[gentoo-commits] proj/sci:master commit in: sci-biology/biobambam2/
commit: d278f615110371626a79ce731cdfb4903fce4417
Author: Andrew Ammerlaan riseup net>
AuthorDate: Mon Feb 1 10:11:38 2021 +
Commit: Andrew Ammerlaan riseup net>
CommitDate: Mon Feb 1 10:11:38 2021 +
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 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}"
[gentoo-commits] proj/sci:master commit in: sci-biology/biobambam2/
commit: 806eb48686efe82aa2ab3aa8409337feb6d7ba71
Author: Horea Christian chymera eu>
AuthorDate: Mon Sep 28 07:26:48 2020 +
Commit: Horea Christian gmail com>
CommitDate: Mon Sep 28 07:26:48 2020 +
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 chymera.eu>
sci-biology/biobambam2/biobambam2-2.0.146.ebuild | 6 ++
sci-biology/biobambam2/biobambam2-2.0.89.ebuild | 6 ++
sci-biology/biobambam2/biobambam2-.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-.ebuild
b/sci-biology/biobambam2/biobambam2-.ebuild
index 59774ca56..bc73dcb65 100644
--- a/sci-biology/biobambam2/biobambam2-.ebuild
+++ b/sci-biology/biobambam2/biobambam2-.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="${DEPEND}"
src_prepare() {
[gentoo-commits] proj/sci:master commit in: sci-biology/biobambam2/
commit: 562893ad174f0517f140907217e55efaf802b6ca
Author: Horea Christian chymera eu>
AuthorDate: Mon Sep 28 07:31:20 2020 +
Commit: Horea Christian gmail com>
CommitDate: Mon Sep 28 07:31:20 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=562893ad
sci-biology/biobambam2: rm old version and dependency version constraint
Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Horea Christian chymera.eu>
sci-biology/biobambam2/biobambam2-2.0.146.ebuild | 2 +-
sci-biology/biobambam2/biobambam2-2.0.89.ebuild | 25
sci-biology/biobambam2/biobambam2-.ebuild| 2 +-
3 files changed, 2 insertions(+), 27 deletions(-)
diff --git a/sci-biology/biobambam2/biobambam2-2.0.146.ebuild
b/sci-biology/biobambam2/biobambam2-2.0.146.ebuild
index a9c27b1cc..fc92d9f84 100644
--- a/sci-biology/biobambam2/biobambam2-2.0.146.ebuild
+++ b/sci-biology/biobambam2/biobambam2-2.0.146.ebuild
@@ -17,7 +17,7 @@ SLOT="0"
KEYWORDS=""
IUSE=""
-DEPEND=">=sci-libs/libmaus2-2.0.683"
+DEPEND="sci-libs/libmaus2"
RDEPEND="${DEPEND}"
S="${WORKDIR}/${P}-release-${release_data}"
diff --git a/sci-biology/biobambam2/biobambam2-2.0.89.ebuild
b/sci-biology/biobambam2/biobambam2-2.0.89.ebuild
deleted file mode 100644
index 391137136..0
--- a/sci-biology/biobambam2/biobambam2-2.0.89.ebuild
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit autotools
-
-DESCRIPTION="Tools for bam file processing (libmaus2)"
-HOMEPAGE="https://gitlab.com/german.tischler/biobambam2
- https://github.com/gt1/biobambam2";
-SRC_URI="https://github.com/gt1/biobambam2/archive/2.0.89-release-20180518145034.tar.gz";
-
-LICENSE="GPL-3 MIT"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND=">=sci-libs/libmaus2-2.0.489"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/biobambam2-2.0.89-release-20180518145034
-
-src_configure(){
- econf --with-libmaus2="${EPREFIX}"
-}
diff --git a/sci-biology/biobambam2/biobambam2-.ebuild
b/sci-biology/biobambam2/biobambam2-.ebuild
index bc73dcb65..69f3ea31c 100644
--- a/sci-biology/biobambam2/biobambam2-.ebuild
+++ b/sci-biology/biobambam2/biobambam2-.ebuild
@@ -15,7 +15,7 @@ SLOT="0"
KEYWORDS=""
IUSE=""
-DEPEND=">=sci-libs/libmaus2-2.0.555"
+DEPEND="sci-libs/libmaus2"
RDEPEND="${DEPEND}"
src_prepare() {
[gentoo-commits] proj/sci:master commit in: sci-biology/biobambam2/
commit: 5b51e6e70104d94d1a287add2206c31eca040da2
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Mon Dec 30 15:33:25 2019 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Mon Dec 30 15:33:25 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=5b51e6e7
sci-biology/biobambam2: version bump to 2.0.146
Package-Manager: Portage-2.3.75, Repoman-2.3.17
Signed-off-by: Martin Mokrejs fold.natur.cuni.cz>
sci-biology/biobambam2/biobambam2-2.0.146.ebuild | 29
1 file changed, 29 insertions(+)
diff --git a/sci-biology/biobambam2/biobambam2-2.0.146.ebuild
b/sci-biology/biobambam2/biobambam2-2.0.146.ebuild
new file mode 100644
index 0..1921fe3b7
--- /dev/null
+++ b/sci-biology/biobambam2/biobambam2-2.0.146.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit autotools
+
+release_data="20191030105216"
+
+DESCRIPTION="Tools for bam file processing (libmaus2)"
+HOMEPAGE="https://gitlab.com/german.tischler/biobambam2
+ https://github.com/gt1/biobambam2";
+SRC_URI="https://gitlab.com/german.tischler/${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/
commit: c136ed4c31ad6688ff68b7f14c8b56f5f8d2504c
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Tue Jan 22 15:35:05 2019 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Tue Jan 22 15:35:05 2019 +
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 fold.natur.cuni.cz>
sci-biology/biobambam2/biobambam2-2.0.89.ebuild | 5 +++--
sci-biology/biobambam2/biobambam2-.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-.ebuild
b/sci-biology/biobambam2/biobambam2-.ebuild
index e2fc6946a..59774ca56 100644
--- a/sci-biology/biobambam2/biobambam2-.ebuild
+++ b/sci-biology/biobambam2/biobambam2-.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="${DEPEND}"
src_prepare() {
[gentoo-commits] proj/sci:master commit in: sci-biology/biobambam2/
commit: 34a0a687d94ea4c3539d81b66558cc816c83cd71
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Fri Dec 14 11:43:36 2018 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Fri Dec 14 11:43:36 2018 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=34a0a687
sci-biology/biobambam2: bring in a release but needs libmaus2 unmasked
Package-Manager: Portage-2.3.52, Repoman-2.3.12
Signed-off-by: Martin Mokrejs fold.natur.cuni.cz>
.../{biobambam2-.ebuild => biobambam2-2.0.89.ebuild} | 15 ++-
sci-biology/biobambam2/biobambam2-.ebuild | 4 ++--
2 files changed, 8 insertions(+), 11 deletions(-)
diff --git a/sci-biology/biobambam2/biobambam2-.ebuild
b/sci-biology/biobambam2/biobambam2-2.0.89.ebuild
similarity index 58%
copy from sci-biology/biobambam2/biobambam2-.ebuild
copy to sci-biology/biobambam2/biobambam2-2.0.89.ebuild
index 8ddae8f97..f4d9679eb 100644
--- a/sci-biology/biobambam2/biobambam2-.ebuild
+++ b/sci-biology/biobambam2/biobambam2-2.0.89.ebuild
@@ -1,13 +1,13 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
-inherit git-r3 autotools
+inherit autotools
DESCRIPTION="Tools for bam file processing (libmaus2)"
HOMEPAGE="https://github.com/gt1/biobambam2";
-EGIT_REPO_URI="https://github.com/gt1/biobambam2.git";
+SRC_URI="https://github.com/gt1/biobambam2/archive/2.0.89-release-20180518145034.tar.gz";
LICENSE="GPL-3 MIT"
SLOT="0"
@@ -16,13 +16,10 @@ IUSE=""
DEPEND="
!sci-biology/biobambam
- >=sci-libs/libmaus2-2.0.225"
+ >=sci-libs/libmaus2-2.0.489"
RDEPEND="${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-.ebuild
b/sci-biology/biobambam2/biobambam2-.ebuild
index 8ddae8f97..e2fc6946a 100644
--- a/sci-biology/biobambam2/biobambam2-.ebuild
+++ b/sci-biology/biobambam2/biobambam2-.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/
commit: da6238be4b7a9b14122d501670264c61723f8235
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Fri Jul 15 10:08:38 2016 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Fri Jul 15 10:08:38 2016 +
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-.ebuild | 30 +++
sci-biology/biobambam2/metadata.xml | 21 +++
2 files changed, 51 insertions(+)
diff --git a/sci-biology/biobambam2/biobambam2-.ebuild
b/sci-biology/biobambam2/biobambam2-.ebuild
new file mode 100644
index 000..80e7206
--- /dev/null
+++ b/sci-biology/biobambam2/biobambam2-.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 000..a3e55a4
--- /dev/null
+++ b/sci-biology/biobambam2/metadata.xml
@@ -0,0 +1,21 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+
+sci-biol...@gentoo.org
+Gentoo Biology Project
+
+
+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
+
+
+gt1/biobambam
+
+
