* [gentoo-commits] proj/sci:master commit in: sci-biology/trinityrnaseq/
@ 2015-04-30 22:48 Martin Mokrejs
0 siblings, 0 replies; 14+ messages in thread
From: Martin Mokrejs @ 2015-04-30 22:48 UTC (permalink / raw
To: gentoo-commits
commit: 5b84166e0195cbf63e9954986da0798f35ad0aee
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Apr 30 22:45:08 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Apr 30 22:45:08 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=5b84166e
sci-biology/trinityrnaseq: added a note and removed broken symlink upon installation
Package-Manager: portage-2.2.18
sci-biology/trinityrnaseq/ChangeLog | 5 +++++
sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild | 3 +++
2 files changed, 8 insertions(+)
diff --git a/sci-biology/trinityrnaseq/ChangeLog b/sci-biology/trinityrnaseq/ChangeLog
index a630ba3..7a31500 100644
--- a/sci-biology/trinityrnaseq/ChangeLog
+++ b/sci-biology/trinityrnaseq/ChangeLog
@@ -2,6 +2,11 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ trinityrnaseq-2.0.6.ebuild:
+ sci-biology/trinityrnaseq: added a note and removed broken symlink upon
+ installation
+
*trinityrnaseq-2.0.6 (30 Apr 2015)
30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild
index 335d075..2ec2290 100644
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild
+++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild
@@ -28,6 +28,8 @@ RDEPEND="${DEPEND}
# ReleaseNotes mentions that <sci-biology/samtools-1.1 is needed
# version of bundled jellyfish is 2.1.4
+# optionally install https://github.com/HpcGridRunner/HpcGridRunner/releases
+
#src_compile(){
# emake all
# emake plugins # bundled copies of TransDecoder, trimmomatic, fastool, parafly
@@ -41,6 +43,7 @@ src_install(){
dodoc trinity-plugins/fstrozzi-Fastool-7c3e034f05/README.md
#
insinto /usr/share/${PN}/util
+ rm -f util/fasta_tool
doins -r util/*
#
dobin Inchworm/bin/*
^ permalink raw reply related [flat|nested] 14+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/trinityrnaseq/
@ 2015-05-02 16:29 Martin Mokrejs
0 siblings, 0 replies; 14+ messages in thread
From: Martin Mokrejs @ 2015-05-02 16:29 UTC (permalink / raw
To: gentoo-commits
commit: fa3f2a761a2d68aee8b6ad302b9c0903a69f2d70
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat May 2 16:14:37 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat May 2 16:14:37 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=fa3f2a76
sci-biology/trinityrnaseq: added missing quotes
Package-Manager: portage-2.2.18
sci-biology/trinityrnaseq/ChangeLog | 4 ++++
sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild | 18 +++++++++---------
2 files changed, 13 insertions(+), 9 deletions(-)
diff --git a/sci-biology/trinityrnaseq/ChangeLog b/sci-biology/trinityrnaseq/ChangeLog
index 7a31500..f4ce466 100644
--- a/sci-biology/trinityrnaseq/ChangeLog
+++ b/sci-biology/trinityrnaseq/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 02 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ trinityrnaseq-2.0.6.ebuild:
+ sci-biology/trinityrnaseq: added missing quotes
+
30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
trinityrnaseq-2.0.6.ebuild:
sci-biology/trinityrnaseq: added a note and removed broken symlink upon
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild
index 2ec2290..6169bfb 100644
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild
+++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild
@@ -42,25 +42,25 @@ src_install(){
dobin trinity-plugins/fstrozzi-Fastool-7c3e034f05/fastool
dodoc trinity-plugins/fstrozzi-Fastool-7c3e034f05/README.md
#
- insinto /usr/share/${PN}/util
+ insinto /usr/share/"${PN}"/util
rm -f util/fasta_tool
doins -r util/*
#
dobin Inchworm/bin/*
cd Chrysalis
dobin MakeDepend checkLock BreakTransByPairs Chrysalis GraphFromFasta IsoformAugment JoinTransByPairs QuantifyGraph ReadsToTranscripts RunButterfly TranscriptomeFromVaryK analysis/ReadsToComponents.pl
- cd ${S} || die
- insinto ${VENDOR_LIB}/${PN}
+ cd "${S}" || die
+ insinto "${VENDOR_LIB}/${PN}"
doins util/misc/PerlLib/*.pm PerlLib/*.pm
- insinto ${VENDOR_LIB}/${PN}/KmerGraphLib
+ insinto "${VENDOR_LIB}/${PN}"/KmerGraphLib
doins PerlLib/KmerGraphLib/*.pm
- insinto ${VENDOR_LIB}/${PN}/CDNA
+ insinto "${VENDOR_LIB}/${PN}"/CDNA
doins PerlLib/CDNA/*.pm
- insinto ${VENDOR_LIB}/${PN}/HPC
+ insinto "${VENDOR_LIB}/${PN}"/HPC
doins PerlLib/HPC/*.pm
- insinto ${VENDOR_LIB}/${PN}/Simulate
+ insinto "${VENDOR_LIB}/${PN}"/Simulate
doins PerlLib/Simulate/*.pm
- insinto ${VENDOR_LIB}/${PN}/CanvasXpress
+ insinto "${VENDOR_LIB}/${PN}"/CanvasXpress
doins PerlLib/CanvasXpress/*.pm
- chmod a+rx -R ${ED}/${VENDOR_LIB}/${PN}
+ chmod a+rx -R "${ED}/${VENDOR_LIB}/${PN}"
}
^ permalink raw reply related [flat|nested] 14+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/trinityrnaseq/
@ 2015-06-06 10:23 Justin Lecher
0 siblings, 0 replies; 14+ messages in thread
From: Justin Lecher @ 2015-06-06 10:23 UTC (permalink / raw
To: gentoo-commits
commit: e765f59ec430f319abf20fb38cd5c887179de9ef
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jun 6 10:13:18 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jun 6 10:13:18 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e765f59e
sci-biology/trinityrnaseq: Add github to remote-id in metadata.xml
Package-Manager: portage-2.2.20
sci-biology/trinityrnaseq/ChangeLog | 3 +++
sci-biology/trinityrnaseq/metadata.xml | 3 +++
2 files changed, 6 insertions(+)
diff --git a/sci-biology/trinityrnaseq/ChangeLog b/sci-biology/trinityrnaseq/ChangeLog
index f4ce466..c8d81e0 100644
--- a/sci-biology/trinityrnaseq/ChangeLog
+++ b/sci-biology/trinityrnaseq/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml:
+ sci-biology/trinityrnaseq: Add github to remote-id in metadata.xml
+
02 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
trinityrnaseq-2.0.6.ebuild:
sci-biology/trinityrnaseq: added missing quotes
diff --git a/sci-biology/trinityrnaseq/metadata.xml b/sci-biology/trinityrnaseq/metadata.xml
index 2bc8930..5fa67e9 100644
--- a/sci-biology/trinityrnaseq/metadata.xml
+++ b/sci-biology/trinityrnaseq/metadata.xml
@@ -6,4 +6,7 @@
<email>mmokrejs@fold.natur.cuni.cz</email>
<name>Martin Mokrejs</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">trinityrnaseq/trinityrnaseq</remote-id>
+ </upstream>
</pkgmetadata>
^ permalink raw reply related [flat|nested] 14+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/trinityrnaseq/
@ 2015-12-31 21:22 Martin Mokrejs
0 siblings, 0 replies; 14+ messages in thread
From: Martin Mokrejs @ 2015-12-31 21:22 UTC (permalink / raw
To: gentoo-commits
commit: 9942cc6d89af0ff581857128d04cd32071880686
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Dec 31 21:21:05 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Dec 31 21:21:05 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=9942cc6d
sci-biology/trinityrnaseq: do not install bundled GAL but DEPEND on it via external package as sci-biology/GAL
sci-biology/trinityrnaseq/ChangeLog | 5 +++++
sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild | 3 ++-
sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild | 3 ++-
3 files changed, 9 insertions(+), 2 deletions(-)
diff --git a/sci-biology/trinityrnaseq/ChangeLog b/sci-biology/trinityrnaseq/ChangeLog
index 405ac83..29796cf 100644
--- a/sci-biology/trinityrnaseq/ChangeLog
+++ b/sci-biology/trinityrnaseq/ChangeLog
@@ -2,6 +2,11 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Id$
+ 31 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ trinityrnaseq-2.0.6.ebuild, trinityrnaseq-2.1.1.ebuild:
+ sci-biology/trinityrnaseq: do not install bundled GAL but DEPEND on it via
+ external package as sci-biology/GAL
+
*trinityrnaseq-2.1.1 (20 Nov 2015)
20 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild
index 9d8558a..44f2843 100644
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild
+++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild
@@ -24,6 +24,7 @@ RDEPEND="${DEPEND}
sci-biology/parafly
=sci-biology/jellyfish-2.1.4
sci-biology/samtools
+ >=sci-biology/GAL-0.2.1
dev-perl/IO-All"
# ReleaseNotes mentions that <sci-biology/samtools-1.1 is needed
# version of bundled jellyfish is 2.1.4
@@ -43,7 +44,7 @@ src_install(){
dodoc trinity-plugins/fstrozzi-Fastool-7c3e034f05/README.md
#
insinto /usr/share/"${PN}"/util
- rm -f util/fasta_tool
+ rm -f trinity-plugins/GAL_0.2.1 util/fasta_tool
doins -r util/*
#
dobin Inchworm/bin/*
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
index 0d5ba53..49d6b89 100644
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
+++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
@@ -25,6 +25,7 @@ RDEPEND="${DEPEND}
>=sci-libs/htslib-1.2.1
<=sci-biology/samtools-1.1
>=sci-biology/trimmomatic-0.32
+ >=sci-biology/GAL-0.2.1
dev-perl/IO-All"
# ReleaseNotes mentions that <sci-biology/samtools-1.1 is needed
# version of bundled jellyfish is 2.1.4
@@ -52,7 +53,7 @@ src_install(){
dodoc trinity-plugins/fstrozzi-Fastool-7c3e034f05/README.md
#
insinto /usr/share/"${PN}"/util
- rm -f util/fasta_tool
+ rm -f trinity-plugins/GAL_0.2.1 util/fasta_tool
doins -r util/*
#
dobin Inchworm/bin/*
^ permalink raw reply related [flat|nested] 14+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/trinityrnaseq/
@ 2016-01-05 8:54 Marius Brehler
0 siblings, 0 replies; 14+ messages in thread
From: Marius Brehler @ 2016-01-05 8:54 UTC (permalink / raw
To: gentoo-commits
commit: 34d8b8ffbcae869875b972bf8fba46b9d75d9fb5
Author: Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Tue Jan 5 08:53:30 2016 +0000
Commit: Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Tue Jan 5 08:53:30 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=34d8b8ff
sci-biology/trinityrnaseq: Drop KEYWORDS (depends on masked package)
Package-Manager: portage-2.2.26
sci-biology/trinityrnaseq/ChangeLog | 6 +++++-
sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild | 4 ++--
2 files changed, 7 insertions(+), 3 deletions(-)
diff --git a/sci-biology/trinityrnaseq/ChangeLog b/sci-biology/trinityrnaseq/ChangeLog
index 29796cf..4e08cbd 100644
--- a/sci-biology/trinityrnaseq/ChangeLog
+++ b/sci-biology/trinityrnaseq/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for sci-biology/trinityrnaseq
-# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2016 Gentoo Foundation; Distributed under the GPL v2
# $Id$
+ 05 Jan 2016; Marius Brehler <marbre@linux.sungazer.de>
+ trinityrnaseq-2.0.6.ebuild:
+ sci-biology/trinityrnaseq: Drop KEYWORDS (depends on masked package)
+
31 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
trinityrnaseq-2.0.6.ebuild, trinityrnaseq-2.1.1.ebuild:
sci-biology/trinityrnaseq: do not install bundled GAL but DEPEND on it via
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild
index 44f2843..642e863 100644
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild
+++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.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
# $Id$
@@ -16,7 +16,7 @@ SRC_URI="https://github.com/${PN}/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="BSD-BroadInstitute"
SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS=""
IUSE=""
DEPEND=""
^ permalink raw reply related [flat|nested] 14+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/trinityrnaseq/
@ 2016-01-05 8:55 Marius Brehler
0 siblings, 0 replies; 14+ messages in thread
From: Marius Brehler @ 2016-01-05 8:55 UTC (permalink / raw
To: gentoo-commits
commit: 947409e4f7403ac77e7207b0d685a1b47e4edcfd
Author: Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Tue Jan 5 08:55:15 2016 +0000
Commit: Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Tue Jan 5 08:55:15 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=947409e4
sci-biology/trinityrnaseq: Add missing die
Package-Manager: portage-2.2.26
sci-biology/trinityrnaseq/ChangeLog | 4 ++++
sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild | 2 +-
sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild | 4 ++--
3 files changed, 7 insertions(+), 3 deletions(-)
diff --git a/sci-biology/trinityrnaseq/ChangeLog b/sci-biology/trinityrnaseq/ChangeLog
index 4e08cbd..ed29a10 100644
--- a/sci-biology/trinityrnaseq/ChangeLog
+++ b/sci-biology/trinityrnaseq/ChangeLog
@@ -3,6 +3,10 @@
# $Id$
05 Jan 2016; Marius Brehler <marbre@linux.sungazer.de>
+ trinityrnaseq-2.0.6.ebuild, trinityrnaseq-2.1.1.ebuild:
+ sci-biology/trinityrnaseq: Add missing die
+
+ 05 Jan 2016; Marius Brehler <marbre@linux.sungazer.de>
trinityrnaseq-2.0.6.ebuild:
sci-biology/trinityrnaseq: Drop KEYWORDS (depends on masked package)
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild
index 642e863..0e93c19 100644
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild
+++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild
@@ -48,7 +48,7 @@ src_install(){
doins -r util/*
#
dobin Inchworm/bin/*
- cd Chrysalis
+ cd Chrysalis || die
dobin MakeDepend checkLock BreakTransByPairs Chrysalis GraphFromFasta IsoformAugment JoinTransByPairs QuantifyGraph ReadsToTranscripts RunButterfly TranscriptomeFromVaryK analysis/ReadsToComponents.pl
cd "${S}" || die
insinto "${VENDOR_LIB}/${PN}"
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
index 49d6b89..b383de4 100644
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
+++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.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
# $Id$
@@ -57,7 +57,7 @@ src_install(){
doins -r util/*
#
dobin Inchworm/bin/*
- cd Chrysalis
+ cd Chrysalis || die
dobin MakeDepend checkLock BreakTransByPairs Chrysalis GraphFromFasta IsoformAugment JoinTransByPairs QuantifyGraph ReadsToTranscripts RunButterfly TranscriptomeFromVaryK analysis/ReadsToComponents.pl
cd "${S}" || die
insinto "${VENDOR_LIB}/${PN}"
^ permalink raw reply related [flat|nested] 14+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/trinityrnaseq/
@ 2016-04-11 19:46 Martin Mokrejs
0 siblings, 0 replies; 14+ messages in thread
From: Martin Mokrejs @ 2016-04-11 19:46 UTC (permalink / raw
To: gentoo-commits
commit: e1714efc4d71beec0428f59ae0fa6ec7b166bd0a
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Apr 11 19:43:14 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Apr 11 19:43:14 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e1714efc
sci-biology/trinityrnaseq: adjust to sci-biology/samtools using SLOTs now;
installation suffers file collision on /usr/bin/fasta_tool , see usptream github issue #126
Package-Manager: portage-2.2.28
sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild | 2 +-
sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild | 2 +-
.../{trinityrnaseq-2.1.1.ebuild => trinityrnaseq-2.2.0.ebuild} | 2 +-
3 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild
index 0e93c19..226fa17 100644
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild
+++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild
@@ -23,7 +23,7 @@ DEPEND=""
RDEPEND="${DEPEND}
sci-biology/parafly
=sci-biology/jellyfish-2.1.4
- sci-biology/samtools
+ sci-biology/samtools:0.1-legacy
>=sci-biology/GAL-0.2.1
dev-perl/IO-All"
# ReleaseNotes mentions that <sci-biology/samtools-1.1 is needed
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
index b383de4..218e4c3 100644
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
+++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
@@ -23,7 +23,7 @@ RDEPEND="${DEPEND}
sci-biology/parafly
=sci-biology/jellyfish-2.1.4
>=sci-libs/htslib-1.2.1
- <=sci-biology/samtools-1.1
+ sci-biology/samtools:0.1-legacy
>=sci-biology/trimmomatic-0.32
>=sci-biology/GAL-0.2.1
dev-perl/IO-All"
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild
similarity index 98%
copy from sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
copy to sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild
index b383de4..218e4c3 100644
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
+++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild
@@ -23,7 +23,7 @@ RDEPEND="${DEPEND}
sci-biology/parafly
=sci-biology/jellyfish-2.1.4
>=sci-libs/htslib-1.2.1
- <=sci-biology/samtools-1.1
+ sci-biology/samtools:0.1-legacy
>=sci-biology/trimmomatic-0.32
>=sci-biology/GAL-0.2.1
dev-perl/IO-All"
^ permalink raw reply related [flat|nested] 14+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/trinityrnaseq/
@ 2016-04-11 19:57 Martin Mokrejs
0 siblings, 0 replies; 14+ messages in thread
From: Martin Mokrejs @ 2016-04-11 19:57 UTC (permalink / raw
To: gentoo-commits
commit: 1f9880950c49a6543a08ca5d285e32b7fb4c4e91
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Apr 11 19:54:33 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Apr 11 19:54:33 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=1f988095
sci-biology/trinityrnaseq: use 'rm -rf' when deleting a subdirectory with bundled GAL-0.2.1
Package-Manager: portage-2.2.28
sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild | 2 +-
sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild | 2 +-
sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild | 2 +-
3 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild
index 226fa17..88c104f 100644
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild
+++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild
@@ -44,7 +44,7 @@ src_install(){
dodoc trinity-plugins/fstrozzi-Fastool-7c3e034f05/README.md
#
insinto /usr/share/"${PN}"/util
- rm -f trinity-plugins/GAL_0.2.1 util/fasta_tool
+ rm -rf trinity-plugins/GAL_0.2.1 util/fasta_tool
doins -r util/*
#
dobin Inchworm/bin/*
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
index 218e4c3..4a51bdf 100644
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
+++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
@@ -53,7 +53,7 @@ src_install(){
dodoc trinity-plugins/fstrozzi-Fastool-7c3e034f05/README.md
#
insinto /usr/share/"${PN}"/util
- rm -f trinity-plugins/GAL_0.2.1 util/fasta_tool
+ rm -rf trinity-plugins/GAL_0.2.1 util/fasta_tool
doins -r util/*
#
dobin Inchworm/bin/*
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild
index 218e4c3..4a51bdf 100644
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild
+++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild
@@ -53,7 +53,7 @@ src_install(){
dodoc trinity-plugins/fstrozzi-Fastool-7c3e034f05/README.md
#
insinto /usr/share/"${PN}"/util
- rm -f trinity-plugins/GAL_0.2.1 util/fasta_tool
+ rm -rf trinity-plugins/GAL_0.2.1 util/fasta_tool
doins -r util/*
#
dobin Inchworm/bin/*
^ permalink raw reply related [flat|nested] 14+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/trinityrnaseq/
@ 2016-12-01 15:57 Martin Mokrejs
0 siblings, 0 replies; 14+ messages in thread
From: Martin Mokrejs @ 2016-12-01 15:57 UTC (permalink / raw
To: gentoo-commits
commit: e827560c61549b25f628da85a51de6261012868b
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Dec 1 15:57:16 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Dec 1 15:57:16 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e827560c
sci-biology/trinityrnaseq: do not install fasta_tool which belongs to sci-biology/GAL
Package-Manager: portage-2.3.2
sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild | 2 +-
sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild | 2 +-
sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild | 2 +-
3 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild
index 88c104f..55c17ee 100644
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild
+++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild
@@ -38,7 +38,7 @@ RDEPEND="${DEPEND}
src_install(){
perl_set_version
- dobin Trinity util/*.pl trinity-plugins/GAL_0.2.1/fasta_tool
+ dobin Trinity util/*.pl
# should become a new package depending on dev-perl/IO-All
dobin trinity-plugins/fstrozzi-Fastool-7c3e034f05/fastool
dodoc trinity-plugins/fstrozzi-Fastool-7c3e034f05/README.md
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
index 4a51bdf..b94e466 100644
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
+++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
@@ -47,7 +47,7 @@ src_prepare(){
src_install(){
perl_set_version
- dobin Trinity util/*.pl trinity-plugins/GAL_0.2.1/fasta_tool
+ dobin Trinity util/*.pl
# should become a new package depending on dev-perl/IO-All
dobin trinity-plugins/fstrozzi-Fastool-7c3e034f05/fastool
dodoc trinity-plugins/fstrozzi-Fastool-7c3e034f05/README.md
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild
index 4a51bdf..b94e466 100644
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild
+++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild
@@ -47,7 +47,7 @@ src_prepare(){
src_install(){
perl_set_version
- dobin Trinity util/*.pl trinity-plugins/GAL_0.2.1/fasta_tool
+ dobin Trinity util/*.pl
# should become a new package depending on dev-perl/IO-All
dobin trinity-plugins/fstrozzi-Fastool-7c3e034f05/fastool
dodoc trinity-plugins/fstrozzi-Fastool-7c3e034f05/README.md
^ permalink raw reply related [flat|nested] 14+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/trinityrnaseq/
@ 2016-12-07 17:51 Martin Mokrejs
0 siblings, 0 replies; 14+ messages in thread
From: Martin Mokrejs @ 2016-12-07 17:51 UTC (permalink / raw
To: gentoo-commits
commit: bbb461d3b960a06f3725deec10fd3d3c2e87f45b
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Dec 7 17:51:31 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Dec 7 17:51:31 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=bbb461d3
sci-biology/trinityrnaseq: upstream removes fasta_tool script in future versions
Package-Manager: portage-2.3.2
sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild | 1 +
1 file changed, 1 insertion(+)
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild
index b94e466..66f905e 100644
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild
+++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild
@@ -52,6 +52,7 @@ src_install(){
dobin trinity-plugins/fstrozzi-Fastool-7c3e034f05/fastool
dodoc trinity-plugins/fstrozzi-Fastool-7c3e034f05/README.md
#
+ # https://github.com/trinityrnaseq/trinityrnaseq/issues/126
insinto /usr/share/"${PN}"/util
rm -rf trinity-plugins/GAL_0.2.1 util/fasta_tool
doins -r util/*
^ permalink raw reply related [flat|nested] 14+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/trinityrnaseq/
@ 2017-01-10 1:04 Martin Mokrejs
0 siblings, 0 replies; 14+ messages in thread
From: Martin Mokrejs @ 2017-01-10 1:04 UTC (permalink / raw
To: gentoo-commits
commit: 7a150bd50eb5360ef6f9e35f42838ba58f32a4d7
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jan 10 01:04:11 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jan 10 01:04:11 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=7a150bd5
sci-biology/trinityrnaseq: slightly relax required version numbers
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild | 4 ++--
sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild | 4 ++--
sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild | 4 ++--
3 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild
index 55c17ee..6542cd9 100644
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild
+++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.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
# $Id$
@@ -22,7 +22,7 @@ IUSE=""
DEPEND=""
RDEPEND="${DEPEND}
sci-biology/parafly
- =sci-biology/jellyfish-2.1.4
+ >=sci-biology/jellyfish-2.1.4
sci-biology/samtools:0.1-legacy
>=sci-biology/GAL-0.2.1
dev-perl/IO-All"
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
index b94e466..19257d3 100644
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
+++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.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
# $Id$
@@ -21,7 +21,7 @@ IUSE=""
DEPEND=""
RDEPEND="${DEPEND}
sci-biology/parafly
- =sci-biology/jellyfish-2.1.4
+ >=sci-biology/jellyfish-2.1.4
>=sci-libs/htslib-1.2.1
sci-biology/samtools:0.1-legacy
>=sci-biology/trimmomatic-0.32
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild
index 66f905e..3f3638b 100644
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild
+++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.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
# $Id$
@@ -21,7 +21,7 @@ IUSE=""
DEPEND=""
RDEPEND="${DEPEND}
sci-biology/parafly
- =sci-biology/jellyfish-2.1.4
+ >=sci-biology/jellyfish-2.1.4
>=sci-libs/htslib-1.2.1
sci-biology/samtools:0.1-legacy
>=sci-biology/trimmomatic-0.32
^ permalink raw reply related [flat|nested] 14+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/trinityrnaseq/
@ 2018-04-21 18:56 Martin Mokrejs
0 siblings, 0 replies; 14+ messages in thread
From: Martin Mokrejs @ 2018-04-21 18:56 UTC (permalink / raw
To: gentoo-commits
commit: f06b6ae4856f27f991bccd3f6d5a6231869a7991
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Apr 21 18:56:02 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Apr 21 18:56:02 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f06b6ae4
sci-biology/trinityrnaseq: rename patch filename
Package-Manager: Portage-2.3.28, Repoman-2.3.9
sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild | 2 +-
sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
index 8f131cb17..05759d02d 100644
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
+++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
@@ -36,7 +36,7 @@ RDEPEND="${DEPEND}
# optionally install https://github.com/HpcGridRunner/HpcGridRunner/releases
src_prepare(){
- epatch "${FILESDIR}"/disable_some_plugins.patch
+ epatch "${FILESDIR}"/trinityrnaseq-2.1.1-disable_some_plugins.patch
}
#src_compile(){
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild
index 19085d752..6d8da6ab9 100644
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild
+++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild
@@ -36,7 +36,7 @@ RDEPEND="${DEPEND}
# optionally install https://github.com/HpcGridRunner/HpcGridRunner/releases
src_prepare(){
- epatch "${FILESDIR}"/disable_some_plugins.patch
+ epatch "${FILESDIR}"/trinityrnaseq-2.1.1-disable_some_plugins.patch
}
#src_compile(){
^ permalink raw reply related [flat|nested] 14+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/trinityrnaseq/
@ 2021-03-18 18:54 Andrew Ammerlaan
0 siblings, 0 replies; 14+ messages in thread
From: Andrew Ammerlaan @ 2021-03-18 18:54 UTC (permalink / raw
To: gentoo-commits
commit: 1f05480bb02af520c73801fd11cc200432e973e5
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Thu Mar 18 18:51:09 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Thu Mar 18 18:51:09 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=1f05480b
sci-biology/trinityrnaseq: use perl_domodule
Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/trinityrnaseq/trinityrnaseq-2.11.0.ebuild | 15 +++++----------
1 file changed, 5 insertions(+), 10 deletions(-)
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.11.0.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.11.0.ebuild
index 4fd8dac9a..30bd4ca62 100644
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.11.0.ebuild
+++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.11.0.ebuild
@@ -61,15 +61,10 @@ src_install(){
cd .. || die
cp -rp support_scripts misc "${ED}"/usr/share/"${PN}"/ || die
cd "${S}" || die
- insinto "${VENDOR_LIB}/${PN}"
- doins util/misc/PerlLib/*.pm PerlLib/*.pm
- insinto "${VENDOR_LIB}/${PN}"/KmerGraphLib
- doins PerlLib/KmerGraphLib/*.pm
- insinto "${VENDOR_LIB}/${PN}"/CDNA
- doins PerlLib/CDNA/*.pm
- insinto "${VENDOR_LIB}/${PN}"/Simulate
- doins PerlLib/Simulate/*.pm
- insinto "${VENDOR_LIB}/${PN}"/CanvasXpress
- doins PerlLib/CanvasXpress/*.pm
+ perl_domodule util/misc/PerlLib/*.pm PerlLib/*.pm
+ perl_domodule PerlLib/KmerGraphLib/*.pm
+ perl_domodule PerlLib/CDNA/*.pm
+ perl_domodule PerlLib/Simulate/*.pm
+ perl_domodule PerlLib/CanvasXpress/*.pm
chmod a+rx -R "${ED}/${VENDOR_LIB}/${PN}"
}
^ permalink raw reply related [flat|nested] 14+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/trinityrnaseq/
@ 2022-01-25 10:20 Andrew Ammerlaan
0 siblings, 0 replies; 14+ messages in thread
From: Andrew Ammerlaan @ 2022-01-25 10:20 UTC (permalink / raw
To: gentoo-commits
commit: 7f5edd6bb6505ec292bf540e7ad1b34fbe9ec59a
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 25 10:19:22 2022 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Jan 25 10:19:22 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=7f5edd6b
sci-biology/trinityrnaseq: bump to 2.1.3.2
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
.../trinityrnaseq/trinityrnaseq-2.11.0.ebuild | 70 ----------------------
.../trinityrnaseq/trinityrnaseq-2.13.2.ebuild | 45 ++++++++++++++
2 files changed, 45 insertions(+), 70 deletions(-)
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.11.0.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.11.0.ebuild
deleted file mode 100644
index 9ecaf24f2..000000000
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.11.0.ebuild
+++ /dev/null
@@ -1,70 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit perl-module
-
-# Butterfly should not require any special compilation, as its written in Java and already provided as portable precompiled software ...
-
-DESCRIPTION="Transcriptome assembler for RNA-seq reads"
-HOMEPAGE="https://github.com/Trinotate/Trinotate.github.io/wiki"
-SRC_URI="https://github.com/trinityrnaseq/trinityrnaseq/releases/download/v${PV}/${PN}-v${PV}.FULL_with_extendedTestData.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD-BroadInstitute"
-SLOT="0"
-KEYWORDS="" # PERL5INC path is wrong when /usr/bin/Trinity is executed
-
-DEPEND=""
-RDEPEND="${DEPEND}
- sci-biology/parafly
- >=sci-biology/jellyfish-2.2.6:2
- >=sci-libs/htslib-1.2.1
- >=sci-biology/samtools-1.3:0
- >=sci-biology/trimmomatic-0.36
- >=sci-biology/GAL-0.2.1
- dev-perl/IO-All
- sci-biology/seqtools"
-# optionally install https://github.com/HpcGridRunner/HpcGridRunner/releases
-# has the following "plugins" (aka bundled 3rd-party code)
-# slclust
-# DEXseq_util
-# COLLECTL
-# ParaFly-0.1.0
-
-S="${WORKDIR}/${PN}-v${PV}"
-
-PATCHES=(
- "${FILESDIR}/${PN}-2.11.0-fix-compilation.patch"
-)
-
-src_compile(){
- emake all
- emake plugins # bundled copies of TransDecoder, trimmomatic, fastool, parafly
-}
-
-src_install(){
- dodoc Chrysalis/chrysalis.notes
- dodoc Changelog.txt
- perl_set_version
- dobin Trinity
- perl_domodule util/*.pl
- dobin Inchworm/bin/*
- cd Chrysalis/bin || die
- dobin BubbleUpClustering Chrysalis CreateIwormFastaBundle GraphFromFasta QuantifyGraph ReadsToTranscripts
- cd ../../util/R || die
- insinto /usr/share/"${PN}"/R
- doins *.R
- cd ../PBS || die
- insinto /usr/share/"${PN}"/PBS
- doins *
- cd .. || die
- cp -rp support_scripts misc "${ED}"/usr/share/"${PN}"/ || die
- cd "${S}" || die
- perl_domodule util/misc/PerlLib/*.pm PerlLib/*.pm
- perl_domodule PerlLib/KmerGraphLib/*.pm
- perl_domodule PerlLib/CDNA/*.pm
- perl_domodule PerlLib/Simulate/*.pm
- perl_domodule PerlLib/CanvasXpress/*.pm
- chmod a+rx -R "${ED}/${VENDOR_LIB}/${PN}"
-}
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.13.2.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.13.2.ebuild
new file mode 100644
index 000000000..3b94d9713
--- /dev/null
+++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.13.2.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit perl-module
+
+DESCRIPTION="Transcriptome assembler for RNA-seq reads"
+HOMEPAGE="https://github.com/Trinotate/Trinotate.github.io/wiki"
+SRC_URI="https://github.com/${PN}/${PN}/releases/download/Trinity-v${PV}/${PN}-v${PV}.FULL_with_extendedTestData.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${PN}-v${PV}"
+
+LICENSE="BSD-BroadInstitute"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND=""
+RDEPEND="${DEPEND}
+ sci-biology/parafly
+ >=sci-biology/jellyfish-2.2.6:2
+ >=sci-libs/htslib-1.2.1
+ >=sci-biology/samtools-1.3:0
+ >=sci-biology/trimmomatic-0.36
+ >=sci-biology/GAL-0.2.1
+ dev-perl/IO-All
+ sci-biology/seqtools
+"
+
+PATCHES=(
+ "${FILESDIR}/${PN}-2.11.0-fix-compilation.patch"
+)
+
+src_compile(){
+ # missing submodule for bamsifter
+ emake no_bamsifter
+ emake plugins
+}
+
+src_install(){
+ # fix the install path
+ sed -e "s:/usr/local/bin:${ED}/usr/bin:g" \
+ -i util/support_scripts/trinity_installer.py || die
+ dodir /usr/bin
+ default
+}
^ permalink raw reply related [flat|nested] 14+ messages in thread
end of thread, other threads:[~2022-01-25 10:20 UTC | newest]
Thread overview: 14+ messages (download: mbox.gz follow: Atom feed
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2015-05-02 16:29 Martin Mokrejs
2015-06-06 10:23 Justin Lecher
2015-12-31 21:22 Martin Mokrejs
2016-01-05 8:54 Marius Brehler
2016-01-05 8:55 Marius Brehler
2016-04-11 19:46 Martin Mokrejs
2016-04-11 19:57 Martin Mokrejs
2016-12-01 15:57 Martin Mokrejs
2016-12-07 17:51 Martin Mokrejs
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