* [gentoo-commits] proj/sci:master commit in: sci-biology/SEECER/
@ 2015-01-07 22:31 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2015-01-07 22:31 UTC (permalink / raw
To: gentoo-commits
commit: 048f49ddebd47dfe85fdffad7ec869913a6ccec7
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jan 7 22:30:38 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jan 7 22:30:38 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=048f49dd
Initial ebuild
---
sci-biology/SEECER/ChangeLog | 10 ++++++++++
sci-biology/SEECER/SEECER-0.1.3.ebuild | 33 +++++++++++++++++++++++++++++++++
sci-biology/SEECER/metadata.xml | 9 +++++++++
3 files changed, 52 insertions(+)
diff --git a/sci-biology/SEECER/ChangeLog b/sci-biology/SEECER/ChangeLog
new file mode 100644
index 0000000..1e865a6
--- /dev/null
+++ b/sci-biology/SEECER/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/SEECER
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*SEECER-0.1.3 (07 Jan 2015)
+
+ 07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +SEECER-0.1.3.ebuild, +metadata.xml:
+ initial ebuild
+
diff --git a/sci-biology/SEECER/SEECER-0.1.3.ebuild b/sci-biology/SEECER/SEECER-0.1.3.ebuild
new file mode 100644
index 0000000..7f3833e
--- /dev/null
+++ b/sci-biology/SEECER/SEECER-0.1.3.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Error corrector for RNA-Seq reads"
+HOMEPAGE="http://sb.cs.cmu.edu/seecer/"
+SRC_URI="http://sb.cs.cmu.edu/seecer/downloads/SEECER-0.1.3.tar.gz
+ http://sb.cs.cmu.edu/seecer/downloads/manual.pdf"
+
+LICENSE=""
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="sci-libs/gsl
+ sci-biology/seqan
+ sci-biology/jellyfish"
+RDEPEND="${DEPEND}"
+
+S="${S}"/SEECER
+
+# doh, it install /usr/bin/seecer (note the lowercase letters)
+
+# checking for x86_64-pc-linux-gnu-gcc option to support OpenMP... -fopenmp
+#
+# Uses:
+# libgomp.so.1 => /usr/lib/gcc/x86_64-pc-linux-gnu/4.8.3/libgomp.so.1 (0x00007f7853faf000)
+
+
+# dobin bin/run_seecer.sh
+# dodoc "${DISTDIR}"/manual.pdf
diff --git a/sci-biology/SEECER/metadata.xml b/sci-biology/SEECER/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/SEECER/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] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/SEECER/
@ 2015-01-10 14:37 Justin Lecher
0 siblings, 0 replies; 7+ messages in thread
From: Justin Lecher @ 2015-01-10 14:37 UTC (permalink / raw
To: gentoo-commits
commit: 495d790cea315b38978ec1d8738f7dd961c118a3
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 10 14:13:39 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jan 10 14:13:39 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=495d790c
sci-biology/SEECER: Fix license
Package-Manager: portage-2.2.15
---
sci-biology/SEECER/ChangeLog | 3 +++
sci-biology/SEECER/SEECER-0.1.3.ebuild | 9 +++++----
2 files changed, 8 insertions(+), 4 deletions(-)
diff --git a/sci-biology/SEECER/ChangeLog b/sci-biology/SEECER/ChangeLog
index 1e865a6..1ac7a38 100644
--- a/sci-biology/SEECER/ChangeLog
+++ b/sci-biology/SEECER/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 10 Jan 2015; Justin Lecher <jlec@gentoo.org> SEECER-0.1.3.ebuild:
+ Fix license
+
*SEECER-0.1.3 (07 Jan 2015)
07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/SEECER/SEECER-0.1.3.ebuild b/sci-biology/SEECER/SEECER-0.1.3.ebuild
index 7f3833e..d415a01 100644
--- a/sci-biology/SEECER/SEECER-0.1.3.ebuild
+++ b/sci-biology/SEECER/SEECER-0.1.3.ebuild
@@ -6,15 +6,17 @@ EAPI=5
DESCRIPTION="Error corrector for RNA-Seq reads"
HOMEPAGE="http://sb.cs.cmu.edu/seecer/"
-SRC_URI="http://sb.cs.cmu.edu/seecer/downloads/SEECER-0.1.3.tar.gz
+SRC_URI="
+ http://sb.cs.cmu.edu/seecer/downloads/SEECER-0.1.3.tar.gz
http://sb.cs.cmu.edu/seecer/downloads/manual.pdf"
-LICENSE=""
+LICENSE="GPL-3"
SLOT="0"
KEYWORDS=""
IUSE=""
-DEPEND="sci-libs/gsl
+DEPEND="
+ sci-libs/gsl
sci-biology/seqan
sci-biology/jellyfish"
RDEPEND="${DEPEND}"
@@ -28,6 +30,5 @@ S="${S}"/SEECER
# Uses:
# libgomp.so.1 => /usr/lib/gcc/x86_64-pc-linux-gnu/4.8.3/libgomp.so.1 (0x00007f7853faf000)
-
# dobin bin/run_seecer.sh
# dodoc "${DISTDIR}"/manual.pdf
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/SEECER/
@ 2015-11-12 0:32 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2015-11-12 0:32 UTC (permalink / raw
To: gentoo-commits
commit: d9df37217fca3b4f9de03d13f3891c9267f5f191
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Nov 12 00:31:36 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Nov 12 00:31:36 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=d9df3721
sci-biology/SEECER: install also the main program wrapper
Package-Manager: portage-2.2.18
sci-biology/SEECER/ChangeLog | 4 ++++
sci-biology/SEECER/SEECER-0.1.3-r1.ebuild | 2 +-
2 files changed, 5 insertions(+), 1 deletion(-)
diff --git a/sci-biology/SEECER/ChangeLog b/sci-biology/SEECER/ChangeLog
index 6776868..eae131d 100644
--- a/sci-biology/SEECER/ChangeLog
+++ b/sci-biology/SEECER/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>
+ SEECER-0.1.3-r1.ebuild:
+ sci-biology/SEECER: install also the main program wrapper
+
*SEECER-0.1.3-r1 (30 Apr 2015)
30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/SEECER/SEECER-0.1.3-r1.ebuild b/sci-biology/SEECER/SEECER-0.1.3-r1.ebuild
index d9f5667..1110b97 100644
--- a/sci-biology/SEECER/SEECER-0.1.3-r1.ebuild
+++ b/sci-biology/SEECER/SEECER-0.1.3-r1.ebuild
@@ -30,6 +30,6 @@ src_prepare(){
}
src_install(){
- dobin bin/seecer bin/random_sub_N bin/replace_ids bin/run_jellyfish.sh
+ dobin bin/seecer bin/random_sub_N bin/replace_ids bin/run_jellyfish.sh bin/run_seecer.sh
dodoc README "${DISTDIR}"/"${PN}"-manual.pdf
}
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/SEECER/
@ 2015-11-15 18:43 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2015-11-15 18:43 UTC (permalink / raw
To: gentoo-commits
commit: e1d13a2f0d3827367a8e5b10813a1dafbcbd46ae
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Nov 15 18:42:06 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Nov 15 18:42:06 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e1d13a2f
sci-biology/SEECER: add einfo() message that default kmer size 17 is suboptimal
Package-Manager: portage-2.2.18
sci-biology/SEECER/ChangeLog | 5 +++++
sci-biology/SEECER/SEECER-0.1.3-r2.ebuild | 13 +++++++++++--
2 files changed, 16 insertions(+), 2 deletions(-)
diff --git a/sci-biology/SEECER/ChangeLog b/sci-biology/SEECER/ChangeLog
index b72cc46..1302cab 100644
--- a/sci-biology/SEECER/ChangeLog
+++ b/sci-biology/SEECER/ChangeLog
@@ -2,6 +2,11 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Id$
+ 15 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ SEECER-0.1.3-r2.ebuild:
+ sci-biology/SEECER: add einfo() message that default kmer size 17 is
+ suboptimal
+
13 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
SEECER-0.1.3-r2.ebuild, files/remove-hardcoded-paths.patch:
sci-biology/SEECER: patch crappy shellscripts to at leats die on error;
diff --git a/sci-biology/SEECER/SEECER-0.1.3-r2.ebuild b/sci-biology/SEECER/SEECER-0.1.3-r2.ebuild
index 3a9138c..8d8e919 100644
--- a/sci-biology/SEECER/SEECER-0.1.3-r2.ebuild
+++ b/sci-biology/SEECER/SEECER-0.1.3-r2.ebuild
@@ -8,13 +8,18 @@ inherit eutils
DESCRIPTION="SEquencing Error Corrector for RNA-Seq reads"
HOMEPAGE="http://sb.cs.cmu.edu/seecer/"
-SRC_URI="
+if [ "$PV" == "9999" ]; then
+ EGIT_REPO_URI="https://github.com/haisonle/SEECER.git"
+ KEYWORDS=""
+else
+ SRC_URI="
http://sb.cs.cmu.edu/seecer/downloads/"${P}".tar.gz
http://sb.cs.cmu.edu/seecer/downloads/manual.pdf -> "${PN}"-manual.pdf"
+ KEYWORDS="~amd64"
+fi
LICENSE="GPL-3"
SLOT="0"
-KEYWORDS="~amd64"
IUSE=""
# although has bundled jellyfish-1.1.11 copy it just calls the executable during runtime
@@ -37,3 +42,7 @@ src_install(){
dobin bin/seecer bin/random_sub_N bin/replace_ids bin/run_jellyfish.sh bin/run_seecer.sh
dodoc README "${DISTDIR}"/"${PN}"-manual.pdf
}
+
+pkg_postinst(){
+ einfo "Note that the default kmer size 17 is terribly suboptimal, use k=31 instead"
+}
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/SEECER/
@ 2017-01-29 14:20 Justin Lecher
0 siblings, 0 replies; 7+ messages in thread
From: Justin Lecher @ 2017-01-29 14:20 UTC (permalink / raw
To: gentoo-commits
commit: c38274779a20385ad70d5c2aa2dac34d8525868d
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jan 29 13:44:25 2017 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jan 29 13:44:25 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c3827477
sci-biology/SEECER: QA fixes
Bump to6 EAPI
drop non active code
add missing slot operator
Package-Manager: Portage-2.3.3, Repoman-2.3.1
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-biology/SEECER/SEECER-0.1.3-r2.ebuild | 23 +++++++++++------------
sci-biology/SEECER/metadata.xml | 2 +-
2 files changed, 12 insertions(+), 13 deletions(-)
diff --git a/sci-biology/SEECER/SEECER-0.1.3-r2.ebuild b/sci-biology/SEECER/SEECER-0.1.3-r2.ebuild
index 8d8e919..f2b5a67 100644
--- a/sci-biology/SEECER/SEECER-0.1.3-r2.ebuild
+++ b/sci-biology/SEECER/SEECER-0.1.3-r2.ebuild
@@ -1,41 +1,40 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
-EAPI=5
+EAPI=6
inherit eutils
DESCRIPTION="SEquencing Error Corrector for RNA-Seq reads"
HOMEPAGE="http://sb.cs.cmu.edu/seecer/"
-if [ "$PV" == "9999" ]; then
- EGIT_REPO_URI="https://github.com/haisonle/SEECER.git"
- KEYWORDS=""
-else
- SRC_URI="
+SRC_URI="
http://sb.cs.cmu.edu/seecer/downloads/"${P}".tar.gz
http://sb.cs.cmu.edu/seecer/downloads/manual.pdf -> "${PN}"-manual.pdf"
- KEYWORDS="~amd64"
-fi
LICENSE="GPL-3"
SLOT="0"
IUSE=""
+KEYWORDS="~amd64"
# although has bundled jellyfish-1.1.11 copy it just calls the executable during runtime
# seems jellyfish-2 does not accept same commandline arguments
DEPEND="
- sci-libs/gsl
- sci-biology/seqan"
+ sci-libs/gsl:0=
+ sci-biology/seqan:0="
RDEPEND="${DEPEND}
=sci-biology/jellyfish-1.1.11"
S="${S}"/SEECER
+PATCHES=(
+ "${FILESDIR}"/remove-hardcoded-paths.patch
+)
+
src_prepare(){
# http://seecer-rna-read-error-correction-mailing-list.21961.x6.nabble.com/Segmentation-fault-in-step-4-td41.html
cp -p "${FILESDIR}"/replace_ids.cc "${S}"/src/ || die
- epatch "${FILESDIR}"/remove-hardcoded-paths.patch
+ default
}
src_install(){
diff --git a/sci-biology/SEECER/metadata.xml b/sci-biology/SEECER/metadata.xml
index 1699e58..f68a1b6 100644
--- a/sci-biology/SEECER/metadata.xml
+++ b/sci-biology/SEECER/metadata.xml
@@ -5,7 +5,7 @@
<email>mmokrejs@fold.natur.cuni.cz</email>
<name>Martin Mokrejs</name>
</maintainer>
-<maintainer type="project">
+ <maintainer type="project">
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/SEECER/
@ 2017-11-21 14:03 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2017-11-21 14:03 UTC (permalink / raw
To: gentoo-commits
commit: 8c3e0095958a9efae40423c93b9b6480152d32b1
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Nov 21 14:03:47 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Nov 21 14:03:47 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=8c3e0095
sci-biology/SEECER: remove stale .swp files from mschulz
Package-Manager: Portage-2.3.14, Repoman-2.3.6
sci-biology/SEECER/SEECER-0.1.3-r2.ebuild | 1 +
1 file changed, 1 insertion(+)
diff --git a/sci-biology/SEECER/SEECER-0.1.3-r2.ebuild b/sci-biology/SEECER/SEECER-0.1.3-r2.ebuild
index ac49a7503..60862d8c8 100644
--- a/sci-biology/SEECER/SEECER-0.1.3-r2.ebuild
+++ b/sci-biology/SEECER/SEECER-0.1.3-r2.ebuild
@@ -33,6 +33,7 @@ PATCHES=(
src_prepare(){
# http://seecer-rna-read-error-correction-mailing-list.21961.x6.nabble.com/Segmentation-fault-in-step-4-td41.html
cp -p "${FILESDIR}"/replace_ids.cc "${S}"/src/ || die
+ rm -f bin/.run*.swp || die
default
}
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/SEECER/
@ 2021-03-05 15:54 Andrew Ammerlaan
0 siblings, 0 replies; 7+ messages in thread
From: Andrew Ammerlaan @ 2021-03-05 15:54 UTC (permalink / raw
To: gentoo-commits
commit: 1a5bc27fa079f59ddf98753103c24b11c8301ce3
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Fri Mar 5 15:51:56 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Fri Mar 5 15:51:56 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=1a5bc27f
sci-biology/SEECER: EAPI bump
Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/SEECER/SEECER-0.1.3-r2.ebuild | 9 +++------
1 file changed, 3 insertions(+), 6 deletions(-)
diff --git a/sci-biology/SEECER/SEECER-0.1.3-r2.ebuild b/sci-biology/SEECER/SEECER-0.1.3-r2.ebuild
index 49ebd3879..c30b872a7 100644
--- a/sci-biology/SEECER/SEECER-0.1.3-r2.ebuild
+++ b/sci-biology/SEECER/SEECER-0.1.3-r2.ebuild
@@ -1,9 +1,7 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
-
-inherit eutils
+EAPI=7
DESCRIPTION="SEquence Error Corrector for RNA-Seq reads"
HOMEPAGE="http://sb.cs.cmu.edu/seecer/"
@@ -13,7 +11,6 @@ SRC_URI="
LICENSE="GPL-3"
SLOT="0"
-IUSE=""
KEYWORDS="~amd64"
# although has bundled jellyfish-1.1.11 copy it just calls the executable during runtime
@@ -24,7 +21,7 @@ DEPEND="
RDEPEND="${DEPEND}
sci-biology/jellyfish:1"
-S="${S}"/SEECER
+S="${WORKDIR}/${P}/SEECER"
PATCHES=(
"${FILESDIR}"/remove-hardcoded-paths.patch
^ permalink raw reply related [flat|nested] 7+ messages in thread
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