sci-biology/samtools: Version bump to 0.1.20

* EAPI=6
* samtools will be slotted with SLOT="legacy", in order
  to be able to install applications that rely on the old
  monolithic library.

Package-Manager: portage-2.2.28

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
+}