diff options
| -rw-r--r-- | sci-biology/samtools/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch | 206 | ||||
| -rw-r--r-- | sci-biology/samtools/samtools-0.1.20.ebuild | 64 |
3 files changed, 271 insertions, 0 deletions
diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest index dae2fbd2272c..fd88ba4947d3 100644 --- a/sci-biology/samtools/Manifest +++ b/sci-biology/samtools/Manifest @@ -1,5 +1,6 @@ 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 diff --git a/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch b/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch new file mode 100644 index 000000000000..dfdd890b1087 --- /dev/null +++ b/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch @@ -0,0 +1,206 @@ +--- samtools-0.1.20/bcftools/Makefile ++++ samtools-0.1.20/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 @@ + .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 @@ + $(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 +--- samtools-0.1.20/Makefile ++++ samtools-0.1.20/Makefile +@@ -4,10 +4,10 @@ + # make git-stamp + VERSION= + +-CC= gcc +-CFLAGS= -g -Wall $(VERSION) -O2 +-#LDFLAGS= -Wl,-rpath,\$$ORIGIN/../lib +-DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 ++CC?= gcc ++CFLAGS?= -g -Wall $(VERSION) -O2 ++#LDFLAGS+= -Wl,-rpath,\$$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 \ +@@ -28,14 +28,14 @@ + .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; +@@ -48,22 +48,22 @@ + .PHONY:all lib clean cleanlocal + .PHONY:all-recur lib-recur clean-recur cleanlocal-recur install-recur + +-lib:libbam.a ++lib:libbam-legacy.a + +-libbam.a:$(LOBJS) ++libbam-legacy.a:$(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 + + 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 $@ + + razip.o:razf.h + bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h +@@ -90,17 +90,17 @@ + faidx_main.o:faidx.h razf.h + + +-libbam.1.dylib-local:$(LOBJS) +- libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz ++libbam-legacy.1.dylib-local:$(LOBJS) ++ libtool -dynamic $(LOBJS) -o libbam-legacy.1.dylib -lc -lz + +-libbam.so.1-local:$(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 $(LOBJS) -lc -lz -lm -lpthread + + dylib: + @$(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;; \ + *) echo 'Unknown OS';; \ + esac + +--- samtools-0.1.20/misc/Makefile ++++ samtools-0.1.20/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 @@ + .SUFFIXES:.c .o + + .c.o: +- $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@ ++ $(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@ + + all:$(PROG) + +@@ -20,7 +20,7 @@ + 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: + + 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 + + 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 +--- samtools-0.1.20/misc/varfilter.py ++++ samtools-0.1.20/misc/varfilter.py +@@ -1,4 +1,4 @@ +-#!/software/bin/python ++#!/usr/bin/env python + + # Author: lh3, converted to python and modified to add -C option by Aylwyn Scally + # diff --git a/sci-biology/samtools/samtools-0.1.20.ebuild b/sci-biology/samtools/samtools-0.1.20.ebuild new file mode 100644 index 000000000000..50ee0b3c0f48 --- /dev/null +++ b/sci-biology/samtools/samtools-0.1.20.ebuild @@ -0,0 +1,64 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=6 + +PYTHON_COMPAT=( python2_7 ) + +inherit eutils python-r1 toolchain-funcs + +DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats" +HOMEPAGE="http://samtools.sourceforge.net/" +SRC_URI="https://github.com/samtools/samtools/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="legacy" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" +IUSE="examples" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND="sys-libs/ncurses:0= + dev-lang/lua:0 + dev-lang/perl" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +PATCHES=( + "${FILESDIR}/${P}-buildsystem.patch" +) + +src_prepare() { + default + sed -i 's~/software/bin/python~/usr/bin/env python~' "${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 $(find bcftools misc -type f -executable) + mv "${ED}"/usr/{bin,${PN}-${SLOT}} || die + mkdir "${ED}"/usr/bin || die + mv "${ED}"/usr/{${PN}-${SLOT},bin/} || die + + mv "${ED}"/usr/bin/${PN}-${SLOT}/varfilter{,-${SLOT}}.py || die + python_replicate_script "${ED}"/usr/bin/${PN}-${SLOT}/varfilter-${SLOT}.py + + dolib.so libbam-${SLOT}$(get_libname 1) + dosym libbam-${SLOT}$(get_libname 1) /usr/$(get_libdir)/libbam-${SLOT}$(get_libname) + + insinto /usr/include/bam-${SLOT} + doins *.h + + mv ${PN}{,-${SLOT}}.1 || die + doman ${PN}-${SLOT}.1 + dodoc AUTHORS NEWS + + use examples && dodoc -r examples +} |