[gentoo-commits] proj/sci:master commit in: sci-biology/bcftools/

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* [gentoo-commits] proj/sci:master commit in: sci-biology/bcftools/
@ 2015-01-14 23:26 Martin Mokrejs
  0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2015-01-14 23:26 UTC (permalink / raw
  To: gentoo-commits

commit:     46558c3fddec519dc1b598612c6aadd022dc2aab
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jan 14 23:25:04 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jan 14 23:25:04 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=46558c3f

sci-biology/bcftools: new package: compiles against bundled sci-libs/htslib-1.1 but does not install it

Package-Manager: portage-2.2.7

---
 sci-biology/bcftools/ChangeLog           | 10 ++++++++++
 sci-biology/bcftools/bcftools-1.1.ebuild | 26 ++++++++++++++++++++++++++
 sci-biology/bcftools/metadata.xml        |  9 +++++++++
 3 files changed, 45 insertions(+)

diff --git a/sci-biology/bcftools/ChangeLog b/sci-biology/bcftools/ChangeLog
new file mode 100644
index 0000000..4e0a781
--- /dev/null
+++ b/sci-biology/bcftools/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/bcftools
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*bcftools-1.1 (14 Jan 2015)
+
+  14 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +bcftools-1.1.ebuild, +metadata.xml:
+  sci-biology/bcftools: new package: compiles against bundled sci-
+  libs/htslib-1.1 but does not install it

diff --git a/sci-biology/bcftools/bcftools-1.1.ebuild b/sci-biology/bcftools/bcftools-1.1.ebuild
new file mode 100644
index 0000000..e3f446f
--- /dev/null
+++ b/sci-biology/bcftools/bcftools-1.1.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
+HOMEPAGE="http://www.htslib.org/bcftools_release_notes"
+SRC_URI="http://sourceforge.net/projects/samtools/files/samtools/1.1/bcftools-1.1.tar.bz2"
+
+LICENSE="MIT-GRL"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND="sci-libs/htslib
+	dev-lang/perl"
+RDEPEND="${DEPEND}"
+
+src_prepare(){
+	sed -e 's#prefix      = /usr/local#prefix      = /usr#' \
+		-e 's@CFLAGS   = -g -Wall -Wc++-compat -O2@#CFLAGS   = -g -Wall -Wc++-compat -O2@' -i Makefile
+
+	sed -e 's#prefix      = /usr/local#prefix      = /usr#' \
+		-e 's@CFLAGS   = -g -Wall -Wc++-compat -O2@#CFLAGS   = -g -Wall -Wc++-compat -O2@' -i htslib-1.1/Makefile
+}

diff --git a/sci-biology/bcftools/metadata.xml b/sci-biology/bcftools/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/bcftools/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+</pkgmetadata>


^ permalink raw reply related	[flat|nested] 10+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/bcftools/
@ 2015-01-15 15:57 Christoph Junghans
  0 siblings, 0 replies; 10+ messages in thread
From: Christoph Junghans @ 2015-01-15 15:57 UTC (permalink / raw
  To: gentoo-commits

commit:     1ed8090c989cf72046e206e4daaf02222c4029a5
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Thu Jan 15 15:56:39 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Thu Jan 15 15:56:39 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1ed8090c

Revert "sci-biology/bcftools: new package: compiles against bundled sci-libs/htslib-1.1 but does not install it"

Missing license.

This reverts commit 46558c3fddec519dc1b598612c6aadd022dc2aab.

---
 sci-biology/bcftools/ChangeLog           | 10 ----------
 sci-biology/bcftools/bcftools-1.1.ebuild | 26 --------------------------
 sci-biology/bcftools/metadata.xml        |  9 ---------
 3 files changed, 45 deletions(-)

diff --git a/sci-biology/bcftools/ChangeLog b/sci-biology/bcftools/ChangeLog
deleted file mode 100644
index 4e0a781..0000000
--- a/sci-biology/bcftools/ChangeLog
+++ /dev/null
@@ -1,10 +0,0 @@
-# ChangeLog for sci-biology/bcftools
-# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
-*bcftools-1.1 (14 Jan 2015)
-
-  14 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
-  +bcftools-1.1.ebuild, +metadata.xml:
-  sci-biology/bcftools: new package: compiles against bundled sci-
-  libs/htslib-1.1 but does not install it

diff --git a/sci-biology/bcftools/bcftools-1.1.ebuild b/sci-biology/bcftools/bcftools-1.1.ebuild
deleted file mode 100644
index e3f446f..0000000
--- a/sci-biology/bcftools/bcftools-1.1.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=5
-
-DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
-HOMEPAGE="http://www.htslib.org/bcftools_release_notes"
-SRC_URI="http://sourceforge.net/projects/samtools/files/samtools/1.1/bcftools-1.1.tar.bz2"
-
-LICENSE="MIT-GRL"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND="sci-libs/htslib
-	dev-lang/perl"
-RDEPEND="${DEPEND}"
-
-src_prepare(){
-	sed -e 's#prefix      = /usr/local#prefix      = /usr#' \
-		-e 's@CFLAGS   = -g -Wall -Wc++-compat -O2@#CFLAGS   = -g -Wall -Wc++-compat -O2@' -i Makefile
-
-	sed -e 's#prefix      = /usr/local#prefix      = /usr#' \
-		-e 's@CFLAGS   = -g -Wall -Wc++-compat -O2@#CFLAGS   = -g -Wall -Wc++-compat -O2@' -i htslib-1.1/Makefile
-}

diff --git a/sci-biology/bcftools/metadata.xml b/sci-biology/bcftools/metadata.xml
deleted file mode 100644
index 2bc8930..0000000
--- a/sci-biology/bcftools/metadata.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <herd>sci-biology</herd>
-  <maintainer>
-    <email>mmokrejs@fold.natur.cuni.cz</email>
-    <name>Martin Mokrejs</name>
-  </maintainer>
-</pkgmetadata>


^ permalink raw reply related	[flat|nested] 10+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/bcftools/
@ 2015-01-15 17:44 Christoph Junghans
  0 siblings, 0 replies; 10+ messages in thread
From: Christoph Junghans @ 2015-01-15 17:44 UTC (permalink / raw
  To: gentoo-commits

commit:     806d5e4ebca3f285986f2e1e0f1125f835fdf196
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Thu Jan 15 17:43:04 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Thu Jan 15 17:43:04 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=806d5e4e

Revert "Revert "sci-biology/bcftools: new package: compiles against bundled sci-libs/htslib-1.1 but does not install it""

This reverts commit 1ed8090c989cf72046e206e4daaf02222c4029a5.

---
 sci-biology/bcftools/ChangeLog           | 10 ++++++++++
 sci-biology/bcftools/bcftools-1.1.ebuild | 26 ++++++++++++++++++++++++++
 sci-biology/bcftools/metadata.xml        |  9 +++++++++
 3 files changed, 45 insertions(+)

diff --git a/sci-biology/bcftools/ChangeLog b/sci-biology/bcftools/ChangeLog
new file mode 100644
index 0000000..4e0a781
--- /dev/null
+++ b/sci-biology/bcftools/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/bcftools
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*bcftools-1.1 (14 Jan 2015)
+
+  14 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +bcftools-1.1.ebuild, +metadata.xml:
+  sci-biology/bcftools: new package: compiles against bundled sci-
+  libs/htslib-1.1 but does not install it

diff --git a/sci-biology/bcftools/bcftools-1.1.ebuild b/sci-biology/bcftools/bcftools-1.1.ebuild
new file mode 100644
index 0000000..e3f446f
--- /dev/null
+++ b/sci-biology/bcftools/bcftools-1.1.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
+HOMEPAGE="http://www.htslib.org/bcftools_release_notes"
+SRC_URI="http://sourceforge.net/projects/samtools/files/samtools/1.1/bcftools-1.1.tar.bz2"
+
+LICENSE="MIT-GRL"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND="sci-libs/htslib
+	dev-lang/perl"
+RDEPEND="${DEPEND}"
+
+src_prepare(){
+	sed -e 's#prefix      = /usr/local#prefix      = /usr#' \
+		-e 's@CFLAGS   = -g -Wall -Wc++-compat -O2@#CFLAGS   = -g -Wall -Wc++-compat -O2@' -i Makefile
+
+	sed -e 's#prefix      = /usr/local#prefix      = /usr#' \
+		-e 's@CFLAGS   = -g -Wall -Wc++-compat -O2@#CFLAGS   = -g -Wall -Wc++-compat -O2@' -i htslib-1.1/Makefile
+}

diff --git a/sci-biology/bcftools/metadata.xml b/sci-biology/bcftools/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/bcftools/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+</pkgmetadata>


^ permalink raw reply related	[flat|nested] 10+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/bcftools/
@ 2015-01-15 17:44 Christoph Junghans
  0 siblings, 0 replies; 10+ messages in thread
From: Christoph Junghans @ 2015-01-15 17:44 UTC (permalink / raw
  To: gentoo-commits

commit:     5f9c2b4185d92def7228f32421ec3952ec48cb3b
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Thu Jan 15 17:43:54 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Thu Jan 15 17:43:54 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5f9c2b41

fixed license

Package-Manager: portage-2.2.14

---
 sci-biology/bcftools/ChangeLog           | 3 +++
 sci-biology/bcftools/bcftools-1.1.ebuild | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/sci-biology/bcftools/ChangeLog b/sci-biology/bcftools/ChangeLog
index 4e0a781..fc2086f 100644
--- a/sci-biology/bcftools/ChangeLog
+++ b/sci-biology/bcftools/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  15 Jan 2015; Christoph Junghans <ottxor@gentoo.org> bcftools-1.1.ebuild:
+  fixed license
+
 *bcftools-1.1 (14 Jan 2015)
 
   14 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>

diff --git a/sci-biology/bcftools/bcftools-1.1.ebuild b/sci-biology/bcftools/bcftools-1.1.ebuild
index e3f446f..7303278 100644
--- a/sci-biology/bcftools/bcftools-1.1.ebuild
+++ b/sci-biology/bcftools/bcftools-1.1.ebuild
@@ -8,7 +8,7 @@ DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
 HOMEPAGE="http://www.htslib.org/bcftools_release_notes"
 SRC_URI="http://sourceforge.net/projects/samtools/files/samtools/1.1/bcftools-1.1.tar.bz2"
 
-LICENSE="MIT-GRL"
+LICENSE="MIT"
 SLOT="0"
 KEYWORDS="~amd64"
 IUSE=""


^ permalink raw reply related	[flat|nested] 10+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/bcftools/
@ 2015-03-02 22:36 Martin Mokrejs
  0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2015-03-02 22:36 UTC (permalink / raw
  To: gentoo-commits

commit:     adb85a2fa58a75fd7a99a24f5fd3458420ba473f
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Mar  2 22:35:23 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Mar  2 22:35:23 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=adb85a2f

version bump, respect CC and CFLAGS

Package-Manager: portage-2.2.15

---
 sci-biology/bcftools/ChangeLog           |  6 ++++++
 sci-biology/bcftools/bcftools-1.1.ebuild | 26 --------------------------
 sci-biology/bcftools/bcftools-1.2.ebuild | 30 ++++++++++++++++++++++++++++++
 3 files changed, 36 insertions(+), 26 deletions(-)

diff --git a/sci-biology/bcftools/ChangeLog b/sci-biology/bcftools/ChangeLog
index fc2086f..f8f7b58 100644
--- a/sci-biology/bcftools/ChangeLog
+++ b/sci-biology/bcftools/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*bcftools-1.2 (02 Mar 2015)
+
+  02 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +bcftools-1.2.ebuild, -bcftools-1.1.ebuild:
+  version bump, respect CC and CFLAGS
+
   15 Jan 2015; Christoph Junghans <ottxor@gentoo.org> bcftools-1.1.ebuild:
   fixed license
 

diff --git a/sci-biology/bcftools/bcftools-1.1.ebuild b/sci-biology/bcftools/bcftools-1.1.ebuild
deleted file mode 100644
index 7303278..0000000
--- a/sci-biology/bcftools/bcftools-1.1.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=5
-
-DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
-HOMEPAGE="http://www.htslib.org/bcftools_release_notes"
-SRC_URI="http://sourceforge.net/projects/samtools/files/samtools/1.1/bcftools-1.1.tar.bz2"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND="sci-libs/htslib
-	dev-lang/perl"
-RDEPEND="${DEPEND}"
-
-src_prepare(){
-	sed -e 's#prefix      = /usr/local#prefix      = /usr#' \
-		-e 's@CFLAGS   = -g -Wall -Wc++-compat -O2@#CFLAGS   = -g -Wall -Wc++-compat -O2@' -i Makefile
-
-	sed -e 's#prefix      = /usr/local#prefix      = /usr#' \
-		-e 's@CFLAGS   = -g -Wall -Wc++-compat -O2@#CFLAGS   = -g -Wall -Wc++-compat -O2@' -i htslib-1.1/Makefile
-}

diff --git a/sci-biology/bcftools/bcftools-1.2.ebuild b/sci-biology/bcftools/bcftools-1.2.ebuild
new file mode 100644
index 0000000..3207a01
--- /dev/null
+++ b/sci-biology/bcftools/bcftools-1.2.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit toolchain-funcs
+
+DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
+HOMEPAGE="http://www.htslib.org"
+SRC_URI="https://github.com/samtools/bcftools/releases/download/"${PV}"/"${P}".tar.bz2"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND="sci-libs/htslib
+	dev-lang/perl"
+RDEPEND="${DEPEND}"
+
+src_prepare(){
+	sed -e "s@gcc@$(tc-getCC)@" \
+		-e 's#prefix      = /usr/local#prefix      = /usr#' \
+		-e "s@CFLAGS   = -g -Wall -Wc++-compat -O2@#CFLAGS   = ${CFLAGS}@" -i Makefile || die
+
+	sed -e "s@gcc@$(tc-getCC)@" \
+		-e 's#prefix      = /usr/local#prefix      = /usr#' \
+		-e "s@CFLAGS   = -g -Wall -O2@#CFLAGS   = ${CFLAGS}@" -i htslib-*/Makefile || die
+}


^ permalink raw reply related	[flat|nested] 10+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/bcftools/
@ 2016-06-23 13:51 Martin Mokrejs
  0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2016-06-23 13:51 UTC (permalink / raw
  To: gentoo-commits

commit:     e6e886f234239519eef70adefa92b3b21b79428c
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jun 23 13:51:37 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jun 23 13:51:37 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e6e886f2

sci-biology/bcftools:  add ${EPREFIX} in front of /usr to fix Gentoo:Prefix QA issue

Package-Manager: portage-2.2.28

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

diff --git a/sci-biology/bcftools/bcftools-1.2.ebuild b/sci-biology/bcftools/bcftools-1.2.ebuild
index 318dbc9..8c60b81 100644
--- a/sci-biology/bcftools/bcftools-1.2.ebuild
+++ b/sci-biology/bcftools/bcftools-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
 # $Id$
 
@@ -21,10 +21,10 @@ RDEPEND="${DEPEND}"
 
 src_prepare(){
 	sed -e "s@gcc@$(tc-getCC)@" \
-		-e 's#prefix      = /usr/local#prefix      = /usr#' \
+		-e 's#prefix      = /usr/local#prefix      = "${EPREFIX}"/usr#' \
 		-e "s@CFLAGS   = -g -Wall -Wc++-compat -O2@#CFLAGS   = ${CFLAGS}@" -i Makefile || die
 
 	sed -e "s@gcc@$(tc-getCC)@" \
-		-e 's#prefix      = /usr/local#prefix      = /usr#' \
+		-e 's#prefix      = /usr/local#prefix      = "${EPREFIX}"/usr#' \
 		-e "s@CFLAGS   = -g -Wall -O2@#CFLAGS   = ${CFLAGS}@" -i htslib-*/Makefile || die
 }


^ permalink raw reply related	[flat|nested] 10+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/bcftools/
@ 2017-02-16 22:16 Martin Mokrejs
  0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2017-02-16 22:16 UTC (permalink / raw
  To: gentoo-commits

commit:     566c68eafce8f41c79f482a701fc93822cd5b539
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Feb 16 22:15:44 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Feb 16 22:15:44 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=566c68ea

sci-biology/bcftools: version bump; removing htslib from DEPEND until we unbundle local copy

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/bcftools/{bcftools-1.2.ebuild => bcftools-1.3.1.ebuild} | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/sci-biology/bcftools/bcftools-1.2.ebuild b/sci-biology/bcftools/bcftools-1.3.1.ebuild
similarity index 83%
rename from sci-biology/bcftools/bcftools-1.2.ebuild
rename to sci-biology/bcftools/bcftools-1.3.1.ebuild
index 8c60b81c4..c5a8e646a 100644
--- a/sci-biology/bcftools/bcftools-1.2.ebuild
+++ b/sci-biology/bcftools/bcftools-1.3.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -15,8 +15,8 @@ SLOT="0"
 KEYWORDS="~amd64"
 IUSE=""
 
-DEPEND="sci-libs/htslib
-	dev-lang/perl"
+# compiles bundled sci-libs/htslib-"${PV}" as a static library and links it into binaries
+DEPEND="dev-lang/perl"
 RDEPEND="${DEPEND}"
 
 src_prepare(){


^ permalink raw reply related	[flat|nested] 10+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/bcftools/
@ 2017-04-30 13:31 Martin Mokrejs
  0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2017-04-30 13:31 UTC (permalink / raw
  To: gentoo-commits

commit:     1aa92f582501092acc6789f0fe818856def206f0
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Apr 30 13:31:11 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Apr 30 13:31:11 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=1aa92f58

sci-biology/bcftools: version bump

Compiles its own static build of htslib-1.4

Package-Manager: Portage-2.3.5, Repoman-2.3.2

 sci-biology/bcftools/bcftools-1.4.ebuild | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/sci-biology/bcftools/bcftools-1.4.ebuild b/sci-biology/bcftools/bcftools-1.4.ebuild
new file mode 100644
index 000000000..b194609b6
--- /dev/null
+++ b/sci-biology/bcftools/bcftools-1.4.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+inherit toolchain-funcs
+
+DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
+HOMEPAGE="http://www.htslib.org"
+SRC_URI="https://github.com/samtools/bcftools/releases/download/"${PV}"/"${P}".tar.bz2"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+# compiles bundled sci-libs/htslib-"${PV}" as a static library and links it into binaries
+DEPEND="dev-lang/perl"
+RDEPEND="${DEPEND}"
+
+src_prepare(){
+	sed -e "s@gcc@$(tc-getCC)@" \
+		-e 's#prefix      = /usr/local#prefix      = "${EPREFIX}"/usr#' \
+		-e "s@CFLAGS   = -g -Wall -Wc++-compat -O2@#CFLAGS   = ${CFLAGS}@" -i Makefile || die
+
+	sed -e "s@gcc@$(tc-getCC)@" \
+		-e 's#prefix      = /usr/local#prefix      = "${EPREFIX}"/usr#' \
+		-e "s@CFLAGS   = -g -Wall -O2@#CFLAGS   = ${CFLAGS}@" -i htslib-*/Makefile || die
+}


^ permalink raw reply related	[flat|nested] 10+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/bcftools/
@ 2017-07-28 20:05 Martin Mokrejs
  0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2017-07-28 20:05 UTC (permalink / raw
  To: gentoo-commits

commit:     7d318bbea490d8786ab6336b355529b08df8ee38
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jul 20 20:14:43 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=7d318bbe

sci-biology/bcftools: version bump

This should be kept unmasked as it uses bundled static lib of htslib-1.5
so practically avoid dependency on sci-libs/htslib-1.5.

Package-Manager: Portage-2.3.6, Repoman-2.3.2

 sci-biology/bcftools/bcftools-1.5.ebuild | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/sci-biology/bcftools/bcftools-1.5.ebuild b/sci-biology/bcftools/bcftools-1.5.ebuild
new file mode 100644
index 000000000..b194609b6
--- /dev/null
+++ b/sci-biology/bcftools/bcftools-1.5.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+inherit toolchain-funcs
+
+DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
+HOMEPAGE="http://www.htslib.org"
+SRC_URI="https://github.com/samtools/bcftools/releases/download/"${PV}"/"${P}".tar.bz2"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+# compiles bundled sci-libs/htslib-"${PV}" as a static library and links it into binaries
+DEPEND="dev-lang/perl"
+RDEPEND="${DEPEND}"
+
+src_prepare(){
+	sed -e "s@gcc@$(tc-getCC)@" \
+		-e 's#prefix      = /usr/local#prefix      = "${EPREFIX}"/usr#' \
+		-e "s@CFLAGS   = -g -Wall -Wc++-compat -O2@#CFLAGS   = ${CFLAGS}@" -i Makefile || die
+
+	sed -e "s@gcc@$(tc-getCC)@" \
+		-e 's#prefix      = /usr/local#prefix      = "${EPREFIX}"/usr#' \
+		-e "s@CFLAGS   = -g -Wall -O2@#CFLAGS   = ${CFLAGS}@" -i htslib-*/Makefile || die
+}


^ permalink raw reply related	[flat|nested] 10+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/bcftools/
@ 2017-09-02 12:46 David Seifert
  0 siblings, 0 replies; 10+ messages in thread
From: David Seifert @ 2017-09-02 12:46 UTC (permalink / raw
  To: gentoo-commits

commit:     c7d12eab1de43f052d778980e5d6b8bc016d9141
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Sep  2 12:45:45 2017 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Sep  2 12:45:45 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c7d12eab

sci-biology/bcftools: Remove old

 sci-biology/bcftools/bcftools-1.3.1.ebuild | 29 -----------------------------
 sci-biology/bcftools/bcftools-1.4.ebuild   | 29 -----------------------------
 sci-biology/bcftools/bcftools-1.5.ebuild   | 29 -----------------------------
 sci-biology/bcftools/metadata.xml          | 15 ---------------
 4 files changed, 102 deletions(-)

diff --git a/sci-biology/bcftools/bcftools-1.3.1.ebuild b/sci-biology/bcftools/bcftools-1.3.1.ebuild
deleted file mode 100644
index b194609b6..000000000
--- a/sci-biology/bcftools/bcftools-1.3.1.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit toolchain-funcs
-
-DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
-HOMEPAGE="http://www.htslib.org"
-SRC_URI="https://github.com/samtools/bcftools/releases/download/"${PV}"/"${P}".tar.bz2"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-# compiles bundled sci-libs/htslib-"${PV}" as a static library and links it into binaries
-DEPEND="dev-lang/perl"
-RDEPEND="${DEPEND}"
-
-src_prepare(){
-	sed -e "s@gcc@$(tc-getCC)@" \
-		-e 's#prefix      = /usr/local#prefix      = "${EPREFIX}"/usr#' \
-		-e "s@CFLAGS   = -g -Wall -Wc++-compat -O2@#CFLAGS   = ${CFLAGS}@" -i Makefile || die
-
-	sed -e "s@gcc@$(tc-getCC)@" \
-		-e 's#prefix      = /usr/local#prefix      = "${EPREFIX}"/usr#' \
-		-e "s@CFLAGS   = -g -Wall -O2@#CFLAGS   = ${CFLAGS}@" -i htslib-*/Makefile || die
-}

diff --git a/sci-biology/bcftools/bcftools-1.4.ebuild b/sci-biology/bcftools/bcftools-1.4.ebuild
deleted file mode 100644
index b194609b6..000000000
--- a/sci-biology/bcftools/bcftools-1.4.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit toolchain-funcs
-
-DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
-HOMEPAGE="http://www.htslib.org"
-SRC_URI="https://github.com/samtools/bcftools/releases/download/"${PV}"/"${P}".tar.bz2"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-# compiles bundled sci-libs/htslib-"${PV}" as a static library and links it into binaries
-DEPEND="dev-lang/perl"
-RDEPEND="${DEPEND}"
-
-src_prepare(){
-	sed -e "s@gcc@$(tc-getCC)@" \
-		-e 's#prefix      = /usr/local#prefix      = "${EPREFIX}"/usr#' \
-		-e "s@CFLAGS   = -g -Wall -Wc++-compat -O2@#CFLAGS   = ${CFLAGS}@" -i Makefile || die
-
-	sed -e "s@gcc@$(tc-getCC)@" \
-		-e 's#prefix      = /usr/local#prefix      = "${EPREFIX}"/usr#' \
-		-e "s@CFLAGS   = -g -Wall -O2@#CFLAGS   = ${CFLAGS}@" -i htslib-*/Makefile || die
-}

diff --git a/sci-biology/bcftools/bcftools-1.5.ebuild b/sci-biology/bcftools/bcftools-1.5.ebuild
deleted file mode 100644
index b194609b6..000000000
--- a/sci-biology/bcftools/bcftools-1.5.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit toolchain-funcs
-
-DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
-HOMEPAGE="http://www.htslib.org"
-SRC_URI="https://github.com/samtools/bcftools/releases/download/"${PV}"/"${P}".tar.bz2"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-# compiles bundled sci-libs/htslib-"${PV}" as a static library and links it into binaries
-DEPEND="dev-lang/perl"
-RDEPEND="${DEPEND}"
-
-src_prepare(){
-	sed -e "s@gcc@$(tc-getCC)@" \
-		-e 's#prefix      = /usr/local#prefix      = "${EPREFIX}"/usr#' \
-		-e "s@CFLAGS   = -g -Wall -Wc++-compat -O2@#CFLAGS   = ${CFLAGS}@" -i Makefile || die
-
-	sed -e "s@gcc@$(tc-getCC)@" \
-		-e 's#prefix      = /usr/local#prefix      = "${EPREFIX}"/usr#' \
-		-e "s@CFLAGS   = -g -Wall -O2@#CFLAGS   = ${CFLAGS}@" -i htslib-*/Makefile || die
-}

diff --git a/sci-biology/bcftools/metadata.xml b/sci-biology/bcftools/metadata.xml
deleted file mode 100644
index d65c87aa3..000000000
--- a/sci-biology/bcftools/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="person">
-    <email>mmokrejs@fold.natur.cuni.cz</email>
-    <name>Martin Mokrejs</name>
-  </maintainer>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="github">samtools/bcftools</remote-id>
-  </upstream>
-</pkgmetadata>


^ permalink raw reply related	[flat|nested] 10+ messages in thread

end of thread, other threads:[~2017-09-02 12:46 UTC | newest]

Thread overview: 10+ messages (download: mbox.gz follow: Atom feed
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2015-01-15 15:57 [gentoo-commits] proj/sci:master commit in: sci-biology/bcftools/ Christoph Junghans
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2017-09-02 12:46 David Seifert
2017-07-28 20:05 Martin Mokrejs
2017-04-30 13:31 Martin Mokrejs
2017-02-16 22:16 Martin Mokrejs
2016-06-23 13:51 Martin Mokrejs
2015-03-02 22:36 Martin Mokrejs
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