* [gentoo-commits] proj/sci:master commit in: sci-biology/sambamba/
@ 2017-02-19 19:39 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2017-02-19 19:39 UTC (permalink / raw
To: gentoo-commits
commit: 6921d365bb6816d75863475baa434d02feec8048
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Feb 19 19:39:05 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Feb 19 19:39:05 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=6921d365
sci-biology/sambamba: multithreaded tool written in D language
The ebuilds are incomplete as I need to figure out how to compile
the thingie. Make does not exit upon error (released tarball does
not contain htslib/).
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/sambamba/metadata.xml | 12 +++++++++++
sci-biology/sambamba/sambamba-0.6.5.ebuild | 32 ++++++++++++++++++++++++++++++
sci-biology/sambamba/sambamba-9999.ebuild | 27 +++++++++++++++++++++++++
3 files changed, 71 insertions(+)
diff --git a/sci-biology/sambamba/metadata.xml b/sci-biology/sambamba/metadata.xml
new file mode 100644
index 000000000..f68a1b6fa
--- /dev/null
+++ b/sci-biology/sambamba/metadata.xml
@@ -0,0 +1,12 @@
+<?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>
+</pkgmetadata>
diff --git a/sci-biology/sambamba/sambamba-0.6.5.ebuild b/sci-biology/sambamba/sambamba-0.6.5.ebuild
new file mode 100644
index 000000000..49a7cb0bb
--- /dev/null
+++ b/sci-biology/sambamba/sambamba-0.6.5.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+DESCRIPTION="Parallell process SAM/BAM/CRAM files faster than samtools"
+HOMEPAGE="http://lomereiter.github.io/sambamba"
+SRC_URI="https://github.com/lomereiter/sambamba/archive/v0.6.5.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-2+"
+SLOT="0"
+KEYWORDS=""
+IUSE="debug"
+
+# needs ldmd2 compiler from LDC package
+# wget https://github.com/ldc-developers/ldc/releases/download/v0.17.1/ldc2-0.17.1-linux-x86_64.tar.xz
+# tar xJf ldc2-0.17.1-linux-x86_64.tar.xz
+# export PATH=~/ldc2-0.17.1-linux-x86_64/bin/:$PATH
+# export LIBRARY_PATH=~/ldc2-0.17.1-linux-x86_64/lib/
+#
+# contains bundled htslib
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+src_compile(){
+ if use debug ; then
+ emake sambamba-ldmd2-debug
+ else
+ emake sambamba-ldmd2-64
+ fi
+}
diff --git a/sci-biology/sambamba/sambamba-9999.ebuild b/sci-biology/sambamba/sambamba-9999.ebuild
new file mode 100644
index 000000000..c19a5053f
--- /dev/null
+++ b/sci-biology/sambamba/sambamba-9999.ebuild
@@ -0,0 +1,27 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit git-r3
+
+DESCRIPTION="Parallell process SAM/BAM/CRAM files faster than samtools"
+HOMEPAGE="http://lomereiter.github.io/sambamba"
+EGIT_REPO_URI="https://github.com/lomereiter/sambamba.git"
+
+LICENSE="GPL-2+"
+SLOT="0"
+KEYWORDS=""
+IUSE="debug"
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+src_compile(){
+ if use debug ; then
+ emake sambamba-ldmd2-debug
+ else
+ emake sambamba-ldmd2-64
+ fi
+}
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/sambamba/
@ 2017-02-19 19:44 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2017-02-19 19:44 UTC (permalink / raw
To: gentoo-commits
commit: 20558e394940348fcf0dcbd1a47f08bf4f654799
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Feb 19 19:43:59 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Feb 19 19:43:59 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=20558e39
sci-biology/sambamba: add a link to ldc-developers Gentoo overlay
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/sambamba/sambamba-0.6.5.ebuild | 6 +-----
sci-biology/sambamba/sambamba-9999.ebuild | 2 ++
2 files changed, 3 insertions(+), 5 deletions(-)
diff --git a/sci-biology/sambamba/sambamba-0.6.5.ebuild b/sci-biology/sambamba/sambamba-0.6.5.ebuild
index 49a7cb0bb..2e8d062e0 100644
--- a/sci-biology/sambamba/sambamba-0.6.5.ebuild
+++ b/sci-biology/sambamba/sambamba-0.6.5.ebuild
@@ -13,11 +13,7 @@ SLOT="0"
KEYWORDS=""
IUSE="debug"
-# needs ldmd2 compiler from LDC package
-# wget https://github.com/ldc-developers/ldc/releases/download/v0.17.1/ldc2-0.17.1-linux-x86_64.tar.xz
-# tar xJf ldc2-0.17.1-linux-x86_64.tar.xz
-# export PATH=~/ldc2-0.17.1-linux-x86_64/bin/:$PATH
-# export LIBRARY_PATH=~/ldc2-0.17.1-linux-x86_64/lib/
+# https://github.com/ldc-developers/gentoo-overlay/tree/master/dev-lang/ldc2
#
# contains bundled htslib
DEPEND=""
diff --git a/sci-biology/sambamba/sambamba-9999.ebuild b/sci-biology/sambamba/sambamba-9999.ebuild
index c19a5053f..0ea89ba23 100644
--- a/sci-biology/sambamba/sambamba-9999.ebuild
+++ b/sci-biology/sambamba/sambamba-9999.ebuild
@@ -18,6 +18,8 @@ IUSE="debug"
DEPEND=""
RDEPEND="${DEPEND}"
+# https://github.com/ldc-developers/gentoo-overlay/tree/master/dev-lang/ldc2
+
src_compile(){
if use debug ; then
emake sambamba-ldmd2-debug
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/sambamba/
@ 2021-02-04 5:23 Andrew Ammerlaan
0 siblings, 0 replies; 5+ messages in thread
From: Andrew Ammerlaan @ 2021-02-04 5:23 UTC (permalink / raw
To: gentoo-commits
commit: 67b756ceafdc4378861efdbf82f83844a31ccf20
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Thu Feb 4 05:23:24 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Thu Feb 4 05:23:24 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=67b756ce
sci-biology/sambamba: version bump, EAPI bump
does not compile, seems to require some other compiler
that is not packaged in ::gentoo at the moment
Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/sambamba/sambamba-0.6.5.ebuild | 27 ----------------------
sci-biology/sambamba/sambamba-0.8.0.ebuild | 36 ++++++++++++++++++++++++++++++
sci-biology/sambamba/sambamba-9999.ebuild | 10 ++++-----
3 files changed, 41 insertions(+), 32 deletions(-)
diff --git a/sci-biology/sambamba/sambamba-0.6.5.ebuild b/sci-biology/sambamba/sambamba-0.6.5.ebuild
deleted file mode 100644
index ab2fb990e..000000000
--- a/sci-biology/sambamba/sambamba-0.6.5.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="Parallell process SAM/BAM/CRAM files faster than samtools"
-HOMEPAGE="http://lomereiter.github.io/sambamba"
-SRC_URI="https://github.com/lomereiter/sambamba/archive/v0.6.5.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-2+"
-SLOT="0"
-KEYWORDS=""
-IUSE="debug"
-
-# https://github.com/ldc-developers/gentoo-overlay/tree/master/dev-lang/ldc2
-#
-# contains bundled htslib
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-src_compile(){
- if use debug ; then
- emake sambamba-ldmd2-debug
- else
- emake sambamba-ldmd2-64
- fi
-}
diff --git a/sci-biology/sambamba/sambamba-0.8.0.ebuild b/sci-biology/sambamba/sambamba-0.8.0.ebuild
new file mode 100644
index 000000000..d6da97806
--- /dev/null
+++ b/sci-biology/sambamba/sambamba-0.8.0.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+LZ4_COMMIT="b3692db46d2b23a7c0af2d5e69988c94f126e10a"
+
+DESCRIPTION="Parallell process SAM/BAM/CRAM files faster than samtools"
+HOMEPAGE="https://lomereiter.github.io/sambamba/"
+SRC_URI="https://github.com/lomereiter/sambamba/archive/v${PV}.tar.gz -> ${P}.tar.gz
+ https://github.com/lz4/lz4/archive/${LZ4_COMMIT}.tar.gz"
+
+LICENSE="GPL-2+"
+SLOT="0"
+KEYWORDS=""
+IUSE="debug"
+
+# https://github.com/ldc-developers/gentoo-overlay/tree/master/dev-lang/ldc2
+#
+# contains bundled htslib
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+src_unpack() {
+ default
+ rm -r "${S}/lz4" || die
+ mv "${WORKDIR}/lz4-${LZ4_COMMIT}" "${S}/lz4" || die
+}
+
+src_compile(){
+ if use debug ; then
+ emake debug all
+ else
+ emake all
+ fi
+}
diff --git a/sci-biology/sambamba/sambamba-9999.ebuild b/sci-biology/sambamba/sambamba-9999.ebuild
index 8cd4c3ba2..e655b10b0 100644
--- a/sci-biology/sambamba/sambamba-9999.ebuild
+++ b/sci-biology/sambamba/sambamba-9999.ebuild
@@ -1,12 +1,12 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
inherit git-r3
DESCRIPTION="Parallell process SAM/BAM/CRAM files faster than samtools"
-HOMEPAGE="http://lomereiter.github.io/sambamba"
+HOMEPAGE="https://lomereiter.github.io/sambamba/"
EGIT_REPO_URI="https://github.com/lomereiter/sambamba.git"
LICENSE="GPL-2+"
@@ -21,8 +21,8 @@ RDEPEND="${DEPEND}"
src_compile(){
if use debug ; then
- emake sambamba-ldmd2-debug
+ emake debug all
else
- emake sambamba-ldmd2-64
+ emake all
fi
}
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/sambamba/
@ 2021-02-04 10:23 Andrew Ammerlaan
0 siblings, 0 replies; 5+ messages in thread
From: Andrew Ammerlaan @ 2021-02-04 10:23 UTC (permalink / raw
To: gentoo-commits
commit: e8ffeeffaf952f9eb70789756a8173f5914444fd
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Thu Feb 4 10:23:06 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Thu Feb 4 10:23:06 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e8ffeeff
sci-biology/sambamba: give tarball a proper name
Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/sambamba/sambamba-0.8.0.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/sambamba/sambamba-0.8.0.ebuild b/sci-biology/sambamba/sambamba-0.8.0.ebuild
index d6da97806..d5f7c1359 100644
--- a/sci-biology/sambamba/sambamba-0.8.0.ebuild
+++ b/sci-biology/sambamba/sambamba-0.8.0.ebuild
@@ -8,7 +8,7 @@ LZ4_COMMIT="b3692db46d2b23a7c0af2d5e69988c94f126e10a"
DESCRIPTION="Parallell process SAM/BAM/CRAM files faster than samtools"
HOMEPAGE="https://lomereiter.github.io/sambamba/"
SRC_URI="https://github.com/lomereiter/sambamba/archive/v${PV}.tar.gz -> ${P}.tar.gz
- https://github.com/lz4/lz4/archive/${LZ4_COMMIT}.tar.gz"
+ https://github.com/lz4/lz4/archive/${LZ4_COMMIT}.tar.gz -> lz4-${P}.tar.gz"
LICENSE="GPL-2+"
SLOT="0"
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/sambamba/
@ 2022-01-25 11:16 Andrew Ammerlaan
0 siblings, 0 replies; 5+ messages in thread
From: Andrew Ammerlaan @ 2022-01-25 11:16 UTC (permalink / raw
To: gentoo-commits
commit: 6131f7f5c445d8c658d59ea1ffa26f1a5f541e0e
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 25 11:16:16 2022 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Jan 25 11:16:16 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=6131f7f5
sci-biology/sambamba: remove package
We need a D compiler for this, not packaged in ::gentoo
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/sambamba/metadata.xml | 15 -------------
sci-biology/sambamba/sambamba-0.8.0.ebuild | 36 ------------------------------
sci-biology/sambamba/sambamba-9999.ebuild | 28 -----------------------
3 files changed, 79 deletions(-)
diff --git a/sci-biology/sambamba/metadata.xml b/sci-biology/sambamba/metadata.xml
deleted file mode 100644
index 3c6df6245..000000000
--- a/sci-biology/sambamba/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">lomereiter/sambamba</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/sambamba/sambamba-0.8.0.ebuild b/sci-biology/sambamba/sambamba-0.8.0.ebuild
deleted file mode 100644
index d5f7c1359..000000000
--- a/sci-biology/sambamba/sambamba-0.8.0.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-LZ4_COMMIT="b3692db46d2b23a7c0af2d5e69988c94f126e10a"
-
-DESCRIPTION="Parallell process SAM/BAM/CRAM files faster than samtools"
-HOMEPAGE="https://lomereiter.github.io/sambamba/"
-SRC_URI="https://github.com/lomereiter/sambamba/archive/v${PV}.tar.gz -> ${P}.tar.gz
- https://github.com/lz4/lz4/archive/${LZ4_COMMIT}.tar.gz -> lz4-${P}.tar.gz"
-
-LICENSE="GPL-2+"
-SLOT="0"
-KEYWORDS=""
-IUSE="debug"
-
-# https://github.com/ldc-developers/gentoo-overlay/tree/master/dev-lang/ldc2
-#
-# contains bundled htslib
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-src_unpack() {
- default
- rm -r "${S}/lz4" || die
- mv "${WORKDIR}/lz4-${LZ4_COMMIT}" "${S}/lz4" || die
-}
-
-src_compile(){
- if use debug ; then
- emake debug all
- else
- emake all
- fi
-}
diff --git a/sci-biology/sambamba/sambamba-9999.ebuild b/sci-biology/sambamba/sambamba-9999.ebuild
deleted file mode 100644
index e655b10b0..000000000
--- a/sci-biology/sambamba/sambamba-9999.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit git-r3
-
-DESCRIPTION="Parallell process SAM/BAM/CRAM files faster than samtools"
-HOMEPAGE="https://lomereiter.github.io/sambamba/"
-EGIT_REPO_URI="https://github.com/lomereiter/sambamba.git"
-
-LICENSE="GPL-2+"
-SLOT="0"
-KEYWORDS=""
-IUSE="debug"
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-# https://github.com/ldc-developers/gentoo-overlay/tree/master/dev-lang/ldc2
-
-src_compile(){
- if use debug ; then
- emake debug all
- else
- emake all
- fi
-}
^ permalink raw reply related [flat|nested] 5+ messages in thread
end of thread, other threads:[~2022-01-25 11:16 UTC | newest]
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