* [gentoo-commits] proj/sci:master commit in: sci-biology/BBmap/
@ 2017-04-03 15:52 Martin Mokrejs
0 siblings, 0 replies; 18+ messages in thread
From: Martin Mokrejs @ 2017-04-03 15:52 UTC (permalink / raw
To: gentoo-commits
commit: f9975865d2ac4175a005d3fd9a315263b07a66c1
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Apr 3 15:52:14 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Apr 3 15:52:14 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f9975865
sci-biology/BBmap: add ~x86 to KEYWORDS, version bump
Package-Manager: Portage-2.3.5, Repoman-2.3.1
sci-biology/BBmap/BBmap-34.97.ebuild | 2 +-
sci-biology/BBmap/BBmap-35.92.ebuild | 2 +-
sci-biology/BBmap/BBmap-36.02.ebuild | 2 +-
sci-biology/BBmap/BBmap-36.86.ebuild | 2 +-
sci-biology/BBmap/{BBmap-35.92.ebuild => BBmap-37.02.ebuild} | 2 +-
5 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/sci-biology/BBmap/BBmap-34.97.ebuild b/sci-biology/BBmap/BBmap-34.97.ebuild
index 7be2990a4..cf80ed6c8 100644
--- a/sci-biology/BBmap/BBmap-34.97.ebuild
+++ b/sci-biology/BBmap/BBmap-34.97.ebuild
@@ -11,7 +11,7 @@ SRC_URI="http://sourceforge.net/projects/bbmap/files/BBMap_"${PV}".tar.gz"
LICENSE="BSD"
SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS="~amd64 ~x86"
IUSE=""
DEPEND="
diff --git a/sci-biology/BBmap/BBmap-35.92.ebuild b/sci-biology/BBmap/BBmap-35.92.ebuild
index f26586885..d8d2042ce 100644
--- a/sci-biology/BBmap/BBmap-35.92.ebuild
+++ b/sci-biology/BBmap/BBmap-35.92.ebuild
@@ -11,7 +11,7 @@ SRC_URI="http://sourceforge.net/projects/bbmap/files/BBMap_"${PV}".tar.gz"
LICENSE="BSD"
SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS="~amd64 ~x86"
IUSE=""
DEPEND="
diff --git a/sci-biology/BBmap/BBmap-36.02.ebuild b/sci-biology/BBmap/BBmap-36.02.ebuild
index f26586885..d8d2042ce 100644
--- a/sci-biology/BBmap/BBmap-36.02.ebuild
+++ b/sci-biology/BBmap/BBmap-36.02.ebuild
@@ -11,7 +11,7 @@ SRC_URI="http://sourceforge.net/projects/bbmap/files/BBMap_"${PV}".tar.gz"
LICENSE="BSD"
SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS="~amd64 ~x86"
IUSE=""
DEPEND="
diff --git a/sci-biology/BBmap/BBmap-36.86.ebuild b/sci-biology/BBmap/BBmap-36.86.ebuild
index f26586885..d8d2042ce 100644
--- a/sci-biology/BBmap/BBmap-36.86.ebuild
+++ b/sci-biology/BBmap/BBmap-36.86.ebuild
@@ -11,7 +11,7 @@ SRC_URI="http://sourceforge.net/projects/bbmap/files/BBMap_"${PV}".tar.gz"
LICENSE="BSD"
SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS="~amd64 ~x86"
IUSE=""
DEPEND="
diff --git a/sci-biology/BBmap/BBmap-35.92.ebuild b/sci-biology/BBmap/BBmap-37.02.ebuild
similarity index 97%
copy from sci-biology/BBmap/BBmap-35.92.ebuild
copy to sci-biology/BBmap/BBmap-37.02.ebuild
index f26586885..d8d2042ce 100644
--- a/sci-biology/BBmap/BBmap-35.92.ebuild
+++ b/sci-biology/BBmap/BBmap-37.02.ebuild
@@ -11,7 +11,7 @@ SRC_URI="http://sourceforge.net/projects/bbmap/files/BBMap_"${PV}".tar.gz"
LICENSE="BSD"
SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS="~amd64 ~x86"
IUSE=""
DEPEND="
^ permalink raw reply related [flat|nested] 18+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/BBmap/
@ 2021-01-19 16:26 Andrew Ammerlaan
0 siblings, 0 replies; 18+ messages in thread
From: Andrew Ammerlaan @ 2021-01-19 16:26 UTC (permalink / raw
To: gentoo-commits
commit: 21c3dbb39084048f2d38dc531824cd57eab82a12
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 16:10:23 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 16:10:23 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=21c3dbb3
sci-biology/BBmap: set use default for openmpi
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/BBmap/BBmap-38.87.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/BBmap/BBmap-38.87.ebuild b/sci-biology/BBmap/BBmap-38.87.ebuild
index 06220b557..7e196a47d 100644
--- a/sci-biology/BBmap/BBmap-38.87.ebuild
+++ b/sci-biology/BBmap/BBmap-38.87.ebuild
@@ -14,7 +14,7 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
DEPEND="
- sys-cluster/openmpi[java]
+ sys-cluster/openmpi[java(-)]
>=virtual/jdk-1.7:*
dev-java/ant-core"
RDEPEND="${DEPEND}
^ permalink raw reply related [flat|nested] 18+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/BBmap/
@ 2017-11-21 14:54 Martin Mokrejs
0 siblings, 0 replies; 18+ messages in thread
From: Martin Mokrejs @ 2017-11-21 14:54 UTC (permalink / raw
To: gentoo-commits
commit: 260aefeda8cec93335beb1bb83e299aff7bc8612
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Nov 21 14:53:47 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Nov 21 14:53:47 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=260aefed
sci-biology/BBmap: version bump
Package-Manager: Portage-2.3.14, Repoman-2.3.6
sci-biology/BBmap/{BBmap-37.22.ebuild => BBmap-37.67.ebuild} | 0
1 file changed, 0 insertions(+), 0 deletions(-)
diff --git a/sci-biology/BBmap/BBmap-37.22.ebuild b/sci-biology/BBmap/BBmap-37.67.ebuild
similarity index 100%
rename from sci-biology/BBmap/BBmap-37.22.ebuild
rename to sci-biology/BBmap/BBmap-37.67.ebuild
^ permalink raw reply [flat|nested] 18+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/BBmap/
@ 2017-05-11 19:13 Martin Mokrejs
0 siblings, 0 replies; 18+ messages in thread
From: Martin Mokrejs @ 2017-05-11 19:13 UTC (permalink / raw
To: gentoo-commits
commit: 28addfe8bee35187068e3cf5ddf95fe91ad1132c
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu May 11 19:13:06 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu May 11 19:13:06 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=28addfe8
sci-biology/BBmap: version bump
Package-Manager: Portage-2.3.5, Repoman-2.3.2
sci-biology/BBmap/{BBmap-37.02.ebuild => BBmap-37.22.ebuild} | 0
1 file changed, 0 insertions(+), 0 deletions(-)
diff --git a/sci-biology/BBmap/BBmap-37.02.ebuild b/sci-biology/BBmap/BBmap-37.22.ebuild
similarity index 100%
rename from sci-biology/BBmap/BBmap-37.02.ebuild
rename to sci-biology/BBmap/BBmap-37.22.ebuild
^ permalink raw reply [flat|nested] 18+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/BBmap/
@ 2017-01-28 16:51 Martin Mokrejs
0 siblings, 0 replies; 18+ messages in thread
From: Martin Mokrejs @ 2017-01-28 16:51 UTC (permalink / raw
To: gentoo-commits
commit: 64a0c52245b6062bae5382c4776c99ef3194befe
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Jan 28 16:51:03 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Jan 28 16:51:03 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=64a0c522
sci-biology/BBmap: version bump
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/BBmap/BBmap-34.97.ebuild | 2 +-
sci-biology/BBmap/BBmap-35.92.ebuild | 2 +-
sci-biology/BBmap/BBmap-36.02.ebuild | 2 +-
sci-biology/BBmap/{BBmap-35.92.ebuild => BBmap-36.86.ebuild} | 2 +-
4 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/sci-biology/BBmap/BBmap-34.97.ebuild b/sci-biology/BBmap/BBmap-34.97.ebuild
index 10cdcb3..d2bad05 100644
--- a/sci-biology/BBmap/BBmap-34.97.ebuild
+++ b/sci-biology/BBmap/BBmap-34.97.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
# $Id$
diff --git a/sci-biology/BBmap/BBmap-35.92.ebuild b/sci-biology/BBmap/BBmap-35.92.ebuild
index fa463a3..8f8b0b3 100644
--- a/sci-biology/BBmap/BBmap-35.92.ebuild
+++ b/sci-biology/BBmap/BBmap-35.92.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
# $Id$
diff --git a/sci-biology/BBmap/BBmap-36.02.ebuild b/sci-biology/BBmap/BBmap-36.02.ebuild
index fa463a3..8f8b0b3 100644
--- a/sci-biology/BBmap/BBmap-36.02.ebuild
+++ b/sci-biology/BBmap/BBmap-36.02.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
# $Id$
diff --git a/sci-biology/BBmap/BBmap-35.92.ebuild b/sci-biology/BBmap/BBmap-36.86.ebuild
similarity index 96%
copy from sci-biology/BBmap/BBmap-35.92.ebuild
copy to sci-biology/BBmap/BBmap-36.86.ebuild
index fa463a3..8f8b0b3 100644
--- a/sci-biology/BBmap/BBmap-35.92.ebuild
+++ b/sci-biology/BBmap/BBmap-36.86.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
# $Id$
^ permalink raw reply related [flat|nested] 18+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/BBmap/
@ 2016-06-22 15:24 Martin Mokrejs
0 siblings, 0 replies; 18+ messages in thread
From: Martin Mokrejs @ 2016-06-22 15:24 UTC (permalink / raw
To: gentoo-commits
commit: 194ebd83e325f228abacc2f5cff6c9dc7fef5dff
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jun 22 15:23:51 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jun 22 15:23:51 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=194ebd83
sci-biology/BBmap: version bump
Package-Manager: portage-2.2.28
sci-biology/BBmap/BBmap-36.02.ebuild | 43 ++++++++++++++++++++++++++++++++++++
1 file changed, 43 insertions(+)
diff --git a/sci-biology/BBmap/BBmap-36.02.ebuild b/sci-biology/BBmap/BBmap-36.02.ebuild
new file mode 100644
index 0000000..fa463a3
--- /dev/null
+++ b/sci-biology/BBmap/BBmap-36.02.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="Short read aligner, K-mer-based error-correct and normalize, FASTA/Q tool"
+HOMEPAGE="http://sourceforge.net/projects/bbmap/"
+SRC_URI="http://sourceforge.net/projects/bbmap/files/BBMap_"${PV}".tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND="
+ sys-cluster/openmpi[java]
+ >=virtual/jdk-1.7:*
+ dev-java/ant-core"
+RDEPEND="${DEPEND}
+ >=virtual/jre-1.7:*"
+
+S="${WORKDIR}"/bbmap
+
+src_prepare(){
+ # fix the line in build.xml to point to mpi.jar location
+ # <property name="mpijar" location="/tmp/mpi.jar" ></property>
+ # see bug #542700
+ sed -e 's#/usr/common/usg/hpc/openmpi/gnu4.6/sge/1.8.1/ib_2.1-1.0.0/lib/mpi.jar#/usr/share/openmpi/lib/mpi.jar#' -i build.xml
+ sed -e 's#compiler="${jcompiler}" ##' -i build.xml
+}
+
+src_compile(){
+ ant dist || die
+}
+
+src_install(){
+ dobin *.sh
+ dodoc docs/readme.txt
+ java-pkg_dojar dist/lib/BBTools.jar
+}
^ permalink raw reply related [flat|nested] 18+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/BBmap/
@ 2016-05-20 21:28 Martin Mokrejs
0 siblings, 0 replies; 18+ messages in thread
From: Martin Mokrejs @ 2016-05-20 21:28 UTC (permalink / raw
To: gentoo-commits
commit: fa0f49dee8098b42a68f30e7671ab1a357cce229
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri May 20 21:28:32 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri May 20 21:28:32 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=fa0f49de
sci-biology/BBmap: version bump, shorten DESCRIPTION line
Package-Manager: portage-2.2.28
sci-biology/BBmap/BBmap-34.97.ebuild | 4 ++--
sci-biology/BBmap/{BBmap-35.85.ebuild => BBmap-35.92.ebuild} | 2 +-
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/BBmap/BBmap-34.97.ebuild b/sci-biology/BBmap/BBmap-34.97.ebuild
index 21fd42f..10cdcb3 100644
--- a/sci-biology/BBmap/BBmap-34.97.ebuild
+++ b/sci-biology/BBmap/BBmap-34.97.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
# $Id$
@@ -6,7 +6,7 @@ EAPI=5
inherit java-pkg-2 java-ant-2
-DESCRIPTION="Short read aligner, K-mer-based error-correction and normalization, FASTA/Q conversion"
+DESCRIPTION="Short read aligner, K-mer-based error-correct and normalize, FASTA/Q tool"
HOMEPAGE="http://sourceforge.net/projects/bbmap/"
SRC_URI="http://sourceforge.net/projects/bbmap/files/BBMap_"${PV}".tar.gz"
diff --git a/sci-biology/BBmap/BBmap-35.85.ebuild b/sci-biology/BBmap/BBmap-35.92.ebuild
similarity index 90%
rename from sci-biology/BBmap/BBmap-35.85.ebuild
rename to sci-biology/BBmap/BBmap-35.92.ebuild
index 86b138c..fa463a3 100644
--- a/sci-biology/BBmap/BBmap-35.85.ebuild
+++ b/sci-biology/BBmap/BBmap-35.92.ebuild
@@ -6,7 +6,7 @@ EAPI=5
inherit java-pkg-2 java-ant-2
-DESCRIPTION="Short read aligner, K-mer-based error-correction and normalization, FASTA/Q conversion"
+DESCRIPTION="Short read aligner, K-mer-based error-correct and normalize, FASTA/Q tool"
HOMEPAGE="http://sourceforge.net/projects/bbmap/"
SRC_URI="http://sourceforge.net/projects/bbmap/files/BBMap_"${PV}".tar.gz"
^ permalink raw reply related [flat|nested] 18+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/BBmap/
@ 2016-03-12 13:53 Martin Mokrejs
0 siblings, 0 replies; 18+ messages in thread
From: Martin Mokrejs @ 2016-03-12 13:53 UTC (permalink / raw
To: gentoo-commits
commit: ce4c591682dc3c3dbe35bfbb87170b52ca142efd
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Mar 12 13:50:06 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Mar 12 13:50:06 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ce4c5916
sci-biology/BBmap: version bump
Package-Manager: portage-2.2.26
sci-biology/BBmap/{BBmap-35.82.ebuild => BBmap-35.85.ebuild} | 0
1 file changed, 0 insertions(+), 0 deletions(-)
diff --git a/sci-biology/BBmap/BBmap-35.82.ebuild b/sci-biology/BBmap/BBmap-35.85.ebuild
similarity index 100%
rename from sci-biology/BBmap/BBmap-35.82.ebuild
rename to sci-biology/BBmap/BBmap-35.85.ebuild
^ permalink raw reply [flat|nested] 18+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/BBmap/
@ 2016-01-06 11:36 Martin Mokrejs
0 siblings, 0 replies; 18+ messages in thread
From: Martin Mokrejs @ 2016-01-06 11:36 UTC (permalink / raw
To: gentoo-commits
commit: 5d1f9491565c8263e298a351f83d00ba9215dc85
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jan 6 11:34:57 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jan 6 11:34:57 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=5d1f9491
sci-biology/BBmap: version bump
Package-Manager: portage-2.2.26
sci-biology/BBmap/{BBmap-35.68.ebuild => BBmap-35.82.ebuild} | 2 +-
sci-biology/BBmap/ChangeLog | 8 +++++++-
2 files changed, 8 insertions(+), 2 deletions(-)
diff --git a/sci-biology/BBmap/BBmap-35.68.ebuild b/sci-biology/BBmap/BBmap-35.82.ebuild
similarity index 96%
rename from sci-biology/BBmap/BBmap-35.68.ebuild
rename to sci-biology/BBmap/BBmap-35.82.ebuild
index a898eff..86b138c 100644
--- a/sci-biology/BBmap/BBmap-35.68.ebuild
+++ b/sci-biology/BBmap/BBmap-35.82.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
# $Id$
diff --git a/sci-biology/BBmap/ChangeLog b/sci-biology/BBmap/ChangeLog
index bac5ec6..15cd8fa 100644
--- a/sci-biology/BBmap/ChangeLog
+++ b/sci-biology/BBmap/ChangeLog
@@ -1,7 +1,13 @@
# ChangeLog for sci-biology/BBmap
-# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2016 Gentoo Foundation; Distributed under the GPL v2
# $Id$
+*BBmap-35.82 (06 Jan 2016)
+
+ 06 Jan 2016; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +BBmap-35.82.ebuild,
+ -BBmap-35.68.ebuild:
+ sci-biology/BBmap: version bump
+
*BBmap-35.68 (19 Nov 2015)
19 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +BBmap-35.68.ebuild,
^ permalink raw reply related [flat|nested] 18+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/BBmap/
@ 2015-11-19 13:15 Martin Mokrejs
0 siblings, 0 replies; 18+ messages in thread
From: Martin Mokrejs @ 2015-11-19 13:15 UTC (permalink / raw
To: gentoo-commits
commit: 24326d33df8d4cdff6eccf14a0057cb075428b12
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Nov 19 13:14:15 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Nov 19 13:14:15 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=24326d33
sci-biology/BBmap: version bump
Package-Manager: portage-2.2.18
sci-biology/BBmap/{BBmap-35.66.ebuild => BBmap-35.68.ebuild} | 3 +--
sci-biology/BBmap/ChangeLog | 6 ++++++
2 files changed, 7 insertions(+), 2 deletions(-)
diff --git a/sci-biology/BBmap/BBmap-35.66.ebuild b/sci-biology/BBmap/BBmap-35.68.ebuild
similarity index 94%
rename from sci-biology/BBmap/BBmap-35.66.ebuild
rename to sci-biology/BBmap/BBmap-35.68.ebuild
index 982c762..a898eff 100644
--- a/sci-biology/BBmap/BBmap-35.66.ebuild
+++ b/sci-biology/BBmap/BBmap-35.68.ebuild
@@ -12,7 +12,7 @@ SRC_URI="http://sourceforge.net/projects/bbmap/files/BBMap_"${PV}".tar.gz"
LICENSE="BSD"
SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64"
IUSE=""
DEPEND="
@@ -30,7 +30,6 @@ src_prepare(){
# see bug #542700
sed -e 's#/usr/common/usg/hpc/openmpi/gnu4.6/sge/1.8.1/ib_2.1-1.0.0/lib/mpi.jar#/usr/share/openmpi/lib/mpi.jar#' -i build.xml
sed -e 's#compiler="${jcompiler}" ##' -i build.xml
- epatch "${FILESDIR}"/UnicodeToAscii.patch
}
src_compile(){
diff --git a/sci-biology/BBmap/ChangeLog b/sci-biology/BBmap/ChangeLog
index 297faef..bac5ec6 100644
--- a/sci-biology/BBmap/ChangeLog
+++ b/sci-biology/BBmap/ChangeLog
@@ -2,6 +2,12 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Id$
+*BBmap-35.68 (19 Nov 2015)
+
+ 19 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +BBmap-35.68.ebuild,
+ -BBmap-35.66.ebuild:
+ sci-biology/BBmap: version bump
+
*BBmap-34.97 (15 Nov 2015)
15 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +BBmap-34.97.ebuild,
^ permalink raw reply related [flat|nested] 18+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/BBmap/
@ 2015-11-15 18:51 Martin Mokrejs
0 siblings, 0 replies; 18+ messages in thread
From: Martin Mokrejs @ 2015-11-15 18:51 UTC (permalink / raw
To: gentoo-commits
commit: 6a6bf4387212cf0113cbb91d6041febf41ebe979
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Nov 15 18:49:47 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Nov 15 18:49:47 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=6a6bf438
sci-biology/BBmap: version bump; apply also the UnicodeToAscii.patch
Package-Manager: portage-2.2.18
sci-biology/BBmap/{BBmap-34.56.ebuild => BBmap-34.97.ebuild} | 1 +
sci-biology/BBmap/ChangeLog | 6 ++++++
2 files changed, 7 insertions(+)
diff --git a/sci-biology/BBmap/BBmap-34.56.ebuild b/sci-biology/BBmap/BBmap-34.97.ebuild
similarity index 96%
rename from sci-biology/BBmap/BBmap-34.56.ebuild
rename to sci-biology/BBmap/BBmap-34.97.ebuild
index a898eff..21fd42f 100644
--- a/sci-biology/BBmap/BBmap-34.56.ebuild
+++ b/sci-biology/BBmap/BBmap-34.97.ebuild
@@ -30,6 +30,7 @@ src_prepare(){
# see bug #542700
sed -e 's#/usr/common/usg/hpc/openmpi/gnu4.6/sge/1.8.1/ib_2.1-1.0.0/lib/mpi.jar#/usr/share/openmpi/lib/mpi.jar#' -i build.xml
sed -e 's#compiler="${jcompiler}" ##' -i build.xml
+ epatch "${FILESDIR}"/UnicodeToAscii.patch
}
src_compile(){
diff --git a/sci-biology/BBmap/ChangeLog b/sci-biology/BBmap/ChangeLog
index 62aa5be..297faef 100644
--- a/sci-biology/BBmap/ChangeLog
+++ b/sci-biology/BBmap/ChangeLog
@@ -2,6 +2,12 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Id$
+*BBmap-34.97 (15 Nov 2015)
+
+ 15 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +BBmap-34.97.ebuild,
+ -BBmap-34.56.ebuild:
+ sci-biology/BBmap: version bump; apply also the UnicodeToAscii.patch
+
12 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> BBmap-34.56.ebuild:
sci-biology/BBmap: drop the call to eclipse jcompiler, added ~amd64 KEYWORD
^ permalink raw reply related [flat|nested] 18+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/BBmap/
@ 2015-11-13 10:07 Martin Mokrejs
0 siblings, 0 replies; 18+ messages in thread
From: Martin Mokrejs @ 2015-11-13 10:07 UTC (permalink / raw
To: gentoo-commits
commit: c27391a315f4e6ed4cf3c68e2a07f85adae4d5b1
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Nov 13 10:06:14 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Nov 13 10:06:14 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c27391a3
sci-biology/BBmap-34.56: restoring previous working version
Package-Manager: portage-2.2.18
sci-biology/BBmap/BBmap-34.56.ebuild | 43 ++++++++++++++++++++++++++++++++++++
1 file changed, 43 insertions(+)
diff --git a/sci-biology/BBmap/BBmap-34.56.ebuild b/sci-biology/BBmap/BBmap-34.56.ebuild
new file mode 100644
index 0000000..a898eff
--- /dev/null
+++ b/sci-biology/BBmap/BBmap-34.56.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="Short read aligner, K-mer-based error-correction and normalization, FASTA/Q conversion"
+HOMEPAGE="http://sourceforge.net/projects/bbmap/"
+SRC_URI="http://sourceforge.net/projects/bbmap/files/BBMap_"${PV}".tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND="
+ sys-cluster/openmpi[java]
+ >=virtual/jdk-1.7:*
+ dev-java/ant-core"
+RDEPEND="${DEPEND}
+ >=virtual/jre-1.7:*"
+
+S="${WORKDIR}"/bbmap
+
+src_prepare(){
+ # fix the line in build.xml to point to mpi.jar location
+ # <property name="mpijar" location="/tmp/mpi.jar" ></property>
+ # see bug #542700
+ sed -e 's#/usr/common/usg/hpc/openmpi/gnu4.6/sge/1.8.1/ib_2.1-1.0.0/lib/mpi.jar#/usr/share/openmpi/lib/mpi.jar#' -i build.xml
+ sed -e 's#compiler="${jcompiler}" ##' -i build.xml
+}
+
+src_compile(){
+ ant dist || die
+}
+
+src_install(){
+ dobin *.sh
+ dodoc docs/readme.txt
+ java-pkg_dojar dist/lib/BBTools.jar
+}
^ permalink raw reply related [flat|nested] 18+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/BBmap/
@ 2015-11-12 0:46 Martin Mokrejs
0 siblings, 0 replies; 18+ messages in thread
From: Martin Mokrejs @ 2015-11-12 0:46 UTC (permalink / raw
To: gentoo-commits
commit: 55c60469b0ee22edf2266722f09ac3627e58bac9
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Nov 12 00:45:22 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Nov 12 00:45:22 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=55c60469
sci-biology/BBmap: drop the call to eclipse jcompiler, added ~amd64 KEYWORD
Package-Manager: portage-2.2.18
sci-biology/BBmap/BBmap-34.56.ebuild | 3 ++-
sci-biology/BBmap/ChangeLog | 3 +++
2 files changed, 5 insertions(+), 1 deletion(-)
diff --git a/sci-biology/BBmap/BBmap-34.56.ebuild b/sci-biology/BBmap/BBmap-34.56.ebuild
index 43e6236..a898eff 100644
--- a/sci-biology/BBmap/BBmap-34.56.ebuild
+++ b/sci-biology/BBmap/BBmap-34.56.ebuild
@@ -12,7 +12,7 @@ SRC_URI="http://sourceforge.net/projects/bbmap/files/BBMap_"${PV}".tar.gz"
LICENSE="BSD"
SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64"
IUSE=""
DEPEND="
@@ -29,6 +29,7 @@ src_prepare(){
# <property name="mpijar" location="/tmp/mpi.jar" ></property>
# see bug #542700
sed -e 's#/usr/common/usg/hpc/openmpi/gnu4.6/sge/1.8.1/ib_2.1-1.0.0/lib/mpi.jar#/usr/share/openmpi/lib/mpi.jar#' -i build.xml
+ sed -e 's#compiler="${jcompiler}" ##' -i build.xml
}
src_compile(){
diff --git a/sci-biology/BBmap/ChangeLog b/sci-biology/BBmap/ChangeLog
index 315b333..62aa5be 100644
--- a/sci-biology/BBmap/ChangeLog
+++ b/sci-biology/BBmap/ChangeLog
@@ -3,6 +3,9 @@
# $Id$
12 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> BBmap-34.56.ebuild:
+ sci-biology/BBmap: drop the call to eclipse jcompiler, added ~amd64 KEYWORD
+
+ 12 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> BBmap-34.56.ebuild:
sci-biology/BBmap: provided bug #542700 is resolved we can use mpi.jar from
openmpi package
^ permalink raw reply related [flat|nested] 18+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/BBmap/
@ 2015-11-12 0:34 Martin Mokrejs
0 siblings, 0 replies; 18+ messages in thread
From: Martin Mokrejs @ 2015-11-12 0:34 UTC (permalink / raw
To: gentoo-commits
commit: 7d63183f97ac775659f864b49b981e5b56607065
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Nov 12 00:33:30 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Nov 12 00:33:30 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=7d63183f
sci-biology/BBmap: provided bug #542700 is resolved we can use mpi.jar from openmpi package
Package-Manager: portage-2.2.18
sci-biology/BBmap/BBmap-34.56.ebuild | 11 ++++++-----
sci-biology/BBmap/ChangeLog | 4 ++++
2 files changed, 10 insertions(+), 5 deletions(-)
diff --git a/sci-biology/BBmap/BBmap-34.56.ebuild b/sci-biology/BBmap/BBmap-34.56.ebuild
index f95b7e9..43e6236 100644
--- a/sci-biology/BBmap/BBmap-34.56.ebuild
+++ b/sci-biology/BBmap/BBmap-34.56.ebuild
@@ -15,7 +15,6 @@ SLOT="0"
KEYWORDS=""
IUSE=""
-# needs USE=java, see bug #542700
DEPEND="
sys-cluster/openmpi[java]
>=virtual/jdk-1.7:*
@@ -25,10 +24,12 @@ RDEPEND="${DEPEND}
S="${WORKDIR}"/bbmap
-#src_prepare(){
-# # fix the line in build.xml to point to mpi.jar location
-# # <property name="mpijar" location="/tmp/mpi.jar" ></property>
-#}
+src_prepare(){
+ # fix the line in build.xml to point to mpi.jar location
+ # <property name="mpijar" location="/tmp/mpi.jar" ></property>
+ # see bug #542700
+ sed -e 's#/usr/common/usg/hpc/openmpi/gnu4.6/sge/1.8.1/ib_2.1-1.0.0/lib/mpi.jar#/usr/share/openmpi/lib/mpi.jar#' -i build.xml
+}
src_compile(){
ant dist || die
diff --git a/sci-biology/BBmap/ChangeLog b/sci-biology/BBmap/ChangeLog
index 9dcb3f4..315b333 100644
--- a/sci-biology/BBmap/ChangeLog
+++ b/sci-biology/BBmap/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Id$
+ 12 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> BBmap-34.56.ebuild:
+ sci-biology/BBmap: provided bug #542700 is resolved we can use mpi.jar from
+ openmpi package
+
09 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> BBmap-34.56.ebuild:
new package, needs openmpi with java support to provide mpi.jar, see bug
#542700
^ permalink raw reply related [flat|nested] 18+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/BBmap/
@ 2015-03-09 14:50 Martin Mokrejs
0 siblings, 0 replies; 18+ messages in thread
From: Martin Mokrejs @ 2015-03-09 14:50 UTC (permalink / raw
To: gentoo-commits
commit: 960302060726d9058e835878c42dec29471034e6
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Mar 9 14:49:18 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Mar 9 14:49:18 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=96030206
new package, needs openmpi with java support to provide mpi.jar, see bug #542700
Package-Manager: portage-2.2.15
sci-biology/BBmap/BBmap-34.56.ebuild | 13 ++++++++++---
sci-biology/BBmap/ChangeLog | 4 ++++
2 files changed, 14 insertions(+), 3 deletions(-)
diff --git a/sci-biology/BBmap/BBmap-34.56.ebuild b/sci-biology/BBmap/BBmap-34.56.ebuild
index 674e8f2..e41097f 100644
--- a/sci-biology/BBmap/BBmap-34.56.ebuild
+++ b/sci-biology/BBmap/BBmap-34.56.ebuild
@@ -12,10 +12,12 @@ SRC_URI="http://sourceforge.net/projects/bbmap/files/BBMap_"${PV}".tar.gz"
LICENSE="BSD"
SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS=""
IUSE=""
+# needs USE=java, see bug #542700
DEPEND="
+ sys-cluster/openmpi[java]
>=virtual/jdk-1.7:*
dev-java/ant-core"
RDEPEND="${DEPEND}
@@ -23,12 +25,17 @@ RDEPEND="${DEPEND}
S="${WORKDIR}"/bbmap
+#src_prepare(){
+# # fix the line in build.xml to point to mpi.jar location
+# # <property name="mpijar" location="/tmp/mpi.jar" ></property>
+#}
+
src_compile(){
- ant compile || die
+ ant dist || die
}
src_install(){
dobin *.sh
dodoc docs/readme.txt
- java-pkg_dojar lib/BBTools.jar
+ java-pkg_dojar dist/lib/BBTools.jar
}
diff --git a/sci-biology/BBmap/ChangeLog b/sci-biology/BBmap/ChangeLog
index 8a90f18..8a5e706 100644
--- a/sci-biology/BBmap/ChangeLog
+++ b/sci-biology/BBmap/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 09 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> BBmap-34.56.ebuild:
+ new package, needs openmpi with java support to provide mpi.jar, see bug
+ #542700
+
*BBmap-34.56 (05 Mar 2015)
05 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +BBmap-34.56.ebuild,
^ permalink raw reply related [flat|nested] 18+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/BBmap/
@ 2015-03-05 23:53 Martin Mokrejs
0 siblings, 0 replies; 18+ messages in thread
From: Martin Mokrejs @ 2015-03-05 23:53 UTC (permalink / raw
To: gentoo-commits
commit: a685e8ebaa1adefe32f5dd6db4b3e38c93b1cd07
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Mar 5 23:53:16 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Mar 5 23:53:16 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a685e8eb
version bump
Package-Manager: portage-2.2.15
.../BBmap/{BBmap-31.40.ebuild => BBmap-34.56.ebuild} | 17 +++++++++++++----
sci-biology/BBmap/ChangeLog | 6 ++++++
2 files changed, 19 insertions(+), 4 deletions(-)
diff --git a/sci-biology/BBmap/BBmap-31.40.ebuild b/sci-biology/BBmap/BBmap-34.56.ebuild
similarity index 62%
rename from sci-biology/BBmap/BBmap-31.40.ebuild
rename to sci-biology/BBmap/BBmap-34.56.ebuild
index e28c005..674e8f2 100644
--- a/sci-biology/BBmap/BBmap-31.40.ebuild
+++ b/sci-biology/BBmap/BBmap-34.56.ebuild
@@ -6,14 +6,13 @@ EAPI=5
inherit java-pkg-2 java-ant-2
-DESCRIPTION="Short read aligner, K-mer-based error-correction and normalization, FASTA/FASTQ conversion"
+DESCRIPTION="Short read aligner, K-mer-based error-correction and normalization, FASTA/Q conversion"
HOMEPAGE="http://sourceforge.net/projects/bbmap/"
-SRC_URI="http://sourceforge.net/projects/bbmap/files/BBMap_31.40_java7.tar.gz"
-#SRC_URI="http://sourceforge.net/projects/bbmap/files/BBMap_31.40_java6.tar.gz"
+SRC_URI="http://sourceforge.net/projects/bbmap/files/BBMap_"${PV}".tar.gz"
LICENSE="BSD"
SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64"
IUSE=""
DEPEND="
@@ -23,3 +22,13 @@ RDEPEND="${DEPEND}
>=virtual/jre-1.7:*"
S="${WORKDIR}"/bbmap
+
+src_compile(){
+ ant compile || die
+}
+
+src_install(){
+ dobin *.sh
+ dodoc docs/readme.txt
+ java-pkg_dojar lib/BBTools.jar
+}
diff --git a/sci-biology/BBmap/ChangeLog b/sci-biology/BBmap/ChangeLog
index 53acebd..8a90f18 100644
--- a/sci-biology/BBmap/ChangeLog
+++ b/sci-biology/BBmap/ChangeLog
@@ -2,6 +2,12 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*BBmap-34.56 (05 Mar 2015)
+
+ 05 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +BBmap-34.56.ebuild,
+ -BBmap-31.40.ebuild:
+ version bump
+
18 Feb 2015; Justin Lecher <jlec@gentoo.org> BBmap-31.40.ebuild:
sci-biology/BBmap: fix SLOT operators
^ permalink raw reply related [flat|nested] 18+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/BBmap/
@ 2014-09-16 0:26 Christoph Junghans
0 siblings, 0 replies; 18+ messages in thread
From: Christoph Junghans @ 2014-09-16 0:26 UTC (permalink / raw
To: gentoo-commits
commit: 14d3ad22fdf55c46c5603bb939ec783d02595505
Author: Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Tue Sep 16 00:23:26 2014 +0000
Commit: Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Tue Sep 16 00:26:07 2014 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=14d3ad22
added license
Package-Manager: portage-2.2.8-r1
---
sci-biology/BBmap/BBmap-31.40.ebuild | 2 +-
sci-biology/BBmap/ChangeLog | 4 +++-
2 files changed, 4 insertions(+), 2 deletions(-)
diff --git a/sci-biology/BBmap/BBmap-31.40.ebuild b/sci-biology/BBmap/BBmap-31.40.ebuild
index 959d062..66e2d2f 100644
--- a/sci-biology/BBmap/BBmap-31.40.ebuild
+++ b/sci-biology/BBmap/BBmap-31.40.ebuild
@@ -11,7 +11,7 @@ HOMEPAGE="http://sourceforge.net/projects/bbmap/"
SRC_URI="http://sourceforge.net/projects/bbmap/files/BBMap_31.40_java7.tar.gz"
#SRC_URI="http://sourceforge.net/projects/bbmap/files/BBMap_31.40_java6.tar.gz"
-LICENSE=""
+LICENSE="BSD"
SLOT="0"
KEYWORDS=""
IUSE=""
diff --git a/sci-biology/BBmap/ChangeLog b/sci-biology/BBmap/ChangeLog
index 9a2750a..88c9cd1 100644
--- a/sci-biology/BBmap/ChangeLog
+++ b/sci-biology/BBmap/ChangeLog
@@ -2,10 +2,12 @@
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> BBmap-31.40.ebuild:
+ added license
+
*BBmap-31.40 (23 Mar 2014)
23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+BBmap-31.40.ebuild, +metadata.xml:
sci-biology/BBmap: a skeleton for a new package, needs help from java team
for sure
-
^ permalink raw reply related [flat|nested] 18+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/BBmap/
@ 2014-03-23 19:34 Martin Mokrejs
0 siblings, 0 replies; 18+ messages in thread
From: Martin Mokrejs @ 2014-03-23 19:34 UTC (permalink / raw
To: gentoo-commits
commit: 05b20520d7eb65ba90e9582b7315c65d2f4234c1
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 19:33:34 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 19:33:34 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=05b20520
sci-biology/BBmap: a skeleton for a new package, needs help from java team for sure
---
sci-biology/BBmap/BBmap-31.40.ebuild | 25 +++++++++++++++++++++++++
sci-biology/BBmap/ChangeLog | 11 +++++++++++
sci-biology/BBmap/metadata.xml | 9 +++++++++
3 files changed, 45 insertions(+)
diff --git a/sci-biology/BBmap/BBmap-31.40.ebuild b/sci-biology/BBmap/BBmap-31.40.ebuild
new file mode 100644
index 0000000..959d062
--- /dev/null
+++ b/sci-biology/BBmap/BBmap-31.40.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="Short read aligner, K-mer-based error-correction and normalization, FASTA/FASTQ conversion"
+HOMEPAGE="http://sourceforge.net/projects/bbmap/"
+SRC_URI="http://sourceforge.net/projects/bbmap/files/BBMap_31.40_java7.tar.gz"
+#SRC_URI="http://sourceforge.net/projects/bbmap/files/BBMap_31.40_java6.tar.gz"
+
+LICENSE=""
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="
+ >=virtual/jdk-1.7
+ dev-java/ant-core"
+RDEPEND="${DEPEND}
+ >=virtual/jre-1.7"
+
+S="${WORKDIR}"/bbmap
diff --git a/sci-biology/BBmap/ChangeLog b/sci-biology/BBmap/ChangeLog
new file mode 100644
index 0000000..9a2750a
--- /dev/null
+++ b/sci-biology/BBmap/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for sci-biology/BBmap
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*BBmap-31.40 (23 Mar 2014)
+
+ 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +BBmap-31.40.ebuild, +metadata.xml:
+ sci-biology/BBmap: a skeleton for a new package, needs help from java team
+ for sure
+
diff --git a/sci-biology/BBmap/metadata.xml b/sci-biology/BBmap/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/BBmap/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] 18+ messages in thread
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