH_HTSLIB into its own file - ---- samtools-1.3/configure.ac -+++ samtools-1.3/configure.ac -@@ -28,6 +28,7 @@ - AC_PREREQ([2.63]) dnl This version introduced 4-argument AC_CHECK_HEADER - AC_CONFIG_SRCDIR([bamtk.c]) - AC_CONFIG_HEADERS([config.h]) -+AC_CONFIG_MACRO_DIR([m4]) - - dnl Copyright notice to be copied into the generated configure script - AC_COPYRIGHT([Portions copyright (C) 2015 Genome Research Ltd. ---- samtools-1.3/m4/ax_with_curses.m4 -+++ samtools-1.3/m4/ax_with_curses.m4 -@@ -0,0 +1,578 @@ -+# =========================================================================== -+# http://www.gnu.org/software/autoconf-archive/ax_with_curses.html -+# =========================================================================== -+# -+# SYNOPSIS -+# -+# AX_WITH_CURSES -+# -+# DESCRIPTION -+# -+# This macro checks whether a SysV or X/Open-compatible Curses library is -+# present, along with the associated header file. The NcursesW -+# (wide-character) library is searched for first, followed by Ncurses, -+# then the system-default plain Curses. The first library found is the -+# one returned. Finding libraries will first be attempted by using -+# pkg-config, and should the pkg-config files not be available, will -+# fallback to combinations of known flags itself. -+# -+# The following options are understood: --with-ncursesw, --with-ncurses, -+# --without-ncursesw, --without-ncurses. The "--with" options force the -+# macro to use that particular library, terminating with an error if not -+# found. The "--without" options simply skip the check for that library. -+# The effect on the search pattern is: -+# -+# (no options) - NcursesW, Ncurses, Curses -+# --with-ncurses --with-ncursesw - NcursesW only [*] -+# --without-ncurses --with-ncursesw - NcursesW only [*] -+# --with-ncursesw - NcursesW only [*] -+# --with-ncurses --without-ncursesw - Ncurses only [*] -+# --with-ncurses - NcursesW, Ncurses [**] -+# --without-ncurses --without-ncursesw - Curses only -+# --without-ncursesw - Ncurses, Curses -+# --without-ncurses - NcursesW, Curses -+# -+# [*] If the library is not found, abort the configure script. -+# -+# [**] If the second library (Ncurses) is not found, abort configure. -+# -+# The following preprocessor symbols may be defined by this macro if the -+# appropriate conditions are met: -+# -+# HAVE_CURSES - if any SysV or X/Open Curses library found -+# HAVE_CURSES_ENHANCED - if library supports X/Open Enhanced functions -+# HAVE_CURSES_COLOR - if library supports color (enhanced functions) -+# HAVE_CURSES_OBSOLETE - if library supports certain obsolete features -+# HAVE_NCURSESW - if NcursesW (wide char) library is to be used -+# HAVE_NCURSES - if the Ncurses library is to be used -+# -+# HAVE_CURSES_H - if <curses.h> is present and should be used -+# HAVE_NCURSESW_H - if <ncursesw.h> should be used -+# HAVE_NCURSES_H - if <ncurses.h> should be used -+# HAVE_NCURSESW_CURSES_H - if <ncursesw/curses.h> should be used -+# HAVE_NCURSES_CURSES_H - if <ncurses/curses.h> should be used -+# -+# (These preprocessor symbols are discussed later in this document.) -+# -+# The following output variables are defined by this macro; they are -+# precious and may be overridden on the ./configure command line: -+# -+# CURSES_LIB - library to add to xxx_LDADD -+# CURSES_CPPFLAGS - include paths to add to xxx_CPPFLAGS -+# -+# Neither the library listed in CURSES_LIB, nor the flags in -+# CURSES_CPPFLAGS are added to LIBS, respectively CPPFLAGS, by default. -+# You need to add both to the appropriate xxx_LDADD/xxx_CPPFLAGS line in -+# your Makefile.am. For example: -+# -+# prog_LDADD = @CURSES_LIB@ -+# prog_CPPFLAGS = @CURSES_CPPFLAGS@ -+# -+# If CURSES_LIB is set on the configure command line (such as by running -+# "./configure CURSES_LIB=-lmycurses"), then the only header searched for -+# is <curses.h>. If the user needs to specify an alternative path for a -+# library (such as for a non-standard NcurseW), the user should use the -+# LDFLAGS variable. -+# -+# The following shell variables may be defined by this macro: -+# -+# ax_cv_curses - set to "yes" if any Curses library found -+# ax_cv_curses_enhanced - set to "yes" if Enhanced functions present -+# ax_cv_curses_color - set to "yes" if color functions present -+# ax_cv_curses_obsolete - set to "yes" if obsolete features present -+# -+# ax_cv_ncursesw - set to "yes" if NcursesW library found -+# ax_cv_ncurses - set to "yes" if Ncurses library found -+# ax_cv_plaincurses - set to "yes" if plain Curses library found -+# ax_cv_curses_which - set to "ncursesw", "ncurses", "plaincurses" or "no" -+# -+# These variables can be used in your configure.ac to determine the level -+# of support you need from the Curses library. For example, if you must -+# have either Ncurses or NcursesW, you could include: -+# -+# AX_WITH_CURSES -+# if test "x$ax_cv_ncursesw" != xyes && test "x$ax_cv_ncurses" != xyes; then -+# AC_MSG_ERROR([requires either NcursesW or Ncurses library]) -+# fi -+# -+# If any Curses library will do (but one must be present and must support -+# color), you could use: -+# -+# AX_WITH_CURSES -+# if test "x$ax_cv_curses" != xyes || test "x$ax_cv_curses_color" != xyes; then -+# AC_MSG_ERROR([requires an X/Open-compatible Curses library with color]) -+# fi -+# -+# Certain preprocessor symbols and shell variables defined by this macro -+# can be used to determine various features of the Curses library. In -+# particular, HAVE_CURSES and ax_cv_curses are defined if the Curses -+# library found conforms to the traditional SysV and/or X/Open Base Curses -+# definition. Any working Curses library conforms to this level. -+# -+# HAVE_CURSES_ENHANCED and ax_cv_curses_enhanced are defined if the -+# library supports the X/Open Enhanced Curses definition. In particular, -+# the wide-character types attr_t, cchar_t and wint_t, the functions -+# wattr_set() and wget_wch() and the macros WA_NORMAL and _XOPEN_CURSES -+# are checked. The Ncurses library does NOT conform to this definition, -+# although NcursesW does. -+# -+# HAVE_CURSES_COLOR and ax_cv_curses_color are defined if the library -+# supports color functions and macros such as COLOR_PAIR, A_COLOR, -+# COLOR_WHITE, COLOR_RED and init_pair(). These are NOT part of the -+# X/Open Base Curses definition, but are part of the Enhanced set of -+# functions. The Ncurses library DOES support these functions, as does -+# NcursesW. -+# -+# HAVE_CURSES_OBSOLETE and ax_cv_curses_obsolete are defined if the -+# library supports certain features present in SysV and BSD Curses but not -+# defined in the X/Open definition. In particular, the functions -+# getattrs(), getcurx() and getmaxx() are checked. -+# -+# To use the HAVE_xxx_H preprocessor symbols, insert the following into -+# your system.h (or equivalent) header file: -+# -+# #if defined HAVE_NCURSESW_CURSES_H -+# # include <ncursesw/curses.h> -+# #elif defined HAVE_NCURSESW_H -+# # include <ncursesw.h> -+# #elif defined HAVE_NCURSES_CURSES_H -+# # include <ncurses/curses.h> -+# #elif defined HAVE_NCURSES_H -+# # include <ncurses.h> -+# #elif defined HAVE_CURSES_H -+# # include <curses.h> -+# #else -+# # error "SysV or X/Open-compatible Curses header file required" -+# #endif -+# -+# For previous users of this macro: you should not need to change anything -+# in your configure.ac or Makefile.am, as the previous (serial 10) -+# semantics are still valid. However, you should update your system.h (or -+# equivalent) header file to the fragment shown above. You are encouraged -+# also to make use of the extended functionality provided by this version -+# of AX_WITH_CURSES, as well as in the additional macros -+# AX_WITH_CURSES_PANEL, AX_WITH_CURSES_MENU and AX_WITH_CURSES_FORM. -+# -+# LICENSE -+# -+# Copyright (c) 2009 Mark Pulford <m...@kyne.com.au> -+# Copyright (c) 2009 Damian Pietras <da...@daper.net> -+# Copyright (c) 2012 Reuben Thomas <r...@sc3d.org> -+# Copyright (c) 2011 John Zaitseff <j.zaits...@zap.org.au> -+# -+# This program is free software: you can redistribute it and/or modify it -+# under the terms of the GNU General Public License as published by the -+# Free Software Foundation, either version 3 of the License, or (at your -+# option) any later version. -+# -+# This program is distributed in the hope that it will be useful, but -+# WITHOUT ANY WARRANTY; without even the implied warranty of -+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General -+# Public License for more details. -+# -+# You should have received a copy of the GNU General Public License along -+# with this program. If not, see <http://www.gnu.org/licenses/>. -+# -+# As a special exception, the respective Autoconf Macro's copyright owner -+# gives unlimited permission to copy, distribute and modify the configure -+# scripts that are the output of Autoconf when processing the Macro. You -+# need not follow the terms of the GNU General Public License when using -+# or distributing such scripts, even though portions of the text of the -+# Macro appear in them. The GNU General Public License (GPL) does govern -+# all other use of the material that constitutes the Autoconf Macro. -+# -+# This special exception to the GPL applies to versions of the Autoconf -+# Macro released by the Autoconf Archive. When you make and distribute a -+# modified version of the Autoconf Macro, you may extend this special -+# exception to the GPL to apply to your modified version as well. -+ -+#serial 16 -+ -+# internal function to factorize common code that is used by both ncurses -+# and ncursesw -+AC_DEFUN([_FIND_CURSES_FLAGS], [ -+ AC_MSG_CHECKING([for $1 via pkg-config]) -+ -+ _PKG_CONFIG([_ax_cv_$1_lib], [libs], [$1]) -+ _PKG_CONFIG([_ax_cv_$1_cppflags], [cflags], [$1]) -+ -+ AS_IF([test "x$pkg_failed" = "xyes" || test "x$pkg_failed" = "xuntried"],[ -+ AC_MSG_RESULT([no]) -+ # No suitable .pc file found, have to find flags via fallback -+ AC_CACHE_CHECK([for $1 via fallback], [ax_cv_$1], [ -+ AS_ECHO() -+ pkg_cv__ax_cv_$1_lib="-l$1" -+ pkg_cv__ax_cv_$1_cppflags="$CURSES_CPPFLAGS" -+ LIBS="$ax_saved_LIBS $pkg_cv__ax_cv_$1_lib" -+ CPPFLAGS="$ax_saved_CPPFLAGS $pkg_cv__ax_cv_$1_cppflags" -+ -+ AC_MSG_CHECKING([for initscr() with $pkg_cv__ax_cv_$1_lib]) -+ AC_LINK_IFELSE([AC_LANG_CALL([], [initscr])], -+ [ -+ AC_MSG_RESULT([yes]) -+ AC_MSG_CHECKING([for nodelay() with $pkg_cv__ax_cv_$1_lib]) -+ AC_LINK_IFELSE([AC_LANG_CALL([], [nodelay])],[ -+ ax_cv_$1=yes -+ ],[ -+ AC_MSG_RESULT([no]) -+ m4_if( -+ [$1],[ncursesw],[pkg_cv__ax_cv_$1_lib="$pkg_cv__ax_cv_$1_lib -ltinfow"], -+ [$1],[ncurses],[pkg_cv__ax_cv_$1_lib="$pkg_cv__ax_cv_$1_lib -ltinfo"] -+ ) -+ LIBS="$ax_saved_LIBS $pkg_cv__ax_cv_$1_lib" -+ -+ AC_MSG_CHECKING([for nodelay() with $pkg_cv__ax_cv_$1_lib]) -+ AC_LINK_IFELSE([AC_LANG_CALL([], [nodelay])],[ -+ ax_cv_$1=yes -+ ],[ -+ ax_cv_$1=no -+ ]) -+ ]) -+ ],[ -+ ax_cv_$1=no -+ ]) -+ ]) -+ ],[ -+ AC_MSG_RESULT([yes]) -+ # Found .pc file, using its information -+ LIBS="$ax_saved_LIBS $pkg_cv__ax_cv_$1_lib" -+ CPPFLAGS="$ax_saved_CPPFLAGS $pkg_cv__ax_cv_$1_cppflags" -+ ax_cv_$1=yes -+ ]) -+]) -+ -+AU_ALIAS([MP_WITH_CURSES], [AX_WITH_CURSES]) -+AC_DEFUN([AX_WITH_CURSES], [ -+ AC_ARG_VAR([CURSES_LIB], [linker library for Curses, e.g. -lcurses]) -+ AC_ARG_VAR([CURSES_CPPFLAGS], [preprocessor flags for Curses, e.g. -I/usr/include/ncursesw]) -+ AC_ARG_WITH([ncurses], [AS_HELP_STRING([--with-ncurses], -+ [force the use of Ncurses or NcursesW])], -+ [], [with_ncurses=check]) -+ AC_ARG_WITH([ncursesw], [AS_HELP_STRING([--without-ncursesw], -+ [do not use NcursesW (wide character support)])], -+ [], [with_ncursesw=check]) -+ AC_REQUIRE([PKG_PROG_PKG_CONFIG]) -+ -+ ax_saved_LIBS=$LIBS -+ ax_saved_CPPFLAGS=$CPPFLAGS -+ -+ AS_IF([test "x$with_ncurses" = xyes || test "x$with_ncursesw" = xyes], -+ [ax_with_plaincurses=no], [ax_with_plaincurses=check]) -+ -+ ax_cv_curses_which=no -+ -+ # Test for NcursesW -+ AS_IF([test "x$CURSES_LIB" = x && test "x$with_ncursesw" != xno], [ -+ _FIND_CURSES_FLAGS([ncursesw]) -+ -+ AS_IF([test "x$ax_cv_ncursesw" = xno && test "x$with_ncursesw" = xyes], [ -+ AC_MSG_ERROR([--with-ncursesw specified but could not find NcursesW library]) -+ ]) -+ -+ AS_IF([test "x$ax_cv_ncursesw" = xyes], [ -+ ax_cv_curses=yes -+ ax_cv_curses_which=ncursesw -+ CURSES_LIB="$pkg_cv__ax_cv_ncursesw_lib" -+ CURSES_CPPFLAGS="$pkg_cv__ax_cv_ncursesw_cppflags" -+ AC_DEFINE([HAVE_NCURSESW], [1], [Define to 1 if the NcursesW library is present]) -+ AC_DEFINE([HAVE_CURSES], [1], [Define to 1 if a SysV or X/Open compatible Curses library is present]) -+ -+ AC_CACHE_CHECK([for working ncursesw/curses.h], [ax_cv_header_ncursesw_curses_h], [ -+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ -+ @%:@define _XOPEN_SOURCE_EXTENDED 1 -+ @%:@include <ncursesw/curses.h> -+ ]], [[ -+ chtype a = A_BOLD; -+ int b = KEY_LEFT; -+ chtype c = COLOR_PAIR(1) & A_COLOR; -+ attr_t d = WA_NORMAL; -+ cchar_t e; -+ wint_t f; -+ int g = getattrs(stdscr); -+ int h = getcurx(stdscr) + getmaxx(stdscr); -+ initscr(); -+ init_pair(1, COLOR_WHITE, COLOR_RED); -+ wattr_set(stdscr, d, 0, NULL); -+ wget_wch(stdscr, &f); -+ ]])], -+ [ax_cv_header_ncursesw_curses_h=yes], -+ [ax_cv_header_ncursesw_curses_h=no]) -+ ]) -+ AS_IF([test "x$ax_cv_header_ncursesw_curses_h" = xyes], [ -+ ax_cv_curses_enhanced=yes -+ ax_cv_curses_color=yes -+ ax_cv_curses_obsolete=yes -+ AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions]) -+ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) -+ AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features]) -+ AC_DEFINE([HAVE_NCURSESW_CURSES_H], [1], [Define to 1 if <ncursesw/curses.h> is present]) -+ ]) -+ -+ AC_CACHE_CHECK([for working ncursesw.h], [ax_cv_header_ncursesw_h], [ -+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ -+ @%:@define _XOPEN_SOURCE_EXTENDED 1 -+ @%:@include <ncursesw.h> -+ ]], [[ -+ chtype a = A_BOLD; -+ int b = KEY_LEFT; -+ chtype c = COLOR_PAIR(1) & A_COLOR; -+ attr_t d = WA_NORMAL; -+ cchar_t e; -+ wint_t f; -+ int g = getattrs(stdscr); -+ int h = getcurx(stdscr) + getmaxx(stdscr); -+ initscr(); -+ init_pair(1, COLOR_WHITE, COLOR_RED); -+ wattr_set(stdscr, d, 0, NULL); -+ wget_wch(stdscr, &f); -+ ]])], -+ [ax_cv_header_ncursesw_h=yes], -+ [ax_cv_header_ncursesw_h=no]) -+ ]) -+ AS_IF([test "x$ax_cv_header_ncursesw_h" = xyes], [ -+ ax_cv_curses_enhanced=yes -+ ax_cv_curses_color=yes -+ ax_cv_curses_obsolete=yes -+ AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions]) -+ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) -+ AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features]) -+ AC_DEFINE([HAVE_NCURSESW_H], [1], [Define to 1 if <ncursesw.h> is present]) -+ ]) -+ -+ AC_CACHE_CHECK([for working ncurses.h], [ax_cv_header_ncurses_h_with_ncursesw], [ -+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ -+ @%:@define _XOPEN_SOURCE_EXTENDED 1 -+ @%:@include <ncurses.h> -+ ]], [[ -+ chtype a = A_BOLD; -+ int b = KEY_LEFT; -+ chtype c = COLOR_PAIR(1) & A_COLOR; -+ attr_t d = WA_NORMAL; -+ cchar_t e; -+ wint_t f; -+ int g = getattrs(stdscr); -+ int h = getcurx(stdscr) + getmaxx(stdscr); -+ initscr(); -+ init_pair(1, COLOR_WHITE, COLOR_RED); -+ wattr_set(stdscr, d, 0, NULL); -+ wget_wch(stdscr, &f); -+ ]])], -+ [ax_cv_header_ncurses_h_with_ncursesw=yes], -+ [ax_cv_header_ncurses_h_with_ncursesw=no]) -+ ]) -+ AS_IF([test "x$ax_cv_header_ncurses_h_with_ncursesw" = xyes], [ -+ ax_cv_curses_enhanced=yes -+ ax_cv_curses_color=yes -+ ax_cv_curses_obsolete=yes -+ AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions]) -+ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) -+ AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features]) -+ AC_DEFINE([HAVE_NCURSES_H], [1], [Define to 1 if <ncurses.h> is present]) -+ ]) -+ -+ AS_IF([test "x$ax_cv_header_ncursesw_curses_h" = xno && test "x$ax_cv_header_ncursesw_h" = xno && test "x$ax_cv_header_ncurses_h_with_ncursesw" = xno], [ -+ AC_MSG_WARN([could not find a working ncursesw/curses.h, ncursesw.h or ncurses.h]) -+ ]) -+ ]) -+ ]) -+ unset pkg_cv__ax_cv_ncursesw_lib -+ unset pkg_cv__ax_cv_ncursesw_cppflags -+ -+ # Test for Ncurses -+ AS_IF([test "x$CURSES_LIB" = x && test "x$with_ncurses" != xno && test "x$ax_cv_curses_which" = xno], [ -+ _FIND_CURSES_FLAGS([ncurses]) -+ -+ AS_IF([test "x$ax_cv_ncurses" = xno && test "x$with_ncurses" = xyes], [ -+ AC_MSG_ERROR([--with-ncurses specified but could not find Ncurses library]) -+ ]) -+ -+ AS_IF([test "x$ax_cv_ncurses" = xyes], [ -+ ax_cv_curses=yes -+ ax_cv_curses_which=ncurses -+ CURSES_LIB="$pkg_cv__ax_cv_ncurses_lib" -+ CURSES_CPPFLAGS="$pkg_cv__ax_cv_ncurses_cppflags" -+ AC_DEFINE([HAVE_NCURSES], [1], [Define to 1 if the Ncurses library is present]) -+ AC_DEFINE([HAVE_CURSES], [1], [Define to 1 if a SysV or X/Open compatible Curses library is present]) -+ -+ AC_CACHE_CHECK([for working ncurses/curses.h], [ax_cv_header_ncurses_curses_h], [ -+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ -+ @%:@include <ncurses/curses.h> -+ ]], [[ -+ chtype a = A_BOLD; -+ int b = KEY_LEFT; -+ chtype c = COLOR_PAIR(1) & A_COLOR; -+ int g = getattrs(stdscr); -+ int h = getcurx(stdscr) + getmaxx(stdscr); -+ initscr(); -+ init_pair(1, COLOR_WHITE, COLOR_RED); -+ ]])], -+ [ax_cv_header_ncurses_curses_h=yes], -+ [ax_cv_header_ncurses_curses_h=no]) -+ ]) -+ AS_IF([test "x$ax_cv_header_ncurses_curses_h" = xyes], [ -+ ax_cv_curses_color=yes -+ ax_cv_curses_obsolete=yes -+ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) -+ AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features]) -+ AC_DEFINE([HAVE_NCURSES_CURSES_H], [1], [Define to 1 if <ncurses/curses.h> is present]) -+ ]) -+ -+ AC_CACHE_CHECK([for working ncurses.h], [ax_cv_header_ncurses_h], [ -+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ -+ @%:@include <ncurses.h> -+ ]], [[ -+ chtype a = A_BOLD; -+ int b = KEY_LEFT; -+ chtype c = COLOR_PAIR(1) & A_COLOR; -+ int g = getattrs(stdscr); -+ int h = getcurx(stdscr) + getmaxx(stdscr); -+ initscr(); -+ init_pair(1, COLOR_WHITE, COLOR_RED); -+ ]])], -+ [ax_cv_header_ncurses_h=yes], -+ [ax_cv_header_ncurses_h=no]) -+ ]) -+ AS_IF([test "x$ax_cv_header_ncurses_h" = xyes], [ -+ ax_cv_curses_color=yes -+ ax_cv_curses_obsolete=yes -+ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) -+ AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features]) -+ AC_DEFINE([HAVE_NCURSES_H], [1], [Define to 1 if <ncurses.h> is present]) -+ ]) -+ -+ AS_IF([test "x$ax_cv_header_ncurses_curses_h" = xno && test "x$ax_cv_header_ncurses_h" = xno], [ -+ AC_MSG_WARN([could not find a working ncurses/curses.h or ncurses.h]) -+ ]) -+ ]) -+ ]) -+ unset pkg_cv__ax_cv_ncurses_lib -+ unset pkg_cv__ax_cv_ncurses_cppflags -+ -+ # Test for plain Curses (or if CURSES_LIB was set by user) -+ AS_IF([test "x$with_plaincurses" != xno && test "x$ax_cv_curses_which" = xno], [ -+ AS_IF([test "x$CURSES_LIB" != x], [ -+ LIBS="$ax_saved_LIBS $CURSES_LIB" -+ ], [ -+ LIBS="$ax_saved_LIBS -lcurses" -+ ]) -+ -+ AC_CACHE_CHECK([for Curses library], [ax_cv_plaincurses], [ -+ AC_LINK_IFELSE([AC_LANG_CALL([], [initscr])], -+ [ax_cv_plaincurses=yes], [ax_cv_plaincurses=no]) -+ ]) -+ -+ AS_IF([test "x$ax_cv_plaincurses" = xyes], [ -+ ax_cv_curses=yes -+ ax_cv_curses_which=plaincurses -+ AS_IF([test "x$CURSES_LIB" = x], [ -+ CURSES_LIB="-lcurses" -+ ]) -+ AC_DEFINE([HAVE_CURSES], [1], [Define to 1 if a SysV or X/Open compatible Curses library is present]) -+ -+ # Check for base conformance (and header file) -+ -+ AC_CACHE_CHECK([for working curses.h], [ax_cv_header_curses_h], [ -+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ -+ @%:@include <curses.h> -+ ]], [[ -+ chtype a = A_BOLD; -+ int b = KEY_LEFT; -+ initscr(); -+ ]])], -+ [ax_cv_header_curses_h=yes], -+ [ax_cv_header_curses_h=no]) -+ ]) -+ AS_IF([test "x$ax_cv_header_curses_h" = xyes], [ -+ AC_DEFINE([HAVE_CURSES_H], [1], [Define to 1 if <curses.h> is present]) -+ -+ # Check for X/Open Enhanced conformance -+ -+ AC_CACHE_CHECK([for X/Open Enhanced Curses conformance], [ax_cv_plaincurses_enhanced], [ -+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ -+ @%:@define _XOPEN_SOURCE_EXTENDED 1 -+ @%:@include <curses.h> -+ @%:@ifndef _XOPEN_CURSES -+ @%:@error "this Curses library is not enhanced" -+ "this Curses library is not enhanced" -+ @%:@endif -+ ]], [[ -+ chtype a = A_BOLD; -+ int b = KEY_LEFT; -+ chtype c = COLOR_PAIR(1) & A_COLOR; -+ attr_t d = WA_NORMAL; -+ cchar_t e; -+ wint_t f; -+ initscr(); -+ init_pair(1, COLOR_WHITE, COLOR_RED); -+ wattr_set(stdscr, d, 0, NULL); -+ wget_wch(stdscr, &f); -+ ]])], -+ [ax_cv_plaincurses_enhanced=yes], -+ [ax_cv_plaincurses_enhanced=no]) -+ ]) -+ AS_IF([test "x$ax_cv_plaincurses_enhanced" = xyes], [ -+ ax_cv_curses_enhanced=yes -+ ax_cv_curses_color=yes -+ AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions]) -+ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) -+ ]) -+ -+ # Check for color functions -+ -+ AC_CACHE_CHECK([for Curses color functions], [ax_cv_plaincurses_color], [ -+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ -+ @%:@define _XOPEN_SOURCE_EXTENDED 1 -+ @%:@include <curses.h> -+ ]], [[ -+ chtype a = A_BOLD; -+ int b = KEY_LEFT; -+ chtype c = COLOR_PAIR(1) & A_COLOR; -+ initscr(); -+ init_pair(1, COLOR_WHITE, COLOR_RED); -+ ]])], -+ [ax_cv_plaincurses_color=yes], -+ [ax_cv_plaincurses_color=no]) -+ ]) -+ AS_IF([test "x$ax_cv_plaincurses_color" = xyes], [ -+ ax_cv_curses_color=yes -+ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) -+ ]) -+ -+ # Check for obsolete functions -+ -+ AC_CACHE_CHECK([for obsolete Curses functions], [ax_cv_plaincurses_obsolete], [ -+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ -+ @%:@include <curses.h> -+ ]], [[ -+ chtype a = A_BOLD; -+ int b = KEY_LEFT; -+ int g = getattrs(stdscr); -+ int h = getcurx(stdscr) + getmaxx(stdscr); -+ initscr(); -+ ]])], -+ [ax_cv_plaincurses_obsolete=yes], -+ [ax_cv_plaincurses_obsolete=no]) -+ ]) -+ AS_IF([test "x$ax_cv_plaincurses_obsolete" = xyes], [ -+ ax_cv_curses_obsolete=yes -+ AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features]) -+ ]) -+ ]) -+ -+ AS_IF([test "x$ax_cv_header_curses_h" = xno], [ -+ AC_MSG_WARN([could not find a working curses.h]) -+ ]) -+ ]) -+ ]) -+ -+ AS_IF([test "x$ax_cv_curses" != xyes], [ax_cv_curses=no]) -+ AS_IF([test "x$ax_cv_curses_enhanced" != xyes], [ax_cv_curses_enhanced=no]) -+ AS_IF([test "x$ax_cv_curses_color" != xyes], [ax_cv_curses_color=no]) -+ AS_IF([test "x$ax_cv_curses_obsolete" != xyes], [ax_cv_curses_obsolete=no]) -+ -+ LIBS=$ax_saved_LIBS -+ CPPFLAGS=$ax_saved_CPPFLAGS -+ -+ unset ax_saved_LIBS -+ unset ax_saved_CPPFLAGS -+])dnl ---- samtools-1.3/m4/ax_with_htslib.m4 -+++ samtools-1.3/m4/ax_with_htslib.m4 -@@ -0,0 +1,140 @@ -+# =========================================================================== -+# http://www.gnu.org/software/autoconf-archive/ax_with_htslib.html -+# =========================================================================== -+# -+# SYNOPSIS -+# -+# AX_WITH_HTSLIB -+# -+# DESCRIPTION -+# -+# This macro checks whether HTSlib <http://www.htslib.org/> is installed -+# or nearby, and adds a --with-htslib=DIR option to the configure script -+# for specifying the location. It locates either an installation prefix -+# (with 'include' and 'lib' subdirectories) or an HTSlib source tree, as -+# HTSlib is fast-moving and users may wish to use an in-development tree. -+# -+# Different checks occur depending on the --with-htslib argument given: -+# -+# With --with-htslib=DIR, checks whether DIR is a source tree or contains -+# a working installation. -+# By default, searches for a source tree (with a name matching htslib*) -+# within or alongside $srcdir. Produces AC_MSG_ERROR if there are -+# several equally-likely candidates. If there are none, checks for -+# a working default installation. -+# With --with-htslib=system, checks for a working default installation. -+# -+# If a source tree is found or specified, it is added to AC_CONFIG_SUBDIRS -+# (which unfortunately may cause a "you should use literals" warning when -+# autoconf is run). -+# -+# The following output variables are set by this macro: -+# -+# HTSDIR Directory containing HTSlib source tree -+# HTSLIB_CPPFLAGS Preprocessor flags for compiling with HTSlib -+# HTSLIB_LDFLAGS Linker flags for linking with HTSlib -+# -+# The following shell variables may be defined: -+# -+# ax_cv_htslib Set to "yes" if HTSlib was found -+# ax_cv_htslib_which Set to "source", "install", or "none" -+# -+# LICENSE -+# -+# Copyright (C) 2015 Genome Research Ltd -+# -+# Copying and distribution of this file, with or without modification, are -+# permitted in any medium without royalty provided the copyright notice -+# and this notice are preserved. This file is offered as-is, without any -+# warranty. -+ -+#serial 1 -+ -+AC_DEFUN([AX_WITH_HTSLIB], -+[AC_ARG_WITH([htslib], -+ [AS_HELP_STRING([--with-htslib=DIR], -+ [use the HTSlib source tree or installation in DIR]) -+dnl Not indented, to avoid extra whitespace outwith AS_HELP_STRING() -+AS_HELP_STRING([--with-htslib=system], -+ [use only a system HTSlib installation])], -+ [], [with_htslib=search]) -+ -+case $with_htslib in -+yes|search) -+ AC_MSG_CHECKING([location of HTSlib source tree]) -+ case $srcdir in -+ .) srcp= ;; -+ *) srcp=$srcdir/ ;; -+ esac -+ found= -+ for dir in ${srcp}htslib* -- ${srcp}../htslib -- ${srcp}../htslib* -+ do -+ if test "$dir" = "--"; then -+ test -n "$found" && break -+ elif test -f "$dir/hts.c" && test -f "$dir/htslib/hts.h"; then -+ found="${found}1" -+ HTSDIR=$dir -+ fi -+ done -+ if test -z "$found"; then -+ AC_MSG_RESULT([none found]) -+ ax_cv_htslib_which=system -+ elif test "$found" = 1; then -+ AC_MSG_RESULT([$HTSDIR]) -+ ax_cv_htslib_which=source -+ else -+ AC_MSG_RESULT([several directories found]) -+ AC_MSG_ERROR([use --with-htslib=DIR to select which HTSlib to use]) -+ fi -+ ;; -+no) ax_cv_htslib_which=none ;; -+system) ax_cv_htslib_which=system ;; -+*) -+ HTSDIR=$with_htslib -+ if test -f "$HTSDIR/hts.c" && test -f "$HTSDIR/htslib/hts.h"; then -+ ax_cv_htslib_which=source -+ else -+ ax_cv_htslib_which=install -+ fi -+ ;; -+esac -+ -+case $ax_cv_htslib_which in -+source) -+ ax_cv_htslib=yes -+ HTSLIB_CPPFLAGS="-I$HTSDIR" -+ HTSLIB_LDFLAGS="-L$HTSDIR" -+ # We can't use a literal, because $HTSDIR is user-provided and variable -+ AC_CONFIG_SUBDIRS($HTSDIR) -+ ;; -+system) -+ AC_CHECK_HEADER([htslib/sam.h], -+ [AC_CHECK_LIB(hts, hts_version, [ax_cv_htslib=yes], [ax_cv_htslib=no])], -+ [ax_cv_htslib=no], [;]) -+ ax_cv_htslib_which=install -+ HTSDIR= -+ HTSLIB_CPPFLAGS= -+ HTSLIB_LDFLAGS= -+ ;; -+install) -+ ax_saved_CPPFLAGS=$CPPFLAGS -+ ax_saved_LDFLAGS=$LDFLAGS -+ HTSLIB_CPPFLAGS="-I$HTSDIR/include" -+ HTSLIB_LDFLAGS="-L$HTSDIR/lib" -+ CPPFLAGS="$CPPFLAGS $HTSLIB_CPPFLAGS" -+ LDFLAGS="$LDFLAGS $HTSLIB_LDFLAGS" -+ AC_CHECK_HEADER([htslib/sam.h], -+ [AC_CHECK_LIB(hts, hts_version, [ax_cv_htslib=yes], [ax_cv_htslib=no])], -+ [ax_cv_htslib=no], [;]) -+ HTSDIR= -+ CPPFLAGS=$ax_saved_CPPFLAGS -+ LDFLAGS=$ax_saved_LDFLAGS -+ ;; -+none) -+ ax_cv_htslib=no -+ ;; -+esac -+ -+AC_SUBST([HTSDIR]) -+AC_SUBST([HTSLIB_CPPFLAGS]) -+AC_SUBST([HTSLIB_LDFLAGS])]) diff --git a/sci-biology/samtools/samtools-0.1.12.ebuild b/sci-biology/samtools/samtools-0.1.12.ebuild deleted file mode 100644 index d32746ae2ba..00000000000 --- a/sci-biology/samtools/samtools-0.1.12.ebuild +++ /dev/null @@ -1,30 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=2 - -MY_P="${P}a" - -DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats" -HOMEPAGE="http://samtools.sourceforge.net/"; -SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.bz2" - -LICENSE="MIT" -SLOT="0" -IUSE="" -KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" - -S="${WORKDIR}/${MY_P}" - -src_prepare() { - sed -i 's/^CFLAGS=/CFLAGS+=/' "${S}"/{Makefile,misc/Makefile} -} - -src_install() { - dobin samtools || die - dobin $(find misc -type f -executable) || die - insinto /usr/share/${PN} - doins -r examples || die - doman ${PN}.1 || die - dodoc AUTHORS ChangeLog NEWS -} diff --git a/sci-biology/samtools/samtools-0.1.19-r2.ebuild b/sci-biology/samtools/samtools-0.1.19-r2.ebuild deleted file mode 100644 index a401e5f9df8..00000000000 --- a/sci-biology/samtools/samtools-0.1.19-r2.ebuild +++ /dev/null @@ -1,60 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit eutils multilib python-r1 toolchain-funcs - -DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats" -HOMEPAGE="http://samtools.sourceforge.net/"; -SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" -IUSE="examples" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -CDEPEND="sys-libs/ncurses:0=" -RDEPEND="${CDEPEND} - dev-lang/lua - dev-lang/perl - ${PYTHON_DEPS}" -DEPEND="${CDEPEND} - virtual/pkgconfig" - -src_prepare() { - epatch "${FILESDIR}"/${P}-buildsystem.patch - - sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die - - tc-export CC AR -} - -src_compile() { - local _ncurses="$($(tc-getPKG_CONFIG) --libs ncurses)" - emake dylib LIBCURSES="${_ncurses}" - emake LIBCURSES="${_ncurses}" -} - -src_install() { - dobin samtools $(find bcftools misc -type f -executable) - - python_replicate_script "${ED}"/usr/bin/varfilter.py - - dolib.so libbam$(get_libname 1) - dosym libbam$(get_libname 1) /usr/$(get_libdir)/libbam$(get_libname) - - insinto /usr/include/bam - doins *.h - - doman ${PN}.1 - dodoc AUTHORS NEWS - - if use examples; then - insinto /usr/share/${PN} - doins -r examples - fi -} diff --git a/sci-biology/samtools/samtools-1.0-r1.ebuild b/sci-biology/samtools/samtools-1.0-r1.ebuild deleted file mode 100644 index b6e1aeb5831..00000000000 --- a/sci-biology/samtools/samtools-1.0-r1.ebuild +++ /dev/null @@ -1,72 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit eutils multilib 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="${PYTHON_REQUIRED_USE}" - -CDEPEND=" - sys-libs/ncurses:0= - sci-libs/htslib" - -RDEPEND="${CDEPEND} - dev-lang/lua - dev-lang/perl - ${PYTHON_DEPS}" -DEPEND="${CDEPEND} - virtual/pkgconfig" - -src_prepare() { - find htslib-1.0 -delete || die - - sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die - - epatch "${FILESDIR}"/${P}-buildsystem.patch - - tc-export CC AR - - sed \ - -e '/htslib.mk/d' \ - -i Makefile || die - -} - -src_compile() { - local mymakeargs=( - LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" - HTSDIR="${EPREFIX}/usr/include" - HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) - BAMLIB="libbam.so" - ) - emake "${mymakeargs[@]}" -} - -src_install() { - dobin samtools $(find misc -type f -executable) - - python_replicate_script "${ED}"/usr/bin/varfilter.py - dolib.so libbam.so* - - insinto /usr/include/bam - doins *.h - - doman ${PN}.1 - dodoc AUTHORS NEWS README - - if use examples; then - insinto /usr/share/${PN} - doins -r examples - fi -} diff --git a/sci-biology/samtools/samtools-1.0.ebuild b/sci-biology/samtools/samtools-1.0.ebuild deleted file mode 100644 index 0fb9d04344b..00000000000 --- a/sci-biology/samtools/samtools-1.0.ebuild +++ /dev/null @@ -1,68 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit eutils multilib 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="${PYTHON_REQUIRED_USE}" - -CDEPEND=" - sys-libs/ncurses:0= - sci-libs/htslib" - -RDEPEND="${CDEPEND} - dev-lang/lua - dev-lang/perl - ${PYTHON_DEPS}" -DEPEND="${CDEPEND} - virtual/pkgconfig" - -src_prepare() { - find htslib-1.0 -delete || die - - sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die - - tc-export CC AR - - sed \ - -e '/htslib.mk/d' \ - -i Makefile || die - -} - -src_compile() { - local mymakeargs=( - LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" - CC="$(tc-getCC)" - LDFLAGS="${LDFLAGS}" - CFLAGS="${CFLAGS}" - HTSDIR="${EPREFIX}/usr/include" - HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) - ) - emake "${mymakeargs[@]}" -} - -src_install() { - dobin samtools $(find misc -type f -executable) - - python_replicate_script "${ED}"/usr/bin/varfilter.py - - doman ${PN}.1 - dodoc AUTHORS NEWS README - - if use examples; then - insinto /usr/share/${PN} - doins -r examples - fi -} diff --git a/sci-biology/samtools/samtools-1.1.ebuild b/sci-biology/samtools/samtools-1.1.ebuild deleted file mode 100644 index ca3e4b46c22..00000000000 --- a/sci-biology/samtools/samtools-1.1.ebuild +++ /dev/null @@ -1,82 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit eutils multilib 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="${PYTHON_REQUIRED_USE}" - -CDEPEND=" - sys-libs/ncurses:0= - ~sci-libs/htslib-${PV}" - -RDEPEND="${CDEPEND} - dev-lang/lua - dev-lang/perl - ${PYTHON_DEPS}" -DEPEND="${CDEPEND} - virtual/pkgconfig" - -src_prepare() { - find htslib-* -delete || die - - sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die - - epatch "${FILESDIR}"/${P}-buildsystem.patch - - tc-export CC AR - - sed \ - -e '/htslib.mk/d' \ - -i Makefile || die - -} - -src_compile() { - local mymakeargs=( - LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" - HTSDIR="${EPREFIX}/usr/include" - HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) - BAMLIB="libbam.so" - ) - emake "${mymakeargs[@]}" -} - -src_test() { - local mymakeargs=( - LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" - HTSDIR="${EPREFIX}/usr/include" - HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) - BAMLIB="libbam.so" - ) - emake "${mymakeargs[@]}" test -} - -src_install() { - dobin samtools $(find misc -type f -executable) - - python_replicate_script "${ED}"/usr/bin/varfilter.py - dolib.so libbam.so* - - insinto /usr/include/bam - doins *.h - - doman ${PN}.1 - dodoc AUTHORS NEWS README - - if use examples; then - insinto /usr/share/${PN} - doins -r examples - fi -} diff --git a/sci-biology/samtools/samtools-1.2.ebuild b/sci-biology/samtools/samtools-1.2.ebuild deleted file mode 100644 index 75dfbfae1f2..00000000000 --- a/sci-biology/samtools/samtools-1.2.ebuild +++ /dev/null @@ -1,82 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit eutils multilib 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="${PYTHON_REQUIRED_USE}" - -CDEPEND=" - sys-libs/ncurses:0= - >=sci-libs/htslib-${PV}" - -RDEPEND="${CDEPEND} - dev-lang/lua - dev-lang/perl - ${PYTHON_DEPS}" -DEPEND="${CDEPEND} - virtual/pkgconfig" - -src_prepare() { - find htslib-* -delete || die - - sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die - - epatch "${FILESDIR}"/${P}-buildsystem.patch - - tc-export CC AR - - sed \ - -e '/htslib.mk/d' \ - -i Makefile || die - -} - -src_compile() { - local mymakeargs=( - LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" - HTSDIR="${EPREFIX}/usr/include" - HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) - BAMLIB="libbam.so" - ) - emake "${mymakeargs[@]}" -} - -src_test() { - local mymakeargs=( - LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" - HTSDIR="${EPREFIX}/usr/include" - HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) - BAMLIB="libbam.so" - ) - LD_LIBRARY_PATH="${S}" emake "${mymakeargs[@]}" test -} - -src_install() { - dobin samtools $(find misc -type f -executable) - - python_replicate_script "${ED}"/usr/bin/varfilter.py - dolib.so libbam.so* - - insinto /usr/include/bam - doins *.h - - doman ${PN}.1 - dodoc AUTHORS NEWS README - - if use examples; then - insinto /usr/share/${PN} - doins -r examples - fi -} diff --git a/sci-biology/samtools/samtools-1.3-r1.ebuild b/sci-biology/samtools/samtools-1.3-r1.ebuild deleted file mode 100644 index 8d25bf84ad3..00000000000 --- a/sci-biology/samtools/samtools-1.3-r1.ebuild +++ /dev/null @@ -1,96 +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="${PYTHON_REQUIRED_USE}" - -RDEPEND="sys-libs/ncurses:0= - =sci-libs/htslib-${PV}* - dev-lang/perl - ${PYTHON_DEPS}" -DEPEND="${RDEPEND} - virtual/pkgconfig" - -PATCHES=( - "${FILESDIR}/${P}-buildsystem.patch" - "${FILESDIR}/${P}-ncurses.patch" -) - -src_prepare() { - default - - # unbundle libs - find htslib-* -delete || die - - sed -i -e 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die - sed -i -e '/htslib.mk/d' -i Makefile || die - - tc-export CC AR - - rm -f aclocal.m4 || die - eautoreconf -} - -src_compile() { - local mymakeargs=( - LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" - HTSDIR="${EPREFIX}/usr/include" - HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) - BAMLIB="libbam.so" - libdir=/usr/$(get_libdir) - ) - emake "${mymakeargs[@]}" -} - -src_test() { - local mymakeargs=( - LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" - HTSDIR="${EPREFIX}/usr/include" - HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) - BAMLIB="libbam.so" - ) - LD_LIBRARY_PATH="${S}" emake "${mymakeargs[@]}" test -} - -src_install() { - dobin samtools $(find misc -type f -executable) - - python_replicate_script "${ED}"usr/bin/varfilter.py - - # fix perl shebangs - pushd "${ED}"usr/bin/ >> /dev/null - local i - for i in plot-bamstats *.pl; do - sed -e '1s:.*:#!/usr/bin/env perl:' -i "${i}" || die - done - - # remove lua scripts - rm -f r2plot.lua vcfutils.lua || die - popd >> /dev/null - - dolib.so libbam.so* - - insinto /usr/include/bam - doins *.h - - doman ${PN}.1 - dodoc AUTHORS NEWS README - - if use examples; then - insinto /usr/share/${PN} - doins -r examples - fi -}
