commit: 861625b2e2c04a19322caab37752a05fe44cde85
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 15:13:20 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 15:13:46 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=861625b2
sci-biology/BBmap: version bump
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
profiles/package.mask | 1 -
sci-biology/BBmap/BBmap-34.97.ebuild | 43 ----------------------
sci-biology/BBmap/BBmap-35.92.ebuild | 42 ---------------------
sci-biology/BBmap/BBmap-36.02.ebuild | 42 ---------------------
sci-biology/BBmap/BBmap-37.67.ebuild | 42 ---------------------
.../{BBmap-36.86.ebuild => BBmap-38.87.ebuild} | 10 ++---
sci-biology/BBmap/files/UnicodeToAscii.patch | 17 ---------
7 files changed, 5 insertions(+), 192 deletions(-)
diff --git a/profiles/package.mask b/profiles/package.mask
index a92b72a94..9abc3dd3c 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -41,4 +41,3 @@ dev-java/hdf-java
sci-biology/aghermann
sci-biology/argo-bin
sci-biology/bambino
-sci-biology/BBmap
diff --git a/sci-biology/BBmap/BBmap-34.97.ebuild
b/sci-biology/BBmap/BBmap-34.97.ebuild
deleted file mode 100644
index 25627cf02..000000000
--- a/sci-biology/BBmap/BBmap-34.97.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Short read aligner, K-mer-based error-correct and normalize,
FASTA/Q tool"
-HOMEPAGE="https://sourceforge.net/projects/bbmap/";
-SRC_URI="https://sourceforge.net/projects/bbmap/files/BBMap_"${PV}".tar.gz";
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="
- sys-cluster/openmpi[java]
- >=virtual/jdk-1.7:*
- dev-java/ant-core"
-RDEPEND="${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
- epatch "${FILESDIR}"/UnicodeToAscii.patch
-}
-
-src_compile(){
- ant dist || die
-}
-
-src_install(){
- dobin *.sh
- dodoc docs/readme.txt
- java-pkg_dojar dist/lib/BBTools.jar
-}
diff --git a/sci-biology/BBmap/BBmap-35.92.ebuild
b/sci-biology/BBmap/BBmap-35.92.ebuild
deleted file mode 100644
index 3bc328b4c..000000000
--- a/sci-biology/BBmap/BBmap-35.92.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Short read aligner, K-mer-based error-correct and normalize,
FASTA/Q tool"
-HOMEPAGE="https://sourceforge.net/projects/bbmap/";
-SRC_URI="https://sourceforge.net/projects/bbmap/files/BBMap_"${PV}".tar.gz";
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-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="${jcompiler}" ##' -i build.xml
-}
-
-src_compile(){
- ant dist || die
-}
-
-src_install(){
- dobin *.sh
- dodoc docs/readme.txt
- java-pkg_dojar dist/lib/BBTools.jar
-}
diff --git a/sci-biology/BBmap/BBmap-36.02.ebuild
b/sci-biology/BBmap/BBmap-36.02.ebuild
deleted file mode 100644
index 3bc328b4c..000000000
--- a/sci-biology/BBmap/BBmap-36.02.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Short read aligner, K-mer-based error-correct and normalize,
FASTA/Q tool"
-HOMEPAGE="https://sourceforge.net/projects/bbmap/";
-SRC_URI="https://sourceforge.net/projects/bbmap/files/BBMap_"${PV}".tar.gz";
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-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="${jcompiler}" ##' -i build.xml
-}
-
-src_compile(){
- ant dist || die
-}
-
-src_install(){
- dobin *.sh
- dodoc docs/readme.txt
- java-pkg_dojar dist/lib/BBTools.jar
-}
diff --git a/sci-biology/BBmap/BBmap-37.67.ebuild
b/sci-biology/BBmap/BBmap-37.67.ebuild
deleted file mode 100644
index 3bc328b4c..000000000
--- a/sci-biology/BBmap/BBmap-37.67.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Short read aligner, K-mer-based error-correct and normalize,
FASTA/Q tool"
-HOMEPAGE="https://sourceforge.net/projects/bbmap/";
-SRC_URI="https://sourceforge.net/projects/bbmap/files/BBMap_"${PV}".tar.gz";
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-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="${jcompiler}" ##' -i build.xml
-}
-
-src_compile(){
- ant dist || die
-}
-
-src_install(){
- dobin *.sh
- dodoc docs/readme.txt
- java-pkg_dojar dist/lib/BBTools.jar
-}
diff --git a/sci-biology/BBmap/BBmap-36.86.ebuild
b/sci-biology/BBmap/BBmap-38.87.ebuild
similarity index 85%
rename from sci-biology/BBmap/BBmap-36.86.ebuild
rename to sci-biology/BBmap/BBmap-38.87.ebuild
index 3bc328b4c..06220b557 100644
--- a/sci-biology/BBmap/BBmap-36.86.ebuild
+++ b/sci-biology/BBmap/BBmap-38.87.ebuild
@@ -1,18 +1,17 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=7
inherit java-pkg-2 java-ant-2
DESCRIPTION="Short read aligner, K-mer-based error-correct and normalize,
FASTA/Q tool"
HOMEPAGE="https://sourceforge.net/projects/bbmap/";
-SRC_URI="https://sourceforge.net/projects/bbmap/files/BBMap_"${PV}".tar.gz";
+SRC_URI="https://sourceforge.net/projects/bbmap/files/BBMap_${PV}.tar.gz";
LICENSE="BSD"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE=""
DEPEND="
sys-cluster/openmpi[java]
@@ -21,9 +20,10 @@ DEPEND="
RDEPEND="${DEPEND}
>=virtual/jre-1.7:*"
-S="${WORKDIR}"/bbmap
+S="${WORKDIR}/bbmap"
src_prepare(){
+ default
# fix the line in build.xml to point to mpi.jar location
# <property name="mpijar" location="/tmp/mpi.jar" ></property>
# see bug #542700
diff --git a/sci-biology/BBmap/files/UnicodeToAscii.patch
b/sci-biology/BBmap/files/UnicodeToAscii.patch
deleted file mode 100644
index 36e5a36e5..000000000
--- a/sci-biology/BBmap/files/UnicodeToAscii.patch
+++ /dev/null
@@ -1,17 +0,0 @@
---- bbmap/current/jgi/UnicodeToAscii.java.ori 2015-11-12 20:24:13.704471341
+0100
-+++ bbmap/current/jgi/UnicodeToAscii.java 2015-11-12 20:27:12.564474322
+0100
-@@ -20,14 +20,6 @@
- public class UnicodeToAscii {
-
- public static void main(String[] args){
--// try {
--// System.err.println("A���C");
--// System.err.println(new String("A���C".getBytes("UTF8"),
"UTF8"));
--// } catch (Exception e) {
--// // TODO Auto-generated catch block
--// e.printStackTrace();
--// }
--// assert(false);
-
- Timer t=new Timer();
- t.start();
