* [gentoo-commits] proj/sci:master commit in: sci-biology/samtools/
@ 2015-06-08 12:19 Justin Lecher
0 siblings, 0 replies; 4+ messages in thread
From: Justin Lecher @ 2015-06-08 12:19 UTC (permalink / raw
To: gentoo-commits
commit: 8c1c38a3d9c37e40df2f906adbf3becfe8fbd751
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jun 8 12:19:42 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jun 8 12:19:42 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=8c1c38a3
sci-biology/samtools: Updating remote-id in metadata.xml
Package-Manager: portage-2.2.20
sci-biology/samtools/ChangeLog | 3 +++
sci-biology/samtools/metadata.xml | 3 +++
2 files changed, 6 insertions(+)
diff --git a/sci-biology/samtools/ChangeLog b/sci-biology/samtools/ChangeLog
index 5e1efce..f5eaa81 100644
--- a/sci-biology/samtools/ChangeLog
+++ b/sci-biology/samtools/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml:
+ sci-biology/samtools: Updating remote-id in metadata.xml
+
*samtools-1.0-r2 (11 May 2015)
*samtools-1.1-r1 (11 May 2015)
*samtools-1.2-r1 (11 May 2015)
diff --git a/sci-biology/samtools/metadata.xml b/sci-biology/samtools/metadata.xml
index f17a827..74dc02b 100644
--- a/sci-biology/samtools/metadata.xml
+++ b/sci-biology/samtools/metadata.xml
@@ -2,4 +2,7 @@
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
+ <upstream>
+ <remote-id type="sourceforge">samtools</remote-id>
+ </upstream>
</pkgmetadata>
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/samtools/
@ 2015-09-21 17:44 Justin Lecher
0 siblings, 0 replies; 4+ messages in thread
From: Justin Lecher @ 2015-09-21 17:44 UTC (permalink / raw
To: gentoo-commits
commit: 3b78eff2b8046466746871467e132507bcf8d013
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Sep 21 17:25:05 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Sep 21 17:25:05 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=3b78eff2
sci-biology/samtools: Add subslot operators
Package-Manager: portage-2.2.20.1
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-biology/samtools/samtools-1.0-r2.ebuild | 8 ++++----
sci-biology/samtools/samtools-1.1-r1.ebuild | 8 ++++----
sci-biology/samtools/samtools-1.2-r1.ebuild | 8 ++++----
3 files changed, 12 insertions(+), 12 deletions(-)
diff --git a/sci-biology/samtools/samtools-1.0-r2.ebuild b/sci-biology/samtools/samtools-1.0-r2.ebuild
index d81f815..b10e681 100644
--- a/sci-biology/samtools/samtools-1.0-r2.ebuild
+++ b/sci-biology/samtools/samtools-1.0-r2.ebuild
@@ -20,7 +20,7 @@ IUSE="examples"
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
CDEPEND="
- sys-libs/ncurses
+ sys-libs/ncurses:0=
sci-libs/htslib"
RDEPEND="${CDEPEND}
@@ -34,15 +34,15 @@ src_prepare() {
sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die
- epatch "${FILESDIR}"/${P}-buildsystem.patch
- epatch "${FILESDIR}"/${P}-rmdup.patch
+ epatch \
+ "${FILESDIR}"/${P}-buildsystem.patch \
+ "${FILESDIR}"/${P}-rmdup.patch
tc-export CC AR
sed \
-e '/htslib.mk/d' \
-i Makefile || die
-
}
src_compile() {
diff --git a/sci-biology/samtools/samtools-1.1-r1.ebuild b/sci-biology/samtools/samtools-1.1-r1.ebuild
index 0d65870..9941156 100644
--- a/sci-biology/samtools/samtools-1.1-r1.ebuild
+++ b/sci-biology/samtools/samtools-1.1-r1.ebuild
@@ -20,7 +20,7 @@ IUSE="examples"
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
CDEPEND="
- sys-libs/ncurses
+ sys-libs/ncurses:0=
~sci-libs/htslib-${PV}"
RDEPEND="${CDEPEND}
@@ -34,15 +34,15 @@ src_prepare() {
sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die
- epatch "${FILESDIR}"/${P}-buildsystem.patch
- epatch "${FILESDIR}"/${P}-rmdup.patch
+ epatch \
+ "${FILESDIR}"/${P}-buildsystem.patch \
+ "${FILESDIR}"/${P}-rmdup.patch
tc-export CC AR
sed \
-e '/htslib.mk/d' \
-i Makefile || die
-
}
src_compile() {
diff --git a/sci-biology/samtools/samtools-1.2-r1.ebuild b/sci-biology/samtools/samtools-1.2-r1.ebuild
index 648032c..dcbd07b 100644
--- a/sci-biology/samtools/samtools-1.2-r1.ebuild
+++ b/sci-biology/samtools/samtools-1.2-r1.ebuild
@@ -20,7 +20,7 @@ IUSE="examples"
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
CDEPEND="
- sys-libs/ncurses
+ sys-libs/ncurses:0=
>=sci-libs/htslib-${PV}"
RDEPEND="${CDEPEND}
@@ -34,15 +34,15 @@ src_prepare() {
sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die
- epatch "${FILESDIR}"/${P}-buildsystem.patch
- epatch "${FILESDIR}"/${P}-rmdup.patch
+ epatch \
+ "${FILESDIR}"/${P}-buildsystem.patch \
+ "${FILESDIR}"/${P}-rmdup.patch
tc-export CC AR
sed \
-e '/htslib.mk/d' \
-i Makefile || die
-
}
src_compile() {
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/samtools/
@ 2017-04-30 13:23 Martin Mokrejs
0 siblings, 0 replies; 4+ messages in thread
From: Martin Mokrejs @ 2017-04-30 13:23 UTC (permalink / raw
To: gentoo-commits
commit: 6948e2872a1c6182e8e325edd5e48a21bd713443
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Apr 30 13:23:16 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Apr 30 13:23:16 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=6948e287
sci-biology/samtools: version bump
Compiles fine against htslib-1.4 but because htslib-1.4 is not KEYWORDed
keeping samtools-1.4 masked as well.
Package-Manager: Portage-2.3.5, Repoman-2.3.2
sci-biology/samtools/samtools-1.4.ebuild | 82 ++++++++++++++++++++++++++++++++
1 file changed, 82 insertions(+)
diff --git a/sci-biology/samtools/samtools-1.4.ebuild b/sci-biology/samtools/samtools-1.4.ebuild
new file mode 100644
index 000000000..b0bd40b82
--- /dev/null
+++ b/sci-biology/samtools/samtools-1.4.ebuild
@@ -0,0 +1,82 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit eutils multilib python-r1 toolchain-funcs
+
+DESCRIPTION="Utilities for SAM (Sequence Alignment/Map) and BAM files"
+HOMEPAGE="http://www.htslib.org/"
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS=""
+# KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+IUSE="examples"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+CDEPEND="
+ sys-libs/ncurses:0=
+ >=sci-libs/htslib-${PV}"
+
+RDEPEND="${CDEPEND}
+ dev-lang/lua
+ dev-lang/perl"
+DEPEND="${CDEPEND}
+ virtual/pkgconfig"
+
+src_prepare() {
+ find htslib-* -delete || die
+
+ sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die
+
+ tc-export CC AR
+
+ sed \
+ -e '/htslib.mk/d' \
+ -i Makefile || die
+}
+
+src_compile() {
+ local mymakeargs=(
+ LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)"
+ HTSDIR="${EPREFIX}/usr/include"
+ HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib)
+ BAMLIB="libbam.so"
+ CC=$(tc-getCC) CFLAGS="${CFLAGS}"
+ )
+ emake "${mymakeargs[@]}"
+}
+
+src_test() {
+ local mymakeargs=(
+ LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)"
+ HTSDIR="${EPREFIX}/usr/include"
+ HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib)
+ BAMLIB="libbam.so"
+ )
+ LD_LIBRARY_PATH="${S}" emake "${mymakeargs[@]}" test
+}
+
+src_install() {
+ dobin samtools $(find misc -type f -executable)
+
+ python_replicate_script "${ED}"/usr/bin/varfilter.py
+ #dolib.so libbam.so*
+ dolib libbam.a
+
+ insinto /usr/include/bam
+ doins *.h
+
+ doman ${PN}.1
+ dodoc AUTHORS NEWS README
+
+ if use examples; then
+ insinto /usr/share/${PN}
+ doins -r examples
+ fi
+}
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/samtools/
@ 2017-07-28 20:05 Martin Mokrejs
0 siblings, 0 replies; 4+ messages in thread
From: Martin Mokrejs @ 2017-07-28 20:05 UTC (permalink / raw
To: gentoo-commits
commit: 22ff29bb13f8e33fd84270dff4dd8ce0a1480f7c
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jul 20 20:16:00 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jul 28 20:05:19 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=22ff29bb
sci-biology/samtools: version bump
Cannot proceed unless htslib-1.5 can be properly installed along existing
htslib-1.3.1 installation.
Package-Manager: Portage-2.3.6, Repoman-2.3.2
sci-biology/samtools/{samtools-1.4.ebuild => samtools-1.5.ebuild} | 0
1 file changed, 0 insertions(+), 0 deletions(-)
diff --git a/sci-biology/samtools/samtools-1.4.ebuild b/sci-biology/samtools/samtools-1.5.ebuild
similarity index 100%
rename from sci-biology/samtools/samtools-1.4.ebuild
rename to sci-biology/samtools/samtools-1.5.ebuild
^ permalink raw reply [flat|nested] 4+ messages in thread
end of thread, other threads:[~2017-07-28 20:05 UTC | newest]
Thread overview: 4+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2015-09-21 17:44 [gentoo-commits] proj/sci:master commit in: sci-biology/samtools/ Justin Lecher
-- strict thread matches above, loose matches on Subject: below --
2017-07-28 20:05 Martin Mokrejs
2017-04-30 13:23 Martin Mokrejs
2015-06-08 12:19 Justin Lecher
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox