[gentoo-commits] proj/sci:master commit in: sci-biology/biobambam2/

[gentoo-commits] proj/sci:master commit in: sci-biology/biobambam2/

[Martin Mokrejs]

commit:     da6238be4b7a9b14122d501670264c61723f8235
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jul 15 10:08:38 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jul 15 10:08:38 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=da6238be

sci-biology/biobambam2: an updated package of sci-biology/biobambam, more ebuild tweaks

Package-Manager: portage-2.2.28

 sci-biology/biobambam2/biobambam2-9999.ebuild | 30 +++++++++++++++++++++++++++
 sci-biology/biobambam2/metadata.xml           | 21 +++++++++++++++++++
 2 files changed, 51 insertions(+)

diff --git a/sci-biology/biobambam2/biobambam2-9999.ebuild b/sci-biology/biobambam2/biobambam2-9999.ebuild
new file mode 100644
index 0000000..80e7206
--- /dev/null
+++ b/sci-biology/biobambam2/biobambam2-9999.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit git-r3 autotools
+
+DESCRIPTION="Tools for bam file processing (libmaus2)"
+HOMEPAGE="https://github.com/gt1/biobambam2"
+EGIT_REPO_URI="https://github.com/gt1/biobambam2.git"
+
+LICENSE="GPL-3 MIT"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="
+	!sci-biology/biobambam
+	>=sci-libs/libmaus2-2.0.225"
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+	eautoreconf
+	eapply_user
+}
+
+src_configure(){
+	econf --with-libmaus2="${EPREFIX}"
+}

diff --git a/sci-biology/biobambam2/metadata.xml b/sci-biology/biobambam2/metadata.xml
new file mode 100644
index 0000000..a3e55a4
--- /dev/null
+++ b/sci-biology/biobambam2/metadata.xml
@@ -0,0 +1,21 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+  <longdescription lang="en">
+This package contains some tools for processing BAM files including
+
+bamcollate2: reads BAM and writes BAM reordered such that alignment or collated by query name
+bammarkduplicates: reads BAM and writes BAM with duplicate alignments marked using the BAM flags field
+bammaskflags: reads BAM and writes BAM while masking (removing) bits from the flags column
+bamrecompress: reads BAM and writes BAM with a defined compression setting. This tool is capable of multi-threading.
+bamsort: reads BAM and writes BAM resorted by coordinates or query name
+bamtofastq: reads BAM and writes FastQ; output can be collated or uncollated by query name
+</longdescription>
+  <upstream>
+    <remote-id type="github">gt1/biobambam</remote-id>
+  </upstream>
+</pkgmetadata>

[gentoo-commits] proj/sci:master commit in: sci-biology/biobambam2/

[Martin Mokrejs]

commit:     34a0a687d94ea4c3539d81b66558cc816c83cd71
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Dec 14 11:43:36 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Dec 14 11:43:36 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=34a0a687

sci-biology/biobambam2: bring in a release but needs libmaus2 unmasked

Package-Manager: Portage-2.3.52, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>

 .../{biobambam2-9999.ebuild => biobambam2-2.0.89.ebuild}  | 15 ++++++---------
 sci-biology/biobambam2/biobambam2-9999.ebuild             |  4 ++--
 2 files changed, 8 insertions(+), 11 deletions(-)

diff --git a/sci-biology/biobambam2/biobambam2-9999.ebuild b/sci-biology/biobambam2/biobambam2-2.0.89.ebuild
similarity index 58%
copy from sci-biology/biobambam2/biobambam2-9999.ebuild
copy to sci-biology/biobambam2/biobambam2-2.0.89.ebuild
index 8ddae8f97..f4d9679eb 100644
--- a/sci-biology/biobambam2/biobambam2-9999.ebuild
+++ b/sci-biology/biobambam2/biobambam2-2.0.89.ebuild
@@ -1,13 +1,13 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-inherit git-r3 autotools
+inherit autotools
 
 DESCRIPTION="Tools for bam file processing (libmaus2)"
 HOMEPAGE="https://github.com/gt1/biobambam2"
-EGIT_REPO_URI="https://github.com/gt1/biobambam2.git"
+SRC_URI="https://github.com/gt1/biobambam2/archive/2.0.89-release-20180518145034.tar.gz"
 
 LICENSE="GPL-3 MIT"
 SLOT="0"
@@ -16,13 +16,10 @@ IUSE=""
 
 DEPEND="
 	!sci-biology/biobambam
-	>=sci-libs/libmaus2-2.0.225"
+	>=sci-libs/libmaus2-2.0.489"
 RDEPEND="${DEPEND}"
 
-src_prepare() {
-	eautoreconf
-	eapply_user
-}
+S="${WORKDIR}"/biobambam2-2.0.89-release-20180518145034
 
 src_configure(){
 	econf --with-libmaus2="${EPREFIX}"

diff --git a/sci-biology/biobambam2/biobambam2-9999.ebuild b/sci-biology/biobambam2/biobambam2-9999.ebuild
index 8ddae8f97..e2fc6946a 100644
--- a/sci-biology/biobambam2/biobambam2-9999.ebuild
+++ b/sci-biology/biobambam2/biobambam2-9999.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 inherit git-r3 autotools
 

[gentoo-commits] proj/sci:master commit in: sci-biology/biobambam2/

[Martin Mokrejs]

commit:     c136ed4c31ad6688ff68b7f14c8b56f5f8d2504c
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jan 22 15:35:05 2019 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jan 22 15:35:05 2019 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c136ed4c

sci-biology/biobambam2: upstream moved from github to gitlab

Package-Manager: Portage-2.3.56, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>

 sci-biology/biobambam2/biobambam2-2.0.89.ebuild |  5 +++--
 sci-biology/biobambam2/biobambam2-9999.ebuild   | 11 ++++++-----
 2 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/sci-biology/biobambam2/biobambam2-2.0.89.ebuild b/sci-biology/biobambam2/biobambam2-2.0.89.ebuild
index f4d9679eb..3ebc9cae5 100644
--- a/sci-biology/biobambam2/biobambam2-2.0.89.ebuild
+++ b/sci-biology/biobambam2/biobambam2-2.0.89.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Authors
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -6,7 +6,8 @@ EAPI=7
 inherit autotools
 
 DESCRIPTION="Tools for bam file processing (libmaus2)"
-HOMEPAGE="https://github.com/gt1/biobambam2"
+HOMEPAGE="https://gitlab.com/german.tischler/biobambam2
+	https://github.com/gt1/biobambam2"
 SRC_URI="https://github.com/gt1/biobambam2/archive/2.0.89-release-20180518145034.tar.gz"
 
 LICENSE="GPL-3 MIT"

diff --git a/sci-biology/biobambam2/biobambam2-9999.ebuild b/sci-biology/biobambam2/biobambam2-9999.ebuild
index e2fc6946a..59774ca56 100644
--- a/sci-biology/biobambam2/biobambam2-9999.ebuild
+++ b/sci-biology/biobambam2/biobambam2-9999.ebuild
@@ -1,13 +1,14 @@
-# Copyright 1999-2018 Gentoo Authors
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
 
 inherit git-r3 autotools
 
-DESCRIPTION="Tools for bam file processing (libmaus2)"
-HOMEPAGE="https://github.com/gt1/biobambam2"
-EGIT_REPO_URI="https://github.com/gt1/biobambam2.git"
+DESCRIPTION="Tools for bam file processing (using libmaus2)"
+HOMEPAGE="https://gitlab.com/german.tischler/biobambam2
+	https://github.com/gt1/biobambam2"
+EGIT_REPO_URI="https://gitlab.com/german.tischler/biobambam2"
 
 LICENSE="GPL-3 MIT"
 SLOT="0"
@@ -16,7 +17,7 @@ IUSE=""
 
 DEPEND="
 	!sci-biology/biobambam
-	>=sci-libs/libmaus2-2.0.225"
+	>=sci-libs/libmaus2-2.0.555"
 RDEPEND="${DEPEND}"
 
 src_prepare() {

[gentoo-commits] proj/sci:master commit in: sci-biology/biobambam2/

[Martin Mokrejs]

commit:     5b51e6e70104d94d1a287add2206c31eca040da2
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Dec 30 15:33:25 2019 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Dec 30 15:33:25 2019 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=5b51e6e7

sci-biology/biobambam2: version bump to 2.0.146

Package-Manager: Portage-2.3.75, Repoman-2.3.17
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>

 sci-biology/biobambam2/biobambam2-2.0.146.ebuild | 29 ++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/sci-biology/biobambam2/biobambam2-2.0.146.ebuild b/sci-biology/biobambam2/biobambam2-2.0.146.ebuild
new file mode 100644
index 000000000..1921fe3b7
--- /dev/null
+++ b/sci-biology/biobambam2/biobambam2-2.0.146.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit autotools
+
+release_data="20191030105216"
+
+DESCRIPTION="Tools for bam file processing (libmaus2)"
+HOMEPAGE="https://gitlab.com/german.tischler/biobambam2
+	https://github.com/gt1/biobambam2"
+SRC_URI="https://gitlab.com/german.tischler/${PN}/-/archive/${PV}-release-${release_data}/${P}-release-${release_data}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3 MIT"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="
+	!sci-biology/biobambam
+	>=sci-libs/libmaus2-2.0.683"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/${P}-release-${release_data}"
+
+src_configure(){
+	econf --with-libmaus2="${EPREFIX}"
+}

[gentoo-commits] proj/sci:master commit in: sci-biology/biobambam2/

[Horea Christian]

commit:     806eb48686efe82aa2ab3aa8409337feb6d7ba71
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Mon Sep 28 07:26:48 2020 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Mon Sep 28 07:26:48 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=806eb486

sci-biology/biobambam2: updated dependencies

Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 sci-biology/biobambam2/biobambam2-2.0.146.ebuild | 6 ++----
 sci-biology/biobambam2/biobambam2-2.0.89.ebuild  | 6 ++----
 sci-biology/biobambam2/biobambam2-9999.ebuild    | 6 ++----
 3 files changed, 6 insertions(+), 12 deletions(-)

diff --git a/sci-biology/biobambam2/biobambam2-2.0.146.ebuild b/sci-biology/biobambam2/biobambam2-2.0.146.ebuild
index 1921fe3b7..a9c27b1cc 100644
--- a/sci-biology/biobambam2/biobambam2-2.0.146.ebuild
+++ b/sci-biology/biobambam2/biobambam2-2.0.146.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -17,9 +17,7 @@ SLOT="0"
 KEYWORDS=""
 IUSE=""
 
-DEPEND="
-	!sci-biology/biobambam
-	>=sci-libs/libmaus2-2.0.683"
+DEPEND=">=sci-libs/libmaus2-2.0.683"
 RDEPEND="${DEPEND}"
 
 S="${WORKDIR}/${P}-release-${release_data}"

diff --git a/sci-biology/biobambam2/biobambam2-2.0.89.ebuild b/sci-biology/biobambam2/biobambam2-2.0.89.ebuild
index 3ebc9cae5..391137136 100644
--- a/sci-biology/biobambam2/biobambam2-2.0.89.ebuild
+++ b/sci-biology/biobambam2/biobambam2-2.0.89.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -15,9 +15,7 @@ SLOT="0"
 KEYWORDS=""
 IUSE=""
 
-DEPEND="
-	!sci-biology/biobambam
-	>=sci-libs/libmaus2-2.0.489"
+DEPEND=">=sci-libs/libmaus2-2.0.489"
 RDEPEND="${DEPEND}"
 
 S="${WORKDIR}"/biobambam2-2.0.89-release-20180518145034

diff --git a/sci-biology/biobambam2/biobambam2-9999.ebuild b/sci-biology/biobambam2/biobambam2-9999.ebuild
index 59774ca56..bc73dcb65 100644
--- a/sci-biology/biobambam2/biobambam2-9999.ebuild
+++ b/sci-biology/biobambam2/biobambam2-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -15,9 +15,7 @@ SLOT="0"
 KEYWORDS=""
 IUSE=""
 
-DEPEND="
-	!sci-biology/biobambam
-	>=sci-libs/libmaus2-2.0.555"
+DEPEND=">=sci-libs/libmaus2-2.0.555"
 RDEPEND="${DEPEND}"
 
 src_prepare() {

[gentoo-commits] proj/sci:master commit in: sci-biology/biobambam2/

[Horea Christian]

commit:     562893ad174f0517f140907217e55efaf802b6ca
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Mon Sep 28 07:31:20 2020 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Mon Sep 28 07:31:20 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=562893ad

sci-biology/biobambam2: rm old version and dependency version constraint

Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 sci-biology/biobambam2/biobambam2-2.0.146.ebuild |  2 +-
 sci-biology/biobambam2/biobambam2-2.0.89.ebuild  | 25 ------------------------
 sci-biology/biobambam2/biobambam2-9999.ebuild    |  2 +-
 3 files changed, 2 insertions(+), 27 deletions(-)

diff --git a/sci-biology/biobambam2/biobambam2-2.0.146.ebuild b/sci-biology/biobambam2/biobambam2-2.0.146.ebuild
index a9c27b1cc..fc92d9f84 100644
--- a/sci-biology/biobambam2/biobambam2-2.0.146.ebuild
+++ b/sci-biology/biobambam2/biobambam2-2.0.146.ebuild
@@ -17,7 +17,7 @@ SLOT="0"
 KEYWORDS=""
 IUSE=""
 
-DEPEND=">=sci-libs/libmaus2-2.0.683"
+DEPEND="sci-libs/libmaus2"
 RDEPEND="${DEPEND}"
 
 S="${WORKDIR}/${P}-release-${release_data}"

diff --git a/sci-biology/biobambam2/biobambam2-2.0.89.ebuild b/sci-biology/biobambam2/biobambam2-2.0.89.ebuild
deleted file mode 100644
index 391137136..000000000
--- a/sci-biology/biobambam2/biobambam2-2.0.89.ebuild
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit autotools
-
-DESCRIPTION="Tools for bam file processing (libmaus2)"
-HOMEPAGE="https://gitlab.com/german.tischler/biobambam2
-	https://github.com/gt1/biobambam2"
-SRC_URI="https://github.com/gt1/biobambam2/archive/2.0.89-release-20180518145034.tar.gz"
-
-LICENSE="GPL-3 MIT"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND=">=sci-libs/libmaus2-2.0.489"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/biobambam2-2.0.89-release-20180518145034
-
-src_configure(){
-	econf --with-libmaus2="${EPREFIX}"
-}

diff --git a/sci-biology/biobambam2/biobambam2-9999.ebuild b/sci-biology/biobambam2/biobambam2-9999.ebuild
index bc73dcb65..69f3ea31c 100644
--- a/sci-biology/biobambam2/biobambam2-9999.ebuild
+++ b/sci-biology/biobambam2/biobambam2-9999.ebuild
@@ -15,7 +15,7 @@ SLOT="0"
 KEYWORDS=""
 IUSE=""
 
-DEPEND=">=sci-libs/libmaus2-2.0.555"
+DEPEND="sci-libs/libmaus2"
 RDEPEND="${DEPEND}"
 
 src_prepare() {

[gentoo-commits] proj/sci:master commit in: sci-biology/biobambam2/

[Andrew Ammerlaan]

commit:     d278f615110371626a79ce731cdfb4903fce4417
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Feb  1 10:11:38 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Feb  1 10:11:38 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=d278f615

sci-biology/biobambam2: add keyword

works for me :D

Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/biobambam2/biobambam2-2.0.146.ebuild | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/sci-biology/biobambam2/biobambam2-2.0.146.ebuild b/sci-biology/biobambam2/biobambam2-2.0.146.ebuild
index fc92d9f84..4b1a7873d 100644
--- a/sci-biology/biobambam2/biobambam2-2.0.146.ebuild
+++ b/sci-biology/biobambam2/biobambam2-2.0.146.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
@@ -8,14 +8,12 @@ inherit autotools
 release_data="20191030105216"
 
 DESCRIPTION="Tools for bam file processing (libmaus2)"
-HOMEPAGE="https://gitlab.com/german.tischler/biobambam2
-	https://github.com/gt1/biobambam2"
+HOMEPAGE="https://gitlab.com/german.tischler/biobambam2"
 SRC_URI="https://gitlab.com/german.tischler/${PN}/-/archive/${PV}-release-${release_data}/${P}-release-${release_data}.tar.gz -> ${P}.tar.gz"
 
 LICENSE="GPL-3 MIT"
 SLOT="0"
-KEYWORDS=""
-IUSE=""
+KEYWORDS="~amd64"
 
 DEPEND="sci-libs/libmaus2"
 RDEPEND="${DEPEND}"