subject:"\[gentoo\-commits\] repo\/gentoo\:master commit in\: sci\-biology\/samtools\/"

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

2024-03-26 Thread David Seifert

commit: 0663dbd3daa9a4f9716f1238a3248e23a97767fa
Author: David Seifert  gentoo  org>
AuthorDate: Tue Mar 26 11:06:21 2024 +
Commit: David Seifert  gentoo  org>
CommitDate: Tue Mar 26 11:06:21 2024 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=0663dbd3

sci-biology/samtools: add 1.19.2

Signed-off-by: David Seifert  gentoo.org>

 sci-biology/samtools/Manifest   |  1 +
 sci-biology/samtools/samtools-1.19.2.ebuild | 47 +
 2 files changed, 48 insertions(+)

diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index 72408c9c9544..09cffe1bb5b0 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1 +1,2 @@
 DIST samtools-1.17.tar.bz2 8605080 BLAKE2B 
09cb0bff7bf7113a77f57fdb879765b28b65461a574e4a1ab20ae2327af46e5616e04f03eb68706d42ba0643e887d7921974a3d78c5f87d296a4c3b691215260
 SHA512 
107a6df858c6bd2556ba4e86cc1922c3184df095f347039fa94bfd24e5ee21e1a4a9fba5a7cce248a06ad47f99978d9aae570efee7e30e165f33ea848a2cd3c3
+DIST samtools-1.19.2.tar.bz2 9150483 BLAKE2B 
fb845b2ccd61f1731ef4cdc180f4b9a4ac75e8c73c1ceaa9409b99e8052ca66b88c73fc71fd1067942aa24964f6df8dcb2d93631e5757e0cc200d7a3b9fad461
 SHA512 
c08d729fed21112855e0acc9cf7f29c7670d38a02ad6b0f2e9b9ef15a18f07e3e194cc4f6913481c98cd3e85dd4dc975dac96155b892da58bbe8ea3679a5270f

diff --git a/sci-biology/samtools/samtools-1.19.2.ebuild 
b/sci-biology/samtools/samtools-1.19.2.ebuild
new file mode 100644
index ..42879b0f8698
--- /dev/null
+++ b/sci-biology/samtools/samtools-1.19.2.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs
+
+DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment 
formats"
+HOMEPAGE="http://www.htslib.org/;
+SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2;
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+
+RDEPEND="
+   dev-lang/perl
+   =sci-libs/htslib-$(ver_cut 1-2)*:=
+   sys-libs/ncurses:=[unicode(+)]
+   sys-libs/zlib"
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
+
+src_prepare() {
+   default
+
+   # remove bundled htslib
+   rm -r htslib-* || die
+}
+
+src_configure() {
+   econf \
+   --with-ncurses \
+   --with-htslib=system \
+   CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw || die)"
+}
+
+src_compile() {
+   emake AR="$(tc-getAR)"
+}
+
+src_install() {
+   default
+
+   dodoc -r examples
+   docompress -x /usr/share/doc/${PF}/examples
+}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/files/, profiles/, sci-biology/samtools/

2023-05-05 Thread David Seifert

commit: f8ed4029d610b62eb95b85692efd9396ab8fd933
Author: David Seifert  gentoo  org>
AuthorDate: Fri May  5 09:19:58 2023 +
Commit: David Seifert  gentoo  org>
CommitDate: Fri May  5 09:19:58 2023 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f8ed4029

sci-biology/samtools: drop 0.1.20-r4

Closes: https://bugs.gentoo.org/862288
Signed-off-by: David Seifert  gentoo.org>

 profiles/package.mask  |   6 -
 sci-biology/samtools/Manifest  |   1 -
 .../files/samtools-0.1.20-buildsystem.patch| 206 -
 sci-biology/samtools/samtools-0.1.20-r4.ebuild |  73 
 4 files changed, 286 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index f381e12c4b19..5b737647d95d 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -283,12 +283,6 @@ dev-ruby/allison
 # Removal on 2023-05-07.  Bug #878655.
 app-misc/wildq
 
-# David Seifert  (2023-04-06)
-# Last release over 7 years ago, abandoned upstream, still depends on
-# dead 0.1-legacy samtools slot. No revdeps in tree.
-# Removal on 2023-05-06. Bug #862288.
-sci-biology/samtools:0.1-legacy
-
 # Ionen Wolkens  (2023-03-30)
 # NVIDIA dropped support for the 390.xx branch in December 2022[1].
 #

diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index 5787a3bb63e6..72408c9c9544 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,2 +1 @@
-DIST samtools-0.1.20.tar.gz 566387 BLAKE2B 
a62d74c408877754af50f5e5fea0e2289ec1e0c9f25013ed0d039bfe8ef61108600d917f8c9d356e98aca632795b4eb0f01ea1b54526a652577fb74a38a433c2
 SHA512 
15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5
 DIST samtools-1.17.tar.bz2 8605080 BLAKE2B 
09cb0bff7bf7113a77f57fdb879765b28b65461a574e4a1ab20ae2327af46e5616e04f03eb68706d42ba0643e887d7921974a3d78c5f87d296a4c3b691215260
 SHA512 
107a6df858c6bd2556ba4e86cc1922c3184df095f347039fa94bfd24e5ee21e1a4a9fba5a7cce248a06ad47f99978d9aae570efee7e30e165f33ea848a2cd3c3

diff --git a/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch 
b/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch
deleted file mode 100644
index eb9f6934a96f..
--- a/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch
+++ /dev/null
@@ -1,206 +0,0 @@
 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)

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

2023-04-06 Thread David Seifert

commit: d3ddf57e6ff7731bc7ceba004419cac3d6efddb1
Author: David Seifert  gentoo  org>
AuthorDate: Thu Apr  6 19:29:07 2023 +
Commit: David Seifert  gentoo  org>
CommitDate: Thu Apr  6 19:29:07 2023 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d3ddf57e

sci-biology/samtools: drop 1.16.1

Signed-off-by: David Seifert  gentoo.org>

 sci-biology/samtools/Manifest   |  1 -
 sci-biology/samtools/samtools-1.16.1.ebuild | 47 -
 2 files changed, 48 deletions(-)

diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index d6c2ed1c0762..5787a3bb63e6 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,3 +1,2 @@
 DIST samtools-0.1.20.tar.gz 566387 BLAKE2B 
a62d74c408877754af50f5e5fea0e2289ec1e0c9f25013ed0d039bfe8ef61108600d917f8c9d356e98aca632795b4eb0f01ea1b54526a652577fb74a38a433c2
 SHA512 
15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5
-DIST samtools-1.16.1.tar.bz2 8217689 BLAKE2B 
51ca62655d1f43dd0c6f9bd38b323b8a9d8f7486ce42496e21186da06ea881d94e096214720f3fb8d1dd12d7a23881bc3b25e27b1a845d56157ac7ffda7130c1
 SHA512 
f9d6b8652234c782a1b369f028073ad4a66c44e9620ae60f0ecb35e0874f04ca633713078b692fdc1a1cc4f884ebdbf3ecae6881f11fb3b4fd3d27c5b8da67ba
 DIST samtools-1.17.tar.bz2 8605080 BLAKE2B 
09cb0bff7bf7113a77f57fdb879765b28b65461a574e4a1ab20ae2327af46e5616e04f03eb68706d42ba0643e887d7921974a3d78c5f87d296a4c3b691215260
 SHA512 
107a6df858c6bd2556ba4e86cc1922c3184df095f347039fa94bfd24e5ee21e1a4a9fba5a7cce248a06ad47f99978d9aae570efee7e30e165f33ea848a2cd3c3

diff --git a/sci-biology/samtools/samtools-1.16.1.ebuild 
b/sci-biology/samtools/samtools-1.16.1.ebuild
deleted file mode 100644
index 8047657df992..
--- a/sci-biology/samtools/samtools-1.16.1.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment 
formats"
-HOMEPAGE="http://www.htslib.org/;
-SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2;
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
-
-RDEPEND="
-   dev-lang/perl
-   =sci-libs/htslib-$(ver_cut 1-2)*:=
-   sys-libs/ncurses:=[unicode(+)]
-   sys-libs/zlib"
-DEPEND="${RDEPEND}"
-BDEPEND="virtual/pkgconfig"
-
-src_prepare() {
-   default
-
-   # remove bundled htslib
-   rm -r htslib-* || die
-}
-
-src_configure() {
-   econf \
-   --with-ncurses \
-   --with-htslib=system \
-   CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw || die)"
-}
-
-src_compile() {
-   emake AR="$(tc-getAR)"
-}
-
-src_install() {
-   default
-
-   dodoc -r examples
-   docompress -x /usr/share/doc/${PF}/examples
-}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

2023-03-30 Thread David Seifert

commit: 6664bbc7a20e0e9662de517ff7aced5dbc2fde9c
Author: David Seifert  gentoo  org>
AuthorDate: Thu Mar 30 11:10:59 2023 +
Commit: David Seifert  gentoo  org>
CommitDate: Thu Mar 30 11:10:59 2023 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6664bbc7

sci-biology/samtools: add 1.17

Signed-off-by: David Seifert  gentoo.org>

 sci-biology/samtools/Manifest |  1 +
 sci-biology/samtools/samtools-1.17.ebuild | 47 +++
 2 files changed, 48 insertions(+)

diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index 098c93fb112b..d6c2ed1c0762 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,2 +1,3 @@
 DIST samtools-0.1.20.tar.gz 566387 BLAKE2B 
a62d74c408877754af50f5e5fea0e2289ec1e0c9f25013ed0d039bfe8ef61108600d917f8c9d356e98aca632795b4eb0f01ea1b54526a652577fb74a38a433c2
 SHA512 
15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5
 DIST samtools-1.16.1.tar.bz2 8217689 BLAKE2B 
51ca62655d1f43dd0c6f9bd38b323b8a9d8f7486ce42496e21186da06ea881d94e096214720f3fb8d1dd12d7a23881bc3b25e27b1a845d56157ac7ffda7130c1
 SHA512 
f9d6b8652234c782a1b369f028073ad4a66c44e9620ae60f0ecb35e0874f04ca633713078b692fdc1a1cc4f884ebdbf3ecae6881f11fb3b4fd3d27c5b8da67ba
+DIST samtools-1.17.tar.bz2 8605080 BLAKE2B 
09cb0bff7bf7113a77f57fdb879765b28b65461a574e4a1ab20ae2327af46e5616e04f03eb68706d42ba0643e887d7921974a3d78c5f87d296a4c3b691215260
 SHA512 
107a6df858c6bd2556ba4e86cc1922c3184df095f347039fa94bfd24e5ee21e1a4a9fba5a7cce248a06ad47f99978d9aae570efee7e30e165f33ea848a2cd3c3

diff --git a/sci-biology/samtools/samtools-1.17.ebuild 
b/sci-biology/samtools/samtools-1.17.ebuild
new file mode 100644
index ..e105621c7865
--- /dev/null
+++ b/sci-biology/samtools/samtools-1.17.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs
+
+DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment 
formats"
+HOMEPAGE="http://www.htslib.org/;
+SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2;
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+
+RDEPEND="
+   dev-lang/perl
+   =sci-libs/htslib-$(ver_cut 1-2)*:=
+   sys-libs/ncurses:=[unicode(+)]
+   sys-libs/zlib"
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
+
+src_prepare() {
+   default
+
+   # remove bundled htslib
+   rm -r htslib-* || die
+}
+
+src_configure() {
+   econf \
+   --with-ncurses \
+   --with-htslib=system \
+   CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw || die)"
+}
+
+src_compile() {
+   emake AR="$(tc-getAR)"
+}
+
+src_install() {
+   default
+
+   dodoc -r examples
+   docompress -x /usr/share/doc/${PF}/examples
+}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

2023-02-19 Thread David Seifert

commit: 5f92906d5b563269d52f9dd1720beb098ba56edb
Author: David Seifert  gentoo  org>
AuthorDate: Sun Feb 19 15:44:19 2023 +
Commit: David Seifert  gentoo  org>
CommitDate: Sun Feb 19 15:44:19 2023 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5f92906d

sci-biology/samtools: drop 1.15.1

Signed-off-by: David Seifert  gentoo.org>

 sci-biology/samtools/Manifest   |  1 -
 sci-biology/samtools/samtools-1.15.1.ebuild | 47 -
 2 files changed, 48 deletions(-)

diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index 6836d74da51a..098c93fb112b 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,3 +1,2 @@
 DIST samtools-0.1.20.tar.gz 566387 BLAKE2B 
a62d74c408877754af50f5e5fea0e2289ec1e0c9f25013ed0d039bfe8ef61108600d917f8c9d356e98aca632795b4eb0f01ea1b54526a652577fb74a38a433c2
 SHA512 
15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5
-DIST samtools-1.15.1.tar.bz2 7831692 BLAKE2B 
0fe94ff05075b219c77d0da8500c64bdffd53927950b5a67f8708c5c326ebc90a40c193b3bcf0baf3d09baed6fa596d9d024cb529340c6887de88614c9ff4bd6
 SHA512 
54a8a394b6b5231bd942236ec353027caaf48b4552a00b35573a1e71d680320d8140a73409bb76066c82e86fe62cf74f2f8f2f1a1e4aec96e4e8b9aff0d44a46
 DIST samtools-1.16.1.tar.bz2 8217689 BLAKE2B 
51ca62655d1f43dd0c6f9bd38b323b8a9d8f7486ce42496e21186da06ea881d94e096214720f3fb8d1dd12d7a23881bc3b25e27b1a845d56157ac7ffda7130c1
 SHA512 
f9d6b8652234c782a1b369f028073ad4a66c44e9620ae60f0ecb35e0874f04ca633713078b692fdc1a1cc4f884ebdbf3ecae6881f11fb3b4fd3d27c5b8da67ba

diff --git a/sci-biology/samtools/samtools-1.15.1.ebuild 
b/sci-biology/samtools/samtools-1.15.1.ebuild
deleted file mode 100644
index 21d2b8a5077d..
--- a/sci-biology/samtools/samtools-1.15.1.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment 
formats"
-HOMEPAGE="http://www.htslib.org/;
-SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2;
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
-
-RDEPEND="
-   dev-lang/perl
-   =sci-libs/htslib-${PV}*:=
-   sys-libs/ncurses:=[unicode(+)]
-   sys-libs/zlib"
-DEPEND="${RDEPEND}"
-BDEPEND="virtual/pkgconfig"
-
-src_prepare() {
-   default
-
-   # remove bundled htslib
-   rm -r htslib-* || die
-}
-
-src_configure() {
-   econf \
-   --with-ncurses \
-   --with-htslib=system \
-   CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw || die)"
-}
-
-src_compile() {
-   emake AR="$(tc-getAR)"
-}
-
-src_install() {
-   default
-
-   dodoc -r examples
-   docompress -x /usr/share/doc/${PF}/examples
-}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

2022-12-26 Thread David Seifert

commit: ec7bfb77b991e596ca13696b7627f49975f8265a
Author: David Seifert  gentoo  org>
AuthorDate: Tue Dec 27 00:06:45 2022 +
Commit: David Seifert  gentoo  org>
CommitDate: Tue Dec 27 00:06:45 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=ec7bfb77

sci-biology/samtools: add 1.16.1

Signed-off-by: David Seifert  gentoo.org>

 sci-biology/samtools/Manifest   |  1 +
 sci-biology/samtools/samtools-1.16.1.ebuild | 47 +
 2 files changed, 48 insertions(+)

diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index 0ff07e0d4f83..6836d74da51a 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,2 +1,3 @@
 DIST samtools-0.1.20.tar.gz 566387 BLAKE2B 
a62d74c408877754af50f5e5fea0e2289ec1e0c9f25013ed0d039bfe8ef61108600d917f8c9d356e98aca632795b4eb0f01ea1b54526a652577fb74a38a433c2
 SHA512 
15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5
 DIST samtools-1.15.1.tar.bz2 7831692 BLAKE2B 
0fe94ff05075b219c77d0da8500c64bdffd53927950b5a67f8708c5c326ebc90a40c193b3bcf0baf3d09baed6fa596d9d024cb529340c6887de88614c9ff4bd6
 SHA512 
54a8a394b6b5231bd942236ec353027caaf48b4552a00b35573a1e71d680320d8140a73409bb76066c82e86fe62cf74f2f8f2f1a1e4aec96e4e8b9aff0d44a46
+DIST samtools-1.16.1.tar.bz2 8217689 BLAKE2B 
51ca62655d1f43dd0c6f9bd38b323b8a9d8f7486ce42496e21186da06ea881d94e096214720f3fb8d1dd12d7a23881bc3b25e27b1a845d56157ac7ffda7130c1
 SHA512 
f9d6b8652234c782a1b369f028073ad4a66c44e9620ae60f0ecb35e0874f04ca633713078b692fdc1a1cc4f884ebdbf3ecae6881f11fb3b4fd3d27c5b8da67ba

diff --git a/sci-biology/samtools/samtools-1.16.1.ebuild 
b/sci-biology/samtools/samtools-1.16.1.ebuild
new file mode 100644
index ..8047657df992
--- /dev/null
+++ b/sci-biology/samtools/samtools-1.16.1.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs
+
+DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment 
formats"
+HOMEPAGE="http://www.htslib.org/;
+SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2;
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+
+RDEPEND="
+   dev-lang/perl
+   =sci-libs/htslib-$(ver_cut 1-2)*:=
+   sys-libs/ncurses:=[unicode(+)]
+   sys-libs/zlib"
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
+
+src_prepare() {
+   default
+
+   # remove bundled htslib
+   rm -r htslib-* || die
+}
+
+src_configure() {
+   econf \
+   --with-ncurses \
+   --with-htslib=system \
+   CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw || die)"
+}
+
+src_compile() {
+   emake AR="$(tc-getAR)"
+}
+
+src_install() {
+   default
+
+   dodoc -r examples
+   docompress -x /usr/share/doc/${PF}/examples
+}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

2022-06-19 Thread David Seifert

commit: d4b7f179a733bc6f4bc223a20f9f40825d920aa2
Author: David Seifert  gentoo  org>
AuthorDate: Sun Jun 19 08:08:45 2022 +
Commit: David Seifert  gentoo  org>
CommitDate: Sun Jun 19 08:08:45 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d4b7f179

sci-biology/samtools: drop 1.13, 1.15

Signed-off-by: David Seifert  gentoo.org>

 sci-biology/samtools/Manifest |  2 --
 sci-biology/samtools/samtools-1.13.ebuild | 47 ---
 sci-biology/samtools/samtools-1.15.ebuild | 47 ---
 3 files changed, 96 deletions(-)

diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index a605c469e6ea..0ff07e0d4f83 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,4 +1,2 @@
 DIST samtools-0.1.20.tar.gz 566387 BLAKE2B 
a62d74c408877754af50f5e5fea0e2289ec1e0c9f25013ed0d039bfe8ef61108600d917f8c9d356e98aca632795b4eb0f01ea1b54526a652577fb74a38a433c2
 SHA512 
15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5
-DIST samtools-1.13.tar.bz2 7984998 BLAKE2B 
e46161c43d4ea51c3ef1d9ed74c40c21b70aef80aa903a49b94b3d468f9211e9147281204eb61b9843c071f09ead08c924e3d624d4df76a1d02ba9ceb318399a
 SHA512 
647fbad2935dfc3e4f85da257a6ee59af40078024a3b77f117dada5f55846e381a096db3cf62a63c04ae95dfc9fadb1d515b8d618e6388bc93f0b2ac85eaf6ea
 DIST samtools-1.15.1.tar.bz2 7831692 BLAKE2B 
0fe94ff05075b219c77d0da8500c64bdffd53927950b5a67f8708c5c326ebc90a40c193b3bcf0baf3d09baed6fa596d9d024cb529340c6887de88614c9ff4bd6
 SHA512 
54a8a394b6b5231bd942236ec353027caaf48b4552a00b35573a1e71d680320d8140a73409bb76066c82e86fe62cf74f2f8f2f1a1e4aec96e4e8b9aff0d44a46
-DIST samtools-1.15.tar.bz2 7832423 BLAKE2B 
5bdfaec750faaa8d84eb601e75f513d726724d3f2f882d9e16edfe4802bd1ad8fee5f1208c93f450fff37125998cb50ff2247fce514d94e580d5d292555da930
 SHA512 
21ce4aff90514a393e685cbb6fa7833c88010b18846be0190d49e8da70995252c2e17b5108113d2313a752706618041c74680efc9ed5539b97ebc0589cb6c6e7

diff --git a/sci-biology/samtools/samtools-1.13.ebuild 
b/sci-biology/samtools/samtools-1.13.ebuild
deleted file mode 100644
index 3165c7b7381c..
--- a/sci-biology/samtools/samtools-1.13.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit 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"
-
-RDEPEND="
-   dev-lang/perl
-   =sci-libs/htslib-${PV}*:=
-   sys-libs/ncurses:=[unicode(+)]
-   sys-libs/zlib"
-DEPEND="${RDEPEND}"
-BDEPEND="virtual/pkgconfig"
-
-src_prepare() {
-   default
-
-   # remove bundled htslib
-   rm -r htslib-* || die
-}
-
-src_configure() {
-   econf \
-   --with-ncurses \
-   --with-htslib=system \
-   CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw || die)"
-}
-
-src_compile() {
-   emake AR="$(tc-getAR)"
-}
-
-src_install() {
-   default
-
-   dodoc -r examples
-   docompress -x /usr/share/doc/${PF}/examples
-}

diff --git a/sci-biology/samtools/samtools-1.15.ebuild 
b/sci-biology/samtools/samtools-1.15.ebuild
deleted file mode 100644
index 74aee5acaaa2..
--- a/sci-biology/samtools/samtools-1.15.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit 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"
-
-RDEPEND="
-   dev-lang/perl
-   =sci-libs/htslib-${PV}*:=
-   sys-libs/ncurses:=[unicode(+)]
-   sys-libs/zlib"
-DEPEND="${RDEPEND}"
-BDEPEND="virtual/pkgconfig"
-
-src_prepare() {
-   default
-
-   # remove bundled htslib
-   rm -r htslib-* || die
-}
-
-src_configure() {
-   econf \
-   --with-ncurses \
-   --with-htslib=system \
-   CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw || die)"
-}
-
-src_compile() {
-   emake AR="$(tc-getAR)"
-}
-
-src_install() {
-   default
-
-   dodoc -r examples
-   docompress -x /usr/share/doc/${PF}/examples
-}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

2022-06-10 Thread David Seifert

commit: b5ba01c508dd2360e176e57e0354694dcde2616b
Author: David Seifert  gentoo  org>
AuthorDate: Fri Jun 10 12:41:46 2022 +
Commit: David Seifert  gentoo  org>
CommitDate: Fri Jun 10 12:41:46 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b5ba01c5

sci-biology/samtools: add 1.15.1

Signed-off-by: David Seifert  gentoo.org>

 sci-biology/samtools/Manifest   |  1 +
 sci-biology/samtools/samtools-1.15.1.ebuild | 47 +
 2 files changed, 48 insertions(+)

diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index d83cc15952b0..a605c469e6ea 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,3 +1,4 @@
 DIST samtools-0.1.20.tar.gz 566387 BLAKE2B 
a62d74c408877754af50f5e5fea0e2289ec1e0c9f25013ed0d039bfe8ef61108600d917f8c9d356e98aca632795b4eb0f01ea1b54526a652577fb74a38a433c2
 SHA512 
15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5
 DIST samtools-1.13.tar.bz2 7984998 BLAKE2B 
e46161c43d4ea51c3ef1d9ed74c40c21b70aef80aa903a49b94b3d468f9211e9147281204eb61b9843c071f09ead08c924e3d624d4df76a1d02ba9ceb318399a
 SHA512 
647fbad2935dfc3e4f85da257a6ee59af40078024a3b77f117dada5f55846e381a096db3cf62a63c04ae95dfc9fadb1d515b8d618e6388bc93f0b2ac85eaf6ea
+DIST samtools-1.15.1.tar.bz2 7831692 BLAKE2B 
0fe94ff05075b219c77d0da8500c64bdffd53927950b5a67f8708c5c326ebc90a40c193b3bcf0baf3d09baed6fa596d9d024cb529340c6887de88614c9ff4bd6
 SHA512 
54a8a394b6b5231bd942236ec353027caaf48b4552a00b35573a1e71d680320d8140a73409bb76066c82e86fe62cf74f2f8f2f1a1e4aec96e4e8b9aff0d44a46
 DIST samtools-1.15.tar.bz2 7832423 BLAKE2B 
5bdfaec750faaa8d84eb601e75f513d726724d3f2f882d9e16edfe4802bd1ad8fee5f1208c93f450fff37125998cb50ff2247fce514d94e580d5d292555da930
 SHA512 
21ce4aff90514a393e685cbb6fa7833c88010b18846be0190d49e8da70995252c2e17b5108113d2313a752706618041c74680efc9ed5539b97ebc0589cb6c6e7

diff --git a/sci-biology/samtools/samtools-1.15.1.ebuild 
b/sci-biology/samtools/samtools-1.15.1.ebuild
new file mode 100644
index ..21d2b8a5077d
--- /dev/null
+++ b/sci-biology/samtools/samtools-1.15.1.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs
+
+DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment 
formats"
+HOMEPAGE="http://www.htslib.org/;
+SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2;
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+
+RDEPEND="
+   dev-lang/perl
+   =sci-libs/htslib-${PV}*:=
+   sys-libs/ncurses:=[unicode(+)]
+   sys-libs/zlib"
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
+
+src_prepare() {
+   default
+
+   # remove bundled htslib
+   rm -r htslib-* || die
+}
+
+src_configure() {
+   econf \
+   --with-ncurses \
+   --with-htslib=system \
+   CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw || die)"
+}
+
+src_compile() {
+   emake AR="$(tc-getAR)"
+}
+
+src_install() {
+   default
+
+   dodoc -r examples
+   docompress -x /usr/share/doc/${PF}/examples
+}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

2022-03-19 Thread David Seifert

commit: 57d20d58a279d301722f1940125c7e216249dfd5
Author: David Seifert  gentoo  org>
AuthorDate: Sat Mar 19 11:38:04 2022 +
Commit: David Seifert  gentoo  org>
CommitDate: Sat Mar 19 11:38:04 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=57d20d58

sci-biology/samtools: add 1.15

Signed-off-by: David Seifert  gentoo.org>

 sci-biology/samtools/Manifest |  1 +
 sci-biology/samtools/samtools-1.15.ebuild | 47 +++
 2 files changed, 48 insertions(+)

diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index 6cee5d727e16..d83cc15952b0 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,2 +1,3 @@
 DIST samtools-0.1.20.tar.gz 566387 BLAKE2B 
a62d74c408877754af50f5e5fea0e2289ec1e0c9f25013ed0d039bfe8ef61108600d917f8c9d356e98aca632795b4eb0f01ea1b54526a652577fb74a38a433c2
 SHA512 
15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5
 DIST samtools-1.13.tar.bz2 7984998 BLAKE2B 
e46161c43d4ea51c3ef1d9ed74c40c21b70aef80aa903a49b94b3d468f9211e9147281204eb61b9843c071f09ead08c924e3d624d4df76a1d02ba9ceb318399a
 SHA512 
647fbad2935dfc3e4f85da257a6ee59af40078024a3b77f117dada5f55846e381a096db3cf62a63c04ae95dfc9fadb1d515b8d618e6388bc93f0b2ac85eaf6ea
+DIST samtools-1.15.tar.bz2 7832423 BLAKE2B 
5bdfaec750faaa8d84eb601e75f513d726724d3f2f882d9e16edfe4802bd1ad8fee5f1208c93f450fff37125998cb50ff2247fce514d94e580d5d292555da930
 SHA512 
21ce4aff90514a393e685cbb6fa7833c88010b18846be0190d49e8da70995252c2e17b5108113d2313a752706618041c74680efc9ed5539b97ebc0589cb6c6e7

diff --git a/sci-biology/samtools/samtools-1.15.ebuild 
b/sci-biology/samtools/samtools-1.15.ebuild
new file mode 100644
index ..74aee5acaaa2
--- /dev/null
+++ b/sci-biology/samtools/samtools-1.15.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit 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"
+
+RDEPEND="
+   dev-lang/perl
+   =sci-libs/htslib-${PV}*:=
+   sys-libs/ncurses:=[unicode(+)]
+   sys-libs/zlib"
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
+
+src_prepare() {
+   default
+
+   # remove bundled htslib
+   rm -r htslib-* || die
+}
+
+src_configure() {
+   econf \
+   --with-ncurses \
+   --with-htslib=system \
+   CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw || die)"
+}
+
+src_compile() {
+   emake AR="$(tc-getAR)"
+}
+
+src_install() {
+   default
+
+   dodoc -r examples
+   docompress -x /usr/share/doc/${PF}/examples
+}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

2021-10-11 Thread David Seifert

commit: 839c7ac1d40d861275bfb91957ce439f9502987b
Author: David Seifert  gentoo  org>
AuthorDate: Mon Oct 11 14:55:10 2021 +
Commit: David Seifert  gentoo  org>
CommitDate: Mon Oct 11 14:55:10 2021 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=839c7ac1

sci-biology/samtools: drop 1.10-r1

Signed-off-by: David Seifert  gentoo.org>

 sci-biology/samtools/Manifest|  1 -
 sci-biology/samtools/samtools-1.10-r1.ebuild | 56 
 2 files changed, 57 deletions(-)

diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index 2128bb6db9c..6cee5d727e1 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,3 +1,2 @@
 DIST samtools-0.1.20.tar.gz 566387 BLAKE2B 
a62d74c408877754af50f5e5fea0e2289ec1e0c9f25013ed0d039bfe8ef61108600d917f8c9d356e98aca632795b4eb0f01ea1b54526a652577fb74a38a433c2
 SHA512 
15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5
-DIST samtools-1.10.tar.bz2 4721173 BLAKE2B 
103c71ec5740eac151a4fc40d67286ee00123c7befd5f654cf5c89812bda44f82b38ab662a4a3216ac84434cabab49500b903612137f97f89a7ea38063e8fc08
 SHA512 
828ec2638592b440e06b81eafc57634416ab54dac6caaecb06f22a90e9bf99da1fd8bb54509cb98591899c4e097ac9038ee5d57ea7bfe1a18967cde4018d840a
 DIST samtools-1.13.tar.bz2 7984998 BLAKE2B 
e46161c43d4ea51c3ef1d9ed74c40c21b70aef80aa903a49b94b3d468f9211e9147281204eb61b9843c071f09ead08c924e3d624d4df76a1d02ba9ceb318399a
 SHA512 
647fbad2935dfc3e4f85da257a6ee59af40078024a3b77f117dada5f55846e381a096db3cf62a63c04ae95dfc9fadb1d515b8d618e6388bc93f0b2ac85eaf6ea

diff --git a/sci-biology/samtools/samtools-1.10-r1.ebuild 
b/sci-biology/samtools/samtools-1.10-r1.ebuild
deleted file mode 100644
index 94089561690..000
--- a/sci-biology/samtools/samtools-1.10-r1.ebuild
+++ /dev/null
@@ -1,56 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit autotools toolchain-funcs
-
-DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment 
formats"
-HOMEPAGE="http://www.htslib.org/;
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
-
-RDEPEND="
-   dev-lang/perl
-   =sci-libs/htslib-${PV}*
-   sys-libs/ncurses:=[unicode(+)]
-   sys-libs/zlib:="
-DEPEND="${RDEPEND}"
-BDEPEND="virtual/pkgconfig"
-
-src_prepare() {
-   default
-
-   # remove bundled htslib
-   rm -r htslib-* || die
-
-   eautoreconf
-}
-
-src_configure() {
-   econf \
-   --with-ncurses \
-   --with-htslib=system \
-   CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw)"
-}
-
-src_compile() {
-   emake AR="$(tc-getAR)"
-}
-
-src_test() {
-   # the tview test diffs expect 80-columns output
-   unset COLUMNS
-
-   default
-}
-
-src_install() {
-   default
-
-   dodoc -r examples
-   docompress -x /usr/share/doc/${PF}/examples
-}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

2021-10-03 Thread David Seifert

commit: e728877de767757bdff23a79092cf0fa15cf5d8a
Author: David Seifert  gentoo  org>
AuthorDate: Sun Oct  3 17:41:37 2021 +
Commit: David Seifert  gentoo  org>
CommitDate: Sun Oct  3 17:41:37 2021 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e728877d

sci-biology/samtools: add 1.13

Signed-off-by: David Seifert  gentoo.org>

 sci-biology/samtools/Manifest |  1 +
 sci-biology/samtools/samtools-1.13.ebuild | 47 +++
 2 files changed, 48 insertions(+)

diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index 622e57502c3..2128bb6db9c 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,2 +1,3 @@
 DIST samtools-0.1.20.tar.gz 566387 BLAKE2B 
a62d74c408877754af50f5e5fea0e2289ec1e0c9f25013ed0d039bfe8ef61108600d917f8c9d356e98aca632795b4eb0f01ea1b54526a652577fb74a38a433c2
 SHA512 
15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5
 DIST samtools-1.10.tar.bz2 4721173 BLAKE2B 
103c71ec5740eac151a4fc40d67286ee00123c7befd5f654cf5c89812bda44f82b38ab662a4a3216ac84434cabab49500b903612137f97f89a7ea38063e8fc08
 SHA512 
828ec2638592b440e06b81eafc57634416ab54dac6caaecb06f22a90e9bf99da1fd8bb54509cb98591899c4e097ac9038ee5d57ea7bfe1a18967cde4018d840a
+DIST samtools-1.13.tar.bz2 7984998 BLAKE2B 
e46161c43d4ea51c3ef1d9ed74c40c21b70aef80aa903a49b94b3d468f9211e9147281204eb61b9843c071f09ead08c924e3d624d4df76a1d02ba9ceb318399a
 SHA512 
647fbad2935dfc3e4f85da257a6ee59af40078024a3b77f117dada5f55846e381a096db3cf62a63c04ae95dfc9fadb1d515b8d618e6388bc93f0b2ac85eaf6ea

diff --git a/sci-biology/samtools/samtools-1.13.ebuild 
b/sci-biology/samtools/samtools-1.13.ebuild
new file mode 100644
index 000..3165c7b7381
--- /dev/null
+++ b/sci-biology/samtools/samtools-1.13.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit 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"
+
+RDEPEND="
+   dev-lang/perl
+   =sci-libs/htslib-${PV}*:=
+   sys-libs/ncurses:=[unicode(+)]
+   sys-libs/zlib"
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
+
+src_prepare() {
+   default
+
+   # remove bundled htslib
+   rm -r htslib-* || die
+}
+
+src_configure() {
+   econf \
+   --with-ncurses \
+   --with-htslib=system \
+   CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw || die)"
+}
+
+src_compile() {
+   emake AR="$(tc-getAR)"
+}
+
+src_install() {
+   default
+
+   dodoc -r examples
+   docompress -x /usr/share/doc/${PF}/examples
+}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

2021-07-17 Thread David Seifert

commit: fe79f96506444e3acc34d0a971c9335026e28c7b
Author: David Seifert  gentoo  org>
AuthorDate: Sat Jul 17 21:30:32 2021 +
Commit: David Seifert  gentoo  org>
CommitDate: Sat Jul 17 21:30:32 2021 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=fe79f965

sci-biology/samtools: Add sys-libs/ncurses[unicode(+)]

Signed-off-by: David Seifert  gentoo.org>

 .../samtools/{samtools-1.10.ebuild => samtools-1.10-r1.ebuild}| 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/samtools/samtools-1.10.ebuild 
b/sci-biology/samtools/samtools-1.10-r1.ebuild
similarity index 93%
rename from sci-biology/samtools/samtools-1.10.ebuild
rename to sci-biology/samtools/samtools-1.10-r1.ebuild
index 0ef5e6c19e8..94089561690 100644
--- a/sci-biology/samtools/samtools-1.10.ebuild
+++ b/sci-biology/samtools/samtools-1.10-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -16,7 +16,7 @@ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
 RDEPEND="
dev-lang/perl
=sci-libs/htslib-${PV}*
-   sys-libs/ncurses:0=[unicode]
+   sys-libs/ncurses:=[unicode(+)]
sys-libs/zlib:="
 DEPEND="${RDEPEND}"
 BDEPEND="virtual/pkgconfig"

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/, sci-biology/samtools/files/

2020-08-03 Thread David Seifert

commit: b6948f3ed9612bc6f11b4ccab40ac4d80f73e397
Author: David Seifert  gentoo  org>
AuthorDate: Mon Aug  3 21:11:18 2020 +
Commit: David Seifert  gentoo  org>
CommitDate: Mon Aug  3 21:11:18 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b6948f3e

sci-biology/samtools: Remove old

Closes: https://bugs.gentoo.org/728018
Package-Manager: Portage-3.0.1, Repoman-2.3.23
Signed-off-by: David Seifert  gentoo.org>

 sci-biology/samtools/Manifest  |   2 -
 .../samtools/files/samtools-1.5-buildsystem.patch  | 413 -
 sci-biology/samtools/samtools-1.5.ebuild   |  61 ---
 sci-biology/samtools/samtools-1.9-r1.ebuild|  49 ---
 4 files changed, 525 deletions(-)

diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index b06f63a40e7..622e57502c3 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,4 +1,2 @@
 DIST samtools-0.1.20.tar.gz 566387 BLAKE2B 
a62d74c408877754af50f5e5fea0e2289ec1e0c9f25013ed0d039bfe8ef61108600d917f8c9d356e98aca632795b4eb0f01ea1b54526a652577fb74a38a433c2
 SHA512 
15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5
 DIST samtools-1.10.tar.bz2 4721173 BLAKE2B 
103c71ec5740eac151a4fc40d67286ee00123c7befd5f654cf5c89812bda44f82b38ab662a4a3216ac84434cabab49500b903612137f97f89a7ea38063e8fc08
 SHA512 
828ec2638592b440e06b81eafc57634416ab54dac6caaecb06f22a90e9bf99da1fd8bb54509cb98591899c4e097ac9038ee5d57ea7bfe1a18967cde4018d840a
-DIST samtools-1.5.tar.bz2 4190142 BLAKE2B 
1d3478f9adf76925a3721e145795ce4a4caf580244f5ba5bc1ddd14d1b13c723c6fddc24cdadf0a23ca5dcd7007a9985f54e7532cb15d5d9433b1164f5a22023
 SHA512 
ff3e39ba867ecbd88f3363b038508c1557e349ea4223483f8f4ecb17ff8864fb53cd193bc2059a147e30f07395bbf53c8518d0f70219e454375c8bffe56e3059
-DIST samtools-1.9.tar.bz2 4440405 BLAKE2B 
409265fed9ff3fcd09096c968224499750da69324eeded754e367430c0f53f9246ccc9a31e166f13ea7bc767fefab499bcfda4d008d5ac82971984c67b533aff
 SHA512 
6c8207754615ae8dad84b278f93e7d57eb40b818efb80f6aff6aba22fde5772247724e86596e765791e3175ffbb683393dd3ddfe7681c73eef4eb4f2342bf68f

diff --git a/sci-biology/samtools/files/samtools-1.5-buildsystem.patch 
b/sci-biology/samtools/files/samtools-1.5-buildsystem.patch
deleted file mode 100644
index c466e66a9d1..000
--- a/sci-biology/samtools/files/samtools-1.5-buildsystem.patch
+++ /dev/null
@@ -1,413 +0,0 @@
 a/config.mk.in
-+++ b/config.mk.in
-@@ -28,27 +28,26 @@
- # in the Makefile to reflect your configuration choices.  If you don't run
- # configure, the main Makefile contains suitable conservative defaults.
- 
--prefix   = @prefix@
--exec_prefix  = @exec_prefix@
--bindir   = @bindir@
--datarootdir  = @datarootdir@
--mandir   = @mandir@
-+prefix  = @prefix@
-+exec_prefix = @exec_prefix@
-+bindir  = @bindir@
-+libdir  = @libdir@
-+datarootdir = @datarootdir@
-+mandir  = @mandir@
-+man1dir = $(mandir)/man1
- 
- CC   = @CC@
-+AR   = @AR@
- CPPFLAGS = @CPPFLAGS@
- CFLAGS   = @CFLAGS@
- LDFLAGS  = @LDFLAGS@
- LIBS = @LIBS@
- 
--@Hsource@HTSDIR = @HTSDIR@
--@Hsource@include $(HTSDIR)/htslib.mk
--@Hsource@include $(HTSDIR)/htslib_static.mk
--@Hsource@HTSLIB = $(HTSDIR)/libhts.a
--@Hsource@HTSLIB_LIB = $(HTSLIB) $(HTSLIB_static_LIBS)
--@Hsource@HTSLIB_LDFLAGS = $(HTSLIB_static_LDFLAGS)
--@Hsource@BGZIP = $(HTSDIR)/bgzip
--HTSLIB_CPPFLAGS = @HTSLIB_CPPFLAGS@
--@Hinstall@HTSLIB_LDFLAGS = @HTSLIB_LDFLAGS@
--@Hinstall@HTSLIB_LIB = -lhts
-+HTSLIB_CFLAGS = @HTSLIB_CFLAGS@
-+HTSLIB_LIBS = @HTSLIB_LIBS@
- 
--CURSES_LIB = @CURSES_LIB@
-+NCURSES_CFLAGS = @NCURSES_CFLAGS@
-+NCURSES_LIBS = @NCURSES_LIBS@
-+
-+ZLIB_CFLAGS = @ZLIB_CFLAGS@
-+ZLIB_LIBS = @ZLIB_LIBS@
 a/configure.ac
-+++ b/configure.ac
-@@ -29,9 +29,6 @@
- AC_CONFIG_SRCDIR([bamtk.c])
- AC_CONFIG_HEADERS([config.h])
- 
--m4_include([m4/ax_with_curses.m4])
--m4_include([m4/ax_with_htslib.m4])
--
- dnl Copyright notice to be copied into the generated configure script
- AC_COPYRIGHT([Portions copyright (C) 2015 Genome Research Ltd.
- 
-@@ -39,73 +36,27 @@
- redistribute it.  There is NO WARRANTY, to the extent permitted by law.])
- 
- AC_PROG_CC
-+AM_PROG_AR
- 
- AC_SYS_LARGEFILE
- 
--AX_WITH_HTSLIB
--if test "$ax_cv_htslib" != yes; then
--  AC_MSG_ERROR([HTSlib development files not found
--
--Samtools uses HTSlib to parse bioinformatics file formats etc.  Building it
--requires an unpacked HTSlib source tree (which will be built in conjunction
--with samtools) or a previously-installed HTSlib.  In either case you may
--need to configure --with-htslib=DIR to locate the appropriate HTSlib.
--
--FAILED.  You must supply an HTSlib in order to build samtools successfully.])
--fi
--
--if test "$ax_cv_htslib_which" = source; then
--  Hsource=
--  Hinstall='#'
--else
--  Hsource='#'
--  Hinstall=
--fi
--AC_SUBST([Hsource])
--AC_SUBST([Hinstall])
-+dnl htslib

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

2020-08-03 Thread David Seifert

commit: b4b33dfa42e5b47cf0bfbf07275fd5b8c576a018
Author: David Seifert  gentoo  org>
AuthorDate: Mon Aug  3 18:17:16 2020 +
Commit: David Seifert  gentoo  org>
CommitDate: Mon Aug  3 18:17:16 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b4b33dfa

sci-biology/samtools: [QA] Fix UnnecessarySlashStrip

Package-Manager: Portage-3.0.1, Repoman-2.3.23
Signed-off-by: David Seifert  gentoo.org>

 sci-biology/samtools/samtools-0.1.20-r4.ebuild | 10 +-
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/sci-biology/samtools/samtools-0.1.20-r4.ebuild 
b/sci-biology/samtools/samtools-0.1.20-r4.ebuild
index 2c76f0580f8..d598a329272 100644
--- a/sci-biology/samtools/samtools-0.1.20-r4.ebuild
+++ b/sci-biology/samtools/samtools-0.1.20-r4.ebuild
@@ -36,16 +36,16 @@ src_install() {
# install executables and hide them away from sight
dobin samtools bcftools/{bcftools,vcfutils.pl} 
misc/{*.py,*.pl,wgsim,ace2sam} \

misc/{md5sum-lite,maq2sam-short,bamcheck,maq2sam-long,md5fa,plot-bamcheck}
-   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}} || die
+   mkdir "${ED}"/usr/bin || die
+   mv "${ED}"/usr/{${PN}-${SLOT},bin/} || die
 
# remove py2 script, has been removed upstream anyways
# https://github.com/samtools/samtools/issues/1125
-   rm "${ED%/}"/usr/bin/${PN}-${SLOT}/varfilter.py || die
+   rm "${ED}"/usr/bin/${PN}-${SLOT}/varfilter.py || die
 
# fix perl shebangs
-   pushd "${ED%/}"/usr/bin/${PN}-${SLOT} >/dev/null || die
+   pushd "${ED}"/usr/bin/${PN}-${SLOT} >/dev/null || die
local i
for i in plot-bamcheck *.pl; do
sed -e '1s:.*:#!/usr/bin/env perl:' -i "${i}" || die

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

2020-08-03 Thread David Seifert

commit: e4e256abcf64dccd8c72ad565bd988ef49e740be
Author: David Seifert  gentoo  org>
AuthorDate: Mon Aug  3 17:39:53 2020 +
Commit: David Seifert  gentoo  org>
CommitDate: Mon Aug  3 17:39:53 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e4e256ab

sci-biology/samtools: Remove ancient py2 varfilter.py script

Closes: https://bugs.gentoo.org/735444
Package-Manager: Portage-3.0.1, Repoman-2.3.23
Signed-off-by: David Seifert  gentoo.org>

 ...-0.1.20-r3.ebuild => samtools-0.1.20-r4.ebuild} | 36 --
 1 file changed, 13 insertions(+), 23 deletions(-)

diff --git a/sci-biology/samtools/samtools-0.1.20-r3.ebuild 
b/sci-biology/samtools/samtools-0.1.20-r4.ebuild
similarity index 66%
rename from sci-biology/samtools/samtools-0.1.20-r3.ebuild
rename to sci-biology/samtools/samtools-0.1.20-r4.ebuild
index 5cfcfd7f6a7..2c76f0580f8 100644
--- a/sci-biology/samtools/samtools-0.1.20-r3.ebuild
+++ b/sci-biology/samtools/samtools-0.1.20-r4.ebuild
@@ -1,11 +1,9 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-PYTHON_COMPAT=( python2_7 )
-
-inherit python-single-r1 toolchain-funcs
+inherit toolchain-funcs
 
 DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment 
formats"
 HOMEPAGE="http://samtools.sourceforge.net/;
@@ -14,23 +12,17 @@ 
SRC_URI="https://github.com/samtools/samtools/archive/${PV}.tar.gz -> ${P}.tar.g
 LICENSE="MIT"
 SLOT="0.1-legacy"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
-IUSE="examples"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
-RDEPEND="${PYTHON_DEPS}
+RDEPEND="
sys-libs/ncurses:0=
dev-lang/perl"
-DEPEND="${RDEPEND}
-   virtual/pkgconfig"
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
 
-PATCHES=(
-   "${FILESDIR}/${P}-buildsystem.patch"
-)
+PATCHES=( "${FILESDIR}"/${P}-buildsystem.patch )
 
 src_prepare() {
default
-   # required, otherwise python_fix_shebang errors out
-   sed -i 's~/software/bin/python~/usr/bin/env python~' misc/varfilter.py 
|| die
tc-export CC AR
 }
 
@@ -48,9 +40,9 @@ src_install() {
mkdir "${ED%/}"/usr/bin || die
mv "${ED%/}"/usr/{${PN}-${SLOT},bin/} || die
 
-   # ... do the same with the python script, but also fix the shebang
-   mv "${ED%/}"/usr/bin/${PN}-${SLOT}/varfilter{,-${SLOT}}.py || die
-   python_fix_shebang "${ED%/}"/usr/bin/${PN}-${SLOT}/varfilter-${SLOT}.py
+   # remove py2 script, has been removed upstream anyways
+   # https://github.com/samtools/samtools/issues/1125
+   rm "${ED%/}"/usr/bin/${PN}-${SLOT}/varfilter.py || die
 
# fix perl shebangs
pushd "${ED%/}"/usr/bin/${PN}-${SLOT} >/dev/null || die
@@ -70,14 +62,12 @@ src_install() {
doman ${PN}-${SLOT}.1
einstalldocs
 
-   if use examples; then
-   dodoc -r examples
-   docompress -x /usr/share/doc/${PF}/examples
-   fi
+   dodoc -r examples
+   docompress -x /usr/share/doc/${PF}/examples
 }
 
 pkg_postinst() {
elog "This version of samtools should *not* be your first choice for 
working"
elog "with NGS data. It is installed solely for programs requiring it."
-   elog "It is recommended that you use >=sci-biology/samtools-1.2."
+   elog "It is recommended that you use >=sci-biology/samtools-1.10."
 }

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

2020-08-03 Thread David Seifert

commit: 90c55f4b6812ba59ca61467380f0a153f3ff2edf
Author: David Seifert  gentoo  org>
AuthorDate: Mon Aug  3 16:54:23 2020 +
Commit: David Seifert  gentoo  org>
CommitDate: Mon Aug  3 16:54:23 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=90c55f4b

sci-biology/samtools: Bump to version 1.10

Bug: https://bugs.gentoo.org/728018
Package-Manager: Portage-3.0.1, Repoman-2.3.23
Signed-off-by: David Seifert  gentoo.org>

 sci-biology/samtools/Manifest |  1 +
 sci-biology/samtools/samtools-1.10.ebuild | 56 +++
 2 files changed, 57 insertions(+)

diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index 7ce21379a95..b06f63a40e7 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,3 +1,4 @@
 DIST samtools-0.1.20.tar.gz 566387 BLAKE2B 
a62d74c408877754af50f5e5fea0e2289ec1e0c9f25013ed0d039bfe8ef61108600d917f8c9d356e98aca632795b4eb0f01ea1b54526a652577fb74a38a433c2
 SHA512 
15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5
+DIST samtools-1.10.tar.bz2 4721173 BLAKE2B 
103c71ec5740eac151a4fc40d67286ee00123c7befd5f654cf5c89812bda44f82b38ab662a4a3216ac84434cabab49500b903612137f97f89a7ea38063e8fc08
 SHA512 
828ec2638592b440e06b81eafc57634416ab54dac6caaecb06f22a90e9bf99da1fd8bb54509cb98591899c4e097ac9038ee5d57ea7bfe1a18967cde4018d840a
 DIST samtools-1.5.tar.bz2 4190142 BLAKE2B 
1d3478f9adf76925a3721e145795ce4a4caf580244f5ba5bc1ddd14d1b13c723c6fddc24cdadf0a23ca5dcd7007a9985f54e7532cb15d5d9433b1164f5a22023
 SHA512 
ff3e39ba867ecbd88f3363b038508c1557e349ea4223483f8f4ecb17ff8864fb53cd193bc2059a147e30f07395bbf53c8518d0f70219e454375c8bffe56e3059
 DIST samtools-1.9.tar.bz2 4440405 BLAKE2B 
409265fed9ff3fcd09096c968224499750da69324eeded754e367430c0f53f9246ccc9a31e166f13ea7bc767fefab499bcfda4d008d5ac82971984c67b533aff
 SHA512 
6c8207754615ae8dad84b278f93e7d57eb40b818efb80f6aff6aba22fde5772247724e86596e765791e3175ffbb683393dd3ddfe7681c73eef4eb4f2342bf68f

diff --git a/sci-biology/samtools/samtools-1.10.ebuild 
b/sci-biology/samtools/samtools-1.10.ebuild
new file mode 100644
index 000..0ef5e6c19e8
--- /dev/null
+++ b/sci-biology/samtools/samtools-1.10.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit autotools toolchain-funcs
+
+DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment 
formats"
+HOMEPAGE="http://www.htslib.org/;
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+
+RDEPEND="
+   dev-lang/perl
+   =sci-libs/htslib-${PV}*
+   sys-libs/ncurses:0=[unicode]
+   sys-libs/zlib:="
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
+
+src_prepare() {
+   default
+
+   # remove bundled htslib
+   rm -r htslib-* || die
+
+   eautoreconf
+}
+
+src_configure() {
+   econf \
+   --with-ncurses \
+   --with-htslib=system \
+   CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw)"
+}
+
+src_compile() {
+   emake AR="$(tc-getAR)"
+}
+
+src_test() {
+   # the tview test diffs expect 80-columns output
+   unset COLUMNS
+
+   default
+}
+
+src_install() {
+   default
+
+   dodoc -r examples
+   docompress -x /usr/share/doc/${PF}/examples
+}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

2020-03-27 Thread David Seifert

commit: d7ff0662f30a752f5b948fda9193a27bfe09099d
Author: David Seifert  gentoo  org>
AuthorDate: Fri Mar 27 10:35:24 2020 +
Commit: David Seifert  gentoo  org>
CommitDate: Fri Mar 27 10:35:24 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d7ff0662

sci-biology/samtools: Remove python dependency

Closes: https://bugs.gentoo.org/710252
Package-Manager: Portage-2.3.96, Repoman-2.3.22
Signed-off-by: David Seifert  gentoo.org>

 .../{samtools-1.9.ebuild => samtools-1.9-r1.ebuild}   | 19 ---
 1 file changed, 8 insertions(+), 11 deletions(-)

diff --git a/sci-biology/samtools/samtools-1.9.ebuild 
b/sci-biology/samtools/samtools-1.9-r1.ebuild
similarity index 72%
rename from sci-biology/samtools/samtools-1.9.ebuild
rename to sci-biology/samtools/samtools-1.9-r1.ebuild
index bdcd115aafe..0d0f993895f 100644
--- a/sci-biology/samtools/samtools-1.9.ebuild
+++ b/sci-biology/samtools/samtools-1.9-r1.ebuild
@@ -1,11 +1,9 @@
-# Copyright 1999-2018 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
 
-PYTHON_COMPAT=( python2_7 )
-
-inherit autotools python-single-r1 toolchain-funcs
+inherit autotools toolchain-funcs
 
 DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment 
formats"
 HOMEPAGE="http://www.htslib.org/;
@@ -15,22 +13,18 @@ LICENSE="MIT"
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
 IUSE="examples"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
 RDEPEND="
dev-lang/perl
=sci-libs/htslib-${PV}*
sys-libs/ncurses:0=
-   sys-libs/zlib:=
-   ${PYTHON_DEPS}"
-DEPEND="${RDEPEND}
-   virtual/pkgconfig"
+   sys-libs/zlib:="
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
 
 src_prepare() {
default
 
-   python_fix_shebang misc/varfilter.py
-
# remove bundled htslib
rm -r htslib-* || die
 
@@ -45,6 +39,9 @@ src_test() {
 src_install() {
default
 
+   # varfilter.py has been retired upstream for being py2 only
+   rm "${ED}"/usr/bin/varfilter.py || die
+
if use examples; then
dodoc -r examples
docompress -x /usr/share/doc/${PF}/examples

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

2018-10-28 Thread David Seifert

commit: 18d496c1b4022e892aae9fcf3350b302b34357ed
Author: David Seifert  gentoo  org>
AuthorDate: Sun Oct 28 20:24:37 2018 +
Commit: David Seifert  gentoo  org>
CommitDate: Sun Oct 28 20:24:37 2018 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=18d496c1

sci-biology/samtools: Version bump to 1.9

Bug: https://bugs.gentoo.org/647714
Signed-off-by: David Seifert  gentoo.org>
Package-Manager: Portage-2.3.50, Repoman-2.3.11

 sci-biology/samtools/Manifest|  1 +
 sci-biology/samtools/samtools-1.9.ebuild | 52 
 2 files changed, 53 insertions(+)

diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index 8269a052050..7ce21379a95 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,2 +1,3 @@
 DIST samtools-0.1.20.tar.gz 566387 BLAKE2B 
a62d74c408877754af50f5e5fea0e2289ec1e0c9f25013ed0d039bfe8ef61108600d917f8c9d356e98aca632795b4eb0f01ea1b54526a652577fb74a38a433c2
 SHA512 
15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5
 DIST samtools-1.5.tar.bz2 4190142 BLAKE2B 
1d3478f9adf76925a3721e145795ce4a4caf580244f5ba5bc1ddd14d1b13c723c6fddc24cdadf0a23ca5dcd7007a9985f54e7532cb15d5d9433b1164f5a22023
 SHA512 
ff3e39ba867ecbd88f3363b038508c1557e349ea4223483f8f4ecb17ff8864fb53cd193bc2059a147e30f07395bbf53c8518d0f70219e454375c8bffe56e3059
+DIST samtools-1.9.tar.bz2 4440405 BLAKE2B 
409265fed9ff3fcd09096c968224499750da69324eeded754e367430c0f53f9246ccc9a31e166f13ea7bc767fefab499bcfda4d008d5ac82971984c67b533aff
 SHA512 
6c8207754615ae8dad84b278f93e7d57eb40b818efb80f6aff6aba22fde5772247724e86596e765791e3175ffbb683393dd3ddfe7681c73eef4eb4f2342bf68f

diff --git a/sci-biology/samtools/samtools-1.9.ebuild 
b/sci-biology/samtools/samtools-1.9.ebuild
new file mode 100644
index 000..bdcd115aafe
--- /dev/null
+++ b/sci-biology/samtools/samtools-1.9.ebuild
@@ -0,0 +1,52 @@
+# Copyright 1999-2018 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit autotools python-single-r1 toolchain-funcs
+
+DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment 
formats"
+HOMEPAGE="http://www.htslib.org/;
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+IUSE="examples"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="
+   dev-lang/perl
+   =sci-libs/htslib-${PV}*
+   sys-libs/ncurses:0=
+   sys-libs/zlib:=
+   ${PYTHON_DEPS}"
+DEPEND="${RDEPEND}
+   virtual/pkgconfig"
+
+src_prepare() {
+   default
+
+   python_fix_shebang misc/varfilter.py
+
+   # remove bundled htslib
+   rm -r htslib-* || die
+
+   eautoreconf
+}
+
+src_test() {
+   local -x LD_LIBRARY_PATH="${S}"
+   default
+}
+
+src_install() {
+   default
+
+   if use examples; then
+   dodoc -r examples
+   docompress -x /usr/share/doc/${PF}/examples
+   fi
+}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/files/

2017-09-02 Thread David Seifert

commit: 06dc3754671e25127fa53a7d8b6c17ab3d254e40
Author: David Seifert  gentoo  org>
AuthorDate: Sat Sep  2 15:01:47 2017 +
Commit: David Seifert  gentoo  org>
CommitDate: Sat Sep  2 15:02:09 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=06dc3754

sci-biology/samtools: Add missing -I. to CPPFLAGS

Bug: https://bugs.gentoo.org/show_bug.cgi?id=629666
Package-Manager: Portage-2.3.8, Repoman-2.3.3

 sci-biology/samtools/files/samtools-1.5-buildsystem.patch | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/samtools/files/samtools-1.5-buildsystem.patch 
b/sci-biology/samtools/files/samtools-1.5-buildsystem.patch
index 248089e09fc..c466e66a9d1 100644
--- a/sci-biology/samtools/files/samtools-1.5-buildsystem.patch
+++ b/sci-biology/samtools/files/samtools-1.5-buildsystem.patch
@@ -196,7 +196,7 @@
$(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ $<
  
 +$(LOBJS):
-+  $(CC) $(CFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $<
++  $(CC) $(CFLAGS) $(ALL_CPPFLAGS) -fPIC -c -o $@ $<
 +
  
  LIBST_OBJS = sam_opts.o sam_utils.o

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/files/, sci-biology/samtools/

2017-09-02 Thread David Seifert

commit: 70386b8c804f2bf2fb7aca4be74d511d765ad1e4
Author: David Seifert  gentoo  org>
AuthorDate: Sat Sep  2 11:07:41 2017 +
Commit: David Seifert  gentoo  org>
CommitDate: Sat Sep  2 12:37:02 2017 +
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..000

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/, sci-biology/samtools/files/

2017-09-02 Thread David Seifert

commit: d401db74e7e270ab7e38d955308cd8d2dbc20a48
Author: David Seifert  gentoo  org>
AuthorDate: Sat Sep  2 09:30:07 2017 +
Commit: David Seifert  gentoo  org>
CommitDate: Sat Sep  2 09:32:42 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d401db74

sci-biology/samtools: Version bump to 1.5

Package-Manager: Portage-2.3.8, Repoman-2.3.3

 sci-biology/samtools/Manifest  |   1 +
 .../samtools/files/samtools-1.5-buildsystem.patch  | 413 +
 sci-biology/samtools/samtools-1.5.ebuild   |  61 +++
 3 files changed, 475 insertions(+)

diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index d25774fee86..791e2050ee7 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -5,3 +5,4 @@ DIST samtools-1.0.tar.bz2 4459669 SHA256 
7340b843663c3f54a902a06f2f73c68198f3a62
 DIST samtools-1.1.tar.bz2 4495373 SHA256 
c24d26c303153d72b5bf3cc11f72c6c375a4ca1140cc485648c8c5473414b7f8 SHA512 
a5552a6c8c4b0808b725b39ddb2fafa36c4f6623bfc7f84faadae7690223e4eec8d722af09c77145796ad9b3f01e04115dd0207207ccfafbb52ffc22d5fc09f0
 WHIRLPOOL 
ed3131b2a8d8b4dab40b53d35a9b00b657670a949dc1597c91fbcd00392c1c1715a85a1d1e49bf0c73ae082738ccfb13d2c6809dbbeba17ff3028f6023ebc449
 DIST samtools-1.2.tar.bz2 4547126 SHA256 
420e7a4a107fe37619b9d300b6379452eb8eb04a4a9b65c3ec69de82ccc26daa SHA512 
4849c3274e732267516b63799f5430c5415d575d46eddf6b704dac51053281094b03b90dd9f5367bcd14c22fb0fb1bd6a412f7d4225f7be5f5385437c5d2101d
 WHIRLPOOL 
273185764a807365a20c381769f987ef02d14ae8e20a3a7fd5af4344769c5fab68d7155523e8c0c8c3cc86092898c2c8454cce8f1560d415bc2b41549cdf04f4
 DIST samtools-1.3.tar.bz2 3978333 SHA256 
beea4003c795a0a25224656815b4036f6864b8753053ed30c590bb052b70b60e SHA512 
72920d4f0f10aa7b54ef448e03e6e769e1e07abd07388a2307d0e52548fa2909c03ca2c7eec5c63cf5b67724b2356833accb0079ce1486bb2ac66a45963a24ea
 WHIRLPOOL 
3f798078100b4ed164f6c89d18cc8f62159437e2cfb2a228ac00f8d08313f7c39ef546214c0796c25a419c0a1065dc21d14b966fed769726b9b1975ec07e3b3e
+DIST samtools-1.5.tar.bz2 4190142 SHA256 
8542da26832ee08c1978713f5f6188ff750635b50d8ab126a0c7bb2ac1ae2df6 SHA512 
ff3e39ba867ecbd88f3363b038508c1557e349ea4223483f8f4ecb17ff8864fb53cd193bc2059a147e30f07395bbf53c8518d0f70219e454375c8bffe56e3059
 WHIRLPOOL 
1a88c9617857f1f6d146df179aef5b5c6bb83de8c9d127c405e5756842ced84c194a3f09f69a4757a8adf6ca623c9fdc972f4bf609649d3e991dda8f616e3582

diff --git a/sci-biology/samtools/files/samtools-1.5-buildsystem.patch 
b/sci-biology/samtools/files/samtools-1.5-buildsystem.patch
new file mode 100644
index 000..248089e09fc
--- /dev/null
+++ b/sci-biology/samtools/files/samtools-1.5-buildsystem.patch
@@ -0,0 +1,413 @@
+--- a/config.mk.in
 b/config.mk.in
+@@ -28,27 +28,26 @@
+ # in the Makefile to reflect your configuration choices.  If you don't run
+ # configure, the main Makefile contains suitable conservative defaults.
+ 
+-prefix   = @prefix@
+-exec_prefix  = @exec_prefix@
+-bindir   = @bindir@
+-datarootdir  = @datarootdir@
+-mandir   = @mandir@
++prefix  = @prefix@
++exec_prefix = @exec_prefix@
++bindir  = @bindir@
++libdir  = @libdir@
++datarootdir = @datarootdir@
++mandir  = @mandir@
++man1dir = $(mandir)/man1
+ 
+ CC   = @CC@
++AR   = @AR@
+ CPPFLAGS = @CPPFLAGS@
+ CFLAGS   = @CFLAGS@
+ LDFLAGS  = @LDFLAGS@
+ LIBS = @LIBS@
+ 
+-@Hsource@HTSDIR = @HTSDIR@
+-@Hsource@include $(HTSDIR)/htslib.mk
+-@Hsource@include $(HTSDIR)/htslib_static.mk
+-@Hsource@HTSLIB = $(HTSDIR)/libhts.a
+-@Hsource@HTSLIB_LIB = $(HTSLIB) $(HTSLIB_static_LIBS)
+-@Hsource@HTSLIB_LDFLAGS = $(HTSLIB_static_LDFLAGS)
+-@Hsource@BGZIP = $(HTSDIR)/bgzip
+-HTSLIB_CPPFLAGS = @HTSLIB_CPPFLAGS@
+-@Hinstall@HTSLIB_LDFLAGS = @HTSLIB_LDFLAGS@
+-@Hinstall@HTSLIB_LIB = -lhts
++HTSLIB_CFLAGS = @HTSLIB_CFLAGS@
++HTSLIB_LIBS = @HTSLIB_LIBS@
+ 
+-CURSES_LIB = @CURSES_LIB@
++NCURSES_CFLAGS = @NCURSES_CFLAGS@
++NCURSES_LIBS = @NCURSES_LIBS@
++
++ZLIB_CFLAGS = @ZLIB_CFLAGS@
++ZLIB_LIBS = @ZLIB_LIBS@
+--- a/configure.ac
 b/configure.ac
+@@ -29,9 +29,6 @@
+ AC_CONFIG_SRCDIR([bamtk.c])
+ AC_CONFIG_HEADERS([config.h])
+ 
+-m4_include([m4/ax_with_curses.m4])
+-m4_include([m4/ax_with_htslib.m4])
+-
+ dnl Copyright notice to be copied into the generated configure script
+ AC_COPYRIGHT([Portions copyright (C) 2015 Genome Research Ltd.
+ 
+@@ -39,73 +36,27 @@
+ redistribute it.  There is NO WARRANTY, to the extent permitted by law.])
+ 
+ AC_PROG_CC
++AM_PROG_AR
+ 
+ AC_SYS_LARGEFILE
+ 
+-AX_WITH_HTSLIB
+-if test "$ax_cv_htslib" != yes; then
+-  AC_MSG_ERROR([HTSlib development files not found
+-
+-Samtools uses HTSlib to parse bioinformatics file formats etc.  Building it
+-requires an unpacked HTSlib source tree (which will be built in conjunction
+-with samtools) or a previously-installed HTSlib.  In either case you may
+-need to configure --with-htslib=DIR to locate the appropriate HTSlib.
+-
+-FAILED.  You must supply an HTSlib in order

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

2016-10-03 Thread David Seifert

commit: 6cd0461e803e777a0b1d91569a25a91b05edc4b1
Author: David Seifert  gentoo  org>
AuthorDate: Mon Oct  3 19:50:27 2016 +
Commit: David Seifert  gentoo  org>
CommitDate: Mon Oct  3 20:21:21 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6cd0461e

sci-biology/samtools: Use 'python-single-r1' instead of 'python-r1'

Package-Manager: portage-2.3.1

 ...-0.1.20-r2.ebuild => samtools-0.1.20-r3.ebuild} | 38 --
 1 file changed, 21 insertions(+), 17 deletions(-)

diff --git a/sci-biology/samtools/samtools-0.1.20-r2.ebuild 
b/sci-biology/samtools/samtools-0.1.20-r3.ebuild
similarity index 60%
rename from sci-biology/samtools/samtools-0.1.20-r2.ebuild
rename to sci-biology/samtools/samtools-0.1.20-r3.ebuild
index e30ed26..787add8 100644
--- a/sci-biology/samtools/samtools-0.1.20-r2.ebuild
+++ b/sci-biology/samtools/samtools-0.1.20-r3.ebuild
@@ -6,7 +6,7 @@ EAPI=6
 
 PYTHON_COMPAT=( python2_7 )
 
-inherit eutils python-r1 toolchain-funcs
+inherit python-single-r1 toolchain-funcs
 
 DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment 
formats"
 HOMEPAGE="http://samtools.sourceforge.net/;
@@ -16,10 +16,10 @@ LICENSE="MIT"
 SLOT="0.1-legacy"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
 IUSE="examples"
-
 REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
-RDEPEND="sys-libs/ncurses:0=
+RDEPEND="${PYTHON_DEPS}
+   sys-libs/ncurses:0=
dev-lang/perl"
 DEPEND="${RDEPEND}
virtual/pkgconfig"
@@ -30,7 +30,8 @@ PATCHES=(
 
 src_prepare() {
default
-   sed -i 's~/software/bin/python~/usr/bin/env python~' 
"${S}"/misc/varfilter.py || die
+   # required, otherwise python_fix_shebang errors out
+   sed -i 's~/software/bin/python~/usr/bin/env python~' misc/varfilter.py 
|| die
tc-export CC AR
 }
 
@@ -41,24 +42,24 @@ src_compile() {
 }
 
 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
+   # install executables and hide them away from sight
+   dobin samtools bcftools/{bcftools,vcfutils.pl} 
misc/{*.py,*.pl,wgsim,ace2sam} \
+   
misc/{md5sum-lite,maq2sam-short,bamcheck,maq2sam-long,md5fa,plot-bamcheck}
+   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
+   # ... do the same with the python script, but also fix the shebang
+   mv "${ED%/}"/usr/bin/${PN}-${SLOT}/varfilter{,-${SLOT}}.py || die
+   python_fix_shebang "${ED%/}"/usr/bin/${PN}-${SLOT}/varfilter-${SLOT}.py
 
# fix perl shebangs
-   pushd "${ED}"usr/bin/"${PN}-${SLOT}"/ >> /dev/null
+   pushd "${ED%/}"/usr/bin/${PN}-${SLOT} >/dev/null || die
local i
for i in plot-bamcheck *.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
+   popd >/dev/null || die
 
dolib.so libbam-${SLOT}$(get_libname 1)
dosym libbam-${SLOT}$(get_libname 1) 
/usr/$(get_libdir)/libbam-${SLOT}$(get_libname)
@@ -68,9 +69,12 @@ src_install() {
 
mv ${PN}{,-${SLOT}}.1 || die
doman ${PN}-${SLOT}.1
-   dodoc AUTHORS NEWS
+   einstalldocs
 
-   use examples && dodoc -r examples
+   if use examples; then
+   dodoc -r examples
+   docompress -x /usr/share/doc/${PF}/examples
+   fi
 }
 
 pkg_postinst() {

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

2016-04-10 Thread David Seifert

commit: 5f3acec053c0f95f355f6c4db5e12994555a4b7a
Author: David Seifert  gentoo  org>
AuthorDate: Sun Apr 10 09:20:56 2016 +
Commit: David Seifert  gentoo  org>
CommitDate: Sun Apr 10 09:21:11 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5f3acec0

sci-biology/samtools: Remove lua dep, fix perl shebangs

Package-Manager: portage-2.2.28

 .../{samtools-1.3.ebuild => samtools-1.3-r1.ebuild} | 17 ++---
 1 file changed, 14 insertions(+), 3 deletions(-)

diff --git a/sci-biology/samtools/samtools-1.3.ebuild 
b/sci-biology/samtools/samtools-1.3-r1.ebuild
similarity index 83%
rename from sci-biology/samtools/samtools-1.3.ebuild
rename to sci-biology/samtools/samtools-1.3-r1.ebuild
index ec510ec..15d6714 100644
--- a/sci-biology/samtools/samtools-1.3.ebuild
+++ b/sci-biology/samtools/samtools-1.3-r1.ebuild
@@ -20,8 +20,7 @@ IUSE="examples"
 REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
 RDEPEND="sys-libs/ncurses:0=
-   >=sci-libs/htslib-${PV}
-   dev-lang/lua:0
+   =sci-libs/htslib-${PV}*
dev-lang/perl"
 DEPEND="${RDEPEND}
virtual/pkgconfig"
@@ -70,7 +69,19 @@ src_test() {
 src_install() {
dobin samtools $(find misc -type f -executable)
 
-   python_replicate_script "${ED}"/usr/bin/varfilter.py
+   python_replicate_script "${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

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

2016-04-09 Thread David Seifert

commit: 0f059b5eb7e03f75705f623dc74e27842540da40
Author: David Seifert  gentoo  org>
AuthorDate: Sat Apr  9 19:58:14 2016 +
Commit: David Seifert  gentoo  org>
CommitDate: Sat Apr  9 19:58:31 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=0f059b5e

sci-biology/samtools: Remove lua dep, fix perl shebangs

Package-Manager: portage-2.2.28

 .../{samtools-0.1.20-r1.ebuild => samtools-0.1.20-r2.ebuild} | 12 +++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/sci-biology/samtools/samtools-0.1.20-r1.ebuild 
b/sci-biology/samtools/samtools-0.1.20-r2.ebuild
similarity index 87%
rename from sci-biology/samtools/samtools-0.1.20-r1.ebuild
rename to sci-biology/samtools/samtools-0.1.20-r2.ebuild
index 744d15f..e30ed26 100644
--- a/sci-biology/samtools/samtools-0.1.20-r1.ebuild
+++ b/sci-biology/samtools/samtools-0.1.20-r2.ebuild
@@ -20,7 +20,6 @@ IUSE="examples"
 REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
 RDEPEND="sys-libs/ncurses:0=
-   dev-lang/lua:0
dev-lang/perl"
 DEPEND="${RDEPEND}
virtual/pkgconfig"
@@ -50,6 +49,17 @@ src_install() {
mv "${ED}"/usr/bin/${PN}-${SLOT}/varfilter{,-${SLOT}}.py || die
python_replicate_script 
"${ED}"/usr/bin/${PN}-${SLOT}/varfilter-${SLOT}.py
 
+   # fix perl shebangs
+   pushd "${ED}"usr/bin/"${PN}-${SLOT}"/ >> /dev/null
+   local i
+   for i in plot-bamcheck *.pl; do
+   sed -e '1s:.*:#!/usr/bin/env perl:' -i "${i}" || die
+   done
+
+   # remove lua scripts
+   rm -f r2plot.lua vcfutils.lua || die
+   popd >> /dev/null
+
dolib.so libbam-${SLOT}$(get_libname 1)
dosym libbam-${SLOT}$(get_libname 1) 
/usr/$(get_libdir)/libbam-${SLOT}$(get_libname)

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/files/, sci-biology/samtools/

2016-03-28 Thread David Seifert

commit: 767b616524e6b171ed4775fe35ecd068f58abc22
Author: David Seifert  gentoo  org>
AuthorDate: Mon Mar 28 19:59:02 2016 +
Commit: David Seifert  gentoo  org>
CommitDate: Mon Mar 28 19:59:24 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=767b6165

sci-biology/samtools: version bump to 1.3, to match htslib

* EAPI=6
* Added modern AX_WITH_CURSES that works with pkg-config
* Fixed incorrect symlinks for libbam.so

Package-Manager: portage-2.2.28

 sci-biology/samtools/Manifest  |   1 +
 .../samtools/files/samtools-1.3-buildsystem.patch  | 174 +
 .../samtools/files/samtools-1.3-ncurses.patch  | 737 +
 sci-biology/samtools/samtools-1.3.ebuild   |  86 +++
 4 files changed, 998 insertions(+)

diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index fd88ba4..d25774f 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -4,3 +4,4 @@ DIST samtools-0.1.20.tar.gz 566387 SHA256 
500019b4d1886ad995513d5ce8b413b14b51f1
 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

diff --git a/sci-biology/samtools/files/samtools-1.3-buildsystem.patch 
b/sci-biology/samtools/files/samtools-1.3-buildsystem.patch
new file mode 100644
index 000..61f6b03
--- /dev/null
+++ b/sci-biology/samtools/files/samtools-1.3-buildsystem.patch
@@ -0,0 +1,174 @@
+--- 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)

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/, sci-biology/samtools/files/

2016-03-27 Thread David Seifert

commit: deaa21ff2b928318d0e1b8fe45aa404411f08086
Author: David Seifert  gentoo  org>
AuthorDate: Sun Mar 27 23:52:51 2016 +
Commit: David Seifert  gentoo  org>
CommitDate: Sun Mar 27 23:52:51 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=deaa21ff

sci-biology/samtools: Move to SLOT="0.1-legacy" for future legacy versions

Package-Manager: portage-2.2.28

 .../samtools/files/samtools-0.1.20-buildsystem.patch | 20 ++--
 ...tools-0.1.20.ebuild => samtools-0.1.20-r1.ebuild} |  2 +-
 2 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch 
b/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch
index dfdd890..eb9f693 100644
--- a/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch
+++ b/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch
@@ -75,15 +75,15 @@
  .PHONY:all-recur lib-recur clean-recur cleanlocal-recur install-recur
  
 -lib:libbam.a
-+lib:libbam-legacy.a
++lib:libbam-0.1-legacy.a
  
 -libbam.a:$(LOBJS)
-+libbam-legacy.a:$(LOBJS)
++libbam-0.1-legacy.a:$(LOBJS)
$(AR) -csru $@ $(LOBJS)
  
  samtools:lib-recur $(AOBJS)
 -  $(CC) $(CFLAGS) -o $@ $(AOBJS) $(LDFLAGS) libbam.a -Lbcftools 
-lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread
-+  $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) libbam-legacy.a 
-Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread
++  $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) -L. -lbam-0.1-legacy 
-Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread
  
  razip:razip.o razf.o $(KNETFILE_O)
 -  $(CC) $(CFLAGS) -o $@ $^ -lz
@@ -105,21 +105,21 @@
  
 -libbam.1.dylib-local:$(LOBJS)
 -  libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz
-+libbam-legacy.1.dylib-local:$(LOBJS)
-+  libtool -dynamic $(LOBJS) -o libbam-legacy.1.dylib -lc -lz
++libbam-0.1-legacy.1.dylib-local:$(LOBJS)
++  libtool -dynamic $(LOBJS) -o libbam-0.1-legacy.1.dylib -lc -lz
  
 -libbam.so.1-local:$(LOBJS)
 -  $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc 
-lz
-+libbam-legacy.so.1-local:$(LOBJS)
-+  $(CC) $(LDFLAGS) -shared -Wl,-soname,libbam-legacy.so -o 
libbam-legacy.so.1 $(LOBJS) -lc -lz -lm -lpthread
++libbam-0.1-legacy.so.1-local:$(LOBJS)
++  $(CC) $(LDFLAGS) -shared -Wl,-soname,libbam-0.1-legacy.so -o 
libbam-0.1-legacy.so.1 $(LOBJS) -lc -lz -lm -lpthread
  
  dylib:
@$(MAKE) cleanlocal; \
case `uname` in \
 -  Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" 
libbam.so.1-local;; \
 -  Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" 
libbam.1.dylib-local;; \
-+  Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" 
libbam-legacy.so.1-local;; \
-+  Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" 
libbam-legacy.1.dylib-local;; \
++  Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" 
libbam-0.1-legacy.so.1-local;; \
++  Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" 
libbam-0.1-legacy.1.dylib-local;; \
*) echo 'Unknown OS';; \
esac
  
@@ -162,7 +162,7 @@
  
  bamcheck:bamcheck.o
 -  $(CC) $(CFLAGS) -o $@ bamcheck.o -L.. -lm -lbam -lpthread -lz
-+  $(CC) $(CFLAGS) $(LDFLAGS) -o $@ bamcheck.o -L.. -lm 
-lbam-legacy -lpthread -lz
++  $(CC) $(CFLAGS) $(LDFLAGS) -o $@ bamcheck.o -L.. -lm 
-lbam-0.1-legacy -lpthread -lz
  
  bamcheck.o:bamcheck.c ../faidx.h ../khash.h ../sam.h ../razf.h
$(CC) $(CFLAGS) -c -I.. -o $@ bamcheck.c

diff --git a/sci-biology/samtools/samtools-0.1.20.ebuild 
b/sci-biology/samtools/samtools-0.1.20-r1.ebuild
similarity index 99%
rename from sci-biology/samtools/samtools-0.1.20.ebuild
rename to sci-biology/samtools/samtools-0.1.20-r1.ebuild
index 3ee9956..744d15f 100644
--- a/sci-biology/samtools/samtools-0.1.20.ebuild
+++ b/sci-biology/samtools/samtools-0.1.20-r1.ebuild
@@ -13,7 +13,7 @@ HOMEPAGE="http://samtools.sourceforge.net/;
 SRC_URI="https://github.com/samtools/samtools/archive/${PV}.tar.gz -> 
${P}.tar.gz"
 
 LICENSE="MIT"
-SLOT="legacy"
+SLOT="0.1-legacy"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
 IUSE="examples"

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

2016-03-27 Thread David Seifert

commit: 5347b1b450f7d7abf30f57adaeeed3f4d6aee5d8
Author: David Seifert  gentoo  org>
AuthorDate: Sun Mar 27 22:53:29 2016 +
Commit: David Seifert  gentoo  org>
CommitDate: Sun Mar 27 22:53:29 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5347b1b4

sci-biology/samtools: Add elog message discouraging direct use

Package-Manager: portage-2.2.28

 sci-biology/samtools/samtools-0.1.20.ebuild | 6 ++
 1 file changed, 6 insertions(+)

diff --git a/sci-biology/samtools/samtools-0.1.20.ebuild 
b/sci-biology/samtools/samtools-0.1.20.ebuild
index 50ee0b3..3ee9956 100644
--- a/sci-biology/samtools/samtools-0.1.20.ebuild
+++ b/sci-biology/samtools/samtools-0.1.20.ebuild
@@ -62,3 +62,9 @@ src_install() {
 
use examples && dodoc -r examples
 }
+
+pkg_postinst() {
+   elog "This version of samtools should *not* be your first choice for 
working"
+   elog "with NGS data. It is installed solely for programs requiring it."
+   elog "It is recommended that you use >=sci-biology/samtools-1.2."
+}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

2016-03-27 Thread David Seifert

commit: 9de6d48e56e90183b53d6bab2e82d288a9cc0792
Author: David Seifert  gentoo  org>
AuthorDate: Sun Mar 27 22:31:29 2016 +
Commit: David Seifert  gentoo  org>
CommitDate: Sun Mar 27 22:39:52 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=9de6d48e

sci-biology/samtools: Trim DESCRIPTION

* Add sub-slot operator for 'sys-libs/ncurses' dependency

Package-Manager: portage-2.2.28

 sci-biology/samtools/samtools-1.0-r1.ebuild | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/sci-biology/samtools/samtools-1.0-r1.ebuild 
b/sci-biology/samtools/samtools-1.0-r1.ebuild
index 279801c..a85053c 100644
--- a/sci-biology/samtools/samtools-1.0-r1.ebuild
+++ b/sci-biology/samtools/samtools-1.0-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -8,7 +8,7 @@ PYTHON_COMPAT=( python2_7 )
 
 inherit eutils multilib python-r1 toolchain-funcs
 
-DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large 
nucleotide sequence alignments"
+DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment 
formats"
 HOMEPAGE="http://www.htslib.org/;
 SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
 
@@ -20,7 +20,7 @@ IUSE="examples"
 REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
 CDEPEND="
-   sys-libs/ncurses
+   sys-libs/ncurses:0=
sci-libs/htslib"
 
 RDEPEND="${CDEPEND}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

2016-03-27 Thread David Seifert

commit: 92e63bcc84ec47131ccefe4f6c7dc224ff43de41
Author: David Seifert  gentoo  org>
AuthorDate: Sun Mar 27 22:32:37 2016 +
Commit: David Seifert  gentoo  org>
CommitDate: Sun Mar 27 22:39:54 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=92e63bcc

sci-biology/samtools: Trim DESCRIPTION

* Add sub-slot operator for 'sys-libs/ncurses' dependency

Package-Manager: portage-2.2.28

 sci-biology/samtools/samtools-1.1.ebuild | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/sci-biology/samtools/samtools-1.1.ebuild 
b/sci-biology/samtools/samtools-1.1.ebuild
index 1f5b82a..235e27f 100644
--- a/sci-biology/samtools/samtools-1.1.ebuild
+++ b/sci-biology/samtools/samtools-1.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -8,7 +8,7 @@ PYTHON_COMPAT=( python2_7 )
 
 inherit eutils multilib python-r1 toolchain-funcs
 
-DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large 
nucleotide sequence alignments"
+DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment 
formats"
 HOMEPAGE="http://www.htslib.org/;
 SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
 
@@ -20,7 +20,7 @@ IUSE="examples"
 REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
 CDEPEND="
-   sys-libs/ncurses
+   sys-libs/ncurses:0=
~sci-libs/htslib-${PV}"
 
 RDEPEND="${CDEPEND}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/files/, sci-biology/samtools/

2016-03-27 Thread David Seifert

commit: f7caa54d3afffe8220d1a5f237b8906a994a0792
Author: David Seifert  gentoo  org>
AuthorDate: Sun Mar 27 22:39:22 2016 +
Commit: David Seifert  gentoo  org>
CommitDate: Sun Mar 27 22:39:58 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f7caa54d

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

 sci-biology/samtools/Manifest  |   1 +
 .../files/samtools-0.1.20-buildsystem.patch| 206 +
 sci-biology/samtools/samtools-0.1.20.ebuild|  64 +++
 3 files changed, 271 insertions(+)

diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index dae2fbd..fd88ba4 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 000..dfdd890
--- /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 $@

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

2016-03-27 Thread David Seifert

commit: 00b1d249875a5f081a74b1a248355c972b423cc3
Author: David Seifert  gentoo  org>
AuthorDate: Sun Mar 27 22:30:25 2016 +
Commit: David Seifert  gentoo  org>
CommitDate: Sun Mar 27 22:39:50 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=00b1d249

sci-biology/samtools: Trim DESCRIPTION

* Add sub-slot operator for 'sys-libs/ncurses' dependency

Package-Manager: portage-2.2.28

 sci-biology/samtools/samtools-1.0.ebuild | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/sci-biology/samtools/samtools-1.0.ebuild 
b/sci-biology/samtools/samtools-1.0.ebuild
index d1f1f50..7a5f026 100644
--- a/sci-biology/samtools/samtools-1.0.ebuild
+++ b/sci-biology/samtools/samtools-1.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -8,7 +8,7 @@ PYTHON_COMPAT=( python2_7 )
 
 inherit eutils multilib python-r1 toolchain-funcs
 
-DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large 
nucleotide sequence alignments"
+DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment 
formats"
 HOMEPAGE="http://www.htslib.org/;
 SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
 
@@ -20,7 +20,7 @@ IUSE="examples"
 REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
 CDEPEND="
-   sys-libs/ncurses
+   sys-libs/ncurses:0=
sci-libs/htslib"
 
 RDEPEND="${CDEPEND}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

2016-03-27 Thread David Seifert

commit: b552f8b45630582714b2ad3df7e814eadf128acb
Author: David Seifert  gentoo  org>
AuthorDate: Sun Mar 27 22:29:08 2016 +
Commit: David Seifert  gentoo  org>
CommitDate: Sun Mar 27 22:39:47 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b552f8b4

sci-biology/samtools: Trim DESCRIPTION

* Add sub-slot operator for 'sys-libs/ncurses' dependency

Package-Manager: portage-2.2.28

 sci-biology/samtools/samtools-0.1.19-r2.ebuild | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/sci-biology/samtools/samtools-0.1.19-r2.ebuild 
b/sci-biology/samtools/samtools-0.1.19-r2.ebuild
index 133abab..9fb708b 100644
--- a/sci-biology/samtools/samtools-0.1.19-r2.ebuild
+++ b/sci-biology/samtools/samtools-0.1.19-r2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -8,7 +8,7 @@ PYTHON_COMPAT=( python2_7 )
 
 inherit eutils multilib python-r1 toolchain-funcs
 
-DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large 
nucleotide sequence alignments"
+DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment 
formats"
 HOMEPAGE="http://samtools.sourceforge.net/;
 SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
 
@@ -19,7 +19,7 @@ IUSE="examples"
 
 REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
-CDEPEND="sys-libs/ncurses"
+CDEPEND="sys-libs/ncurses:0="
 RDEPEND="${CDEPEND}
dev-lang/lua
dev-lang/perl"

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

2016-03-27 Thread David Seifert

commit: 2362d04e9b57b0a3f2c2c4cc98a93fd4d52e976a
Author: David Seifert  gentoo  org>
AuthorDate: Sun Mar 27 22:27:22 2016 +
Commit: David Seifert  gentoo  org>
CommitDate: Sun Mar 27 22:39:45 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=2362d04e

sci-biology/samtools: Trim DESCRIPTION

Package-Manager: portage-2.2.28

 sci-biology/samtools/samtools-0.1.12.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/samtools/samtools-0.1.12.ebuild 
b/sci-biology/samtools/samtools-0.1.12.ebuild
index 34720e4..d057288 100644
--- a/sci-biology/samtools/samtools-0.1.12.ebuild
+++ b/sci-biology/samtools/samtools-0.1.12.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -6,7 +6,7 @@ EAPI=2
 
 MY_P="${P}a"
 
-DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large 
nucleotide sequence alignments"
+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"

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

2016-03-27 Thread David Seifert

commit: 31d61492a851fcda68985b29915584dda2125aa5
Author: David Seifert  gentoo  org>
AuthorDate: Sun Mar 27 22:33:48 2016 +
Commit: David Seifert  gentoo  org>
CommitDate: Sun Mar 27 22:39:56 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=31d61492

sci-biology/samtools: Trim DESCRIPTION

* Add sub-slot operator for 'sys-libs/ncurses' dependency

Package-Manager: portage-2.2.28

 sci-biology/samtools/samtools-1.2.ebuild | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/sci-biology/samtools/samtools-1.2.ebuild 
b/sci-biology/samtools/samtools-1.2.ebuild
index 3a999e0..c905fc9 100644
--- a/sci-biology/samtools/samtools-1.2.ebuild
+++ b/sci-biology/samtools/samtools-1.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -8,7 +8,7 @@ PYTHON_COMPAT=( python2_7 )
 
 inherit eutils multilib python-r1 toolchain-funcs
 
-DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large 
nucleotide sequence alignments"
+DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment 
formats"
 HOMEPAGE="http://www.htslib.org/;
 SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
 
@@ -20,7 +20,7 @@ IUSE="examples"
 REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
 CDEPEND="
-   sys-libs/ncurses
+   sys-libs/ncurses:0=
>=sci-libs/htslib-${PV}"
 
 RDEPEND="${CDEPEND}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

2015-09-24 Thread Agostino Sarubbo

commit: eacfdf7dded3b46636d0f4c422062216f1a6d1eb
Author: Agostino Sarubbo  gentoo  org>
AuthorDate: Thu Sep 24 12:55:27 2015 +
Commit: Agostino Sarubbo  gentoo  org>
CommitDate: Thu Sep 24 12:55:27 2015 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=eacfdf7d

sci-biology/samtools: amd64 stable wrt bug #525630

Package-Manager: portage-2.2.20.1
RepoMan-Options: --include-arches="amd64"

 sci-biology/samtools/samtools-1.0-r1.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/samtools/samtools-1.0-r1.ebuild 
b/sci-biology/samtools/samtools-1.0-r1.ebuild
index 802aefc..279801c 100644
--- a/sci-biology/samtools/samtools-1.0-r1.ebuild
+++ b/sci-biology/samtools/samtools-1.0-r1.ebuild
@@ -14,7 +14,7 @@ SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
 
 LICENSE="MIT"
 SLOT="0"
-KEYWORDS="~amd64 x86 ~amd64-linux ~x86-linux ~x64-macos"
+KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~x64-macos"
 IUSE="examples"
 
 REQUIRED_USE="${PYTHON_REQUIRED_USE}"

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/files/, profiles/, sci-biology/samtools/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/, sci-biology/samtools/files/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/files/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/files/, sci-biology/samtools/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/, sci-biology/samtools/files/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/files/, sci-biology/samtools/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/, sci-biology/samtools/files/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/files/, sci-biology/samtools/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/

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