sci-biology/trinityrnaseq
Transcriptome assembler for RNA-seq reads
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commit 7f5edd6bb6505ec292bf540e7ad1b34fbe9ec59a
Author: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
Date: Tue Jan 25 11:19:22 2022 +0100
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@gentoo.org>
commit 2d72ece0d970ae520b1b54a2d0a32d814e78042a
Author: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
Date: Thu Dec 16 11:38:27 2021 +0100
sci-biology/trinityrnaseq: drop UnusedInherits
Package-Manager: Portage-3.0.28, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
commit 1f05480bb02af520c73801fd11cc200432e973e5
Author: Andrew Ammerlaan <andrewammerlaan@riseup.net>
Date: Thu Mar 18 19:51:09 2021 +0100
sci-biology/trinityrnaseq: use perl_domodule
Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
commit 451b8632c92318dc8aec4ec7b625a968c30a28be
Author: Andrew Ammerlaan <andrewammerlaan@riseup.net>
Date: Mon Feb 1 10:13:31 2021 +0100
sci-biology/trinityrnaseq: version bump 2.11.0
no keywords, because dep GAL is missing them
Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
commit 307a9995cc3b29bd9726ad7ade53132c7c08f7fa
Author: Justin Lecher <jlec@gentoo.org>
Date: Sat Oct 27 21:03:05 2018 +0100
Sort keywords
Signed-off-by: Justin Lecher <jlec@gentoo.org>
commit aef6b7cc29677f3720adb39bebdc124ab6f64aa7
Author: Justin Lecher <jlec@gentoo.org>
Date: Sat Oct 27 20:45:04 2018 +0100
Sort keywords
Signed-off-by: Justin Lecher <jlec@gentoo.org>
commit f06b6ae4856f27f991bccd3f6d5a6231869a7991
Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Sat Apr 21 20:56:02 2018 +0200
sci-biology/trinityrnaseq: rename patch filename
Package-Manager: Portage-2.3.28, Repoman-2.3.9
commit 2dffd7378f16086d11d32432d30d0325d40d3238
Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Sat Apr 21 20:53:23 2018 +0200
sci-biology/trinityrnaseq: version bump (no KEYWORDS set)
The perl include paths are not matching the paths in *.pm files
all *.pm need to be patched so that they could be placed into
site_perl subdirectory.
In brief, the package still does not support installation into
a site-wide directory. users are supposed to executed off the
unpacked tarball directly.
Package-Manager: Portage-2.3.28, Repoman-2.3.9
commit 3072d10e6c4f21185d53e4728d0fa0fad58537e7
Author: Justin Lecher <jlec@gentoo.org>
Date: Sun Dec 10 22:20:38 2017 +0000
Update Manifests to new hashes
Signed-off-by: Justin Lecher <jlec@gentoo.org>
commit bce61aa3e4fe85fe411df858eb30ebe72a3a8f88
Author: Justin Lecher <jlec@gentoo.org>
Date: Sat Nov 18 20:39:44 2017 +0000
Consistently ident with tabs
Signed-off-by: Justin Lecher <jlec@gentoo.org>
commit 3199ec7737e923dc19479e5de7b31bb583071931
Author: Justin Lecher <jlec@gentoo.org>
Date: Sun Apr 30 11:12:48 2017 +0100
Cleanup remote IDs
Signed-off-by: Justin Lecher <jlec@gentoo.org>
commit f69e73182fc7cdc6c600a72fceb88ae1626db25d
Author: Justin Lecher <jlec@gentoo.org>
Date: Sat Feb 25 16:50:59 2017 +0000
Drop leftover from CVS in HEADER
Signed-off-by: Justin Lecher <jlec@gentoo.org>
commit 7a150bd50eb5360ef6f9e35f42838ba58f32a4d7
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Tue Jan 10 02:04:11 2017 +0100
sci-biology/trinityrnaseq: slightly relax required version numbers
Package-Manager: Portage-2.3.3, Repoman-2.3.1
commit bbb461d3b960a06f3725deec10fd3d3c2e87f45b
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Wed Dec 7 18:51:31 2016 +0100
sci-biology/trinityrnaseq: upstream removes fasta_tool script in future versions
Package-Manager: portage-2.3.2
commit e827560c61549b25f628da85a51de6261012868b
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Thu Dec 1 16:57:16 2016 +0100
sci-biology/trinityrnaseq: do not install fasta_tool which belongs to sci-biology/GAL
Package-Manager: portage-2.3.2
commit 1f9880950c49a6543a08ca5d285e32b7fb4c4e91
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Mon Apr 11 21:54:33 2016 +0200
sci-biology/trinityrnaseq: use 'rm -rf' when deleting a subdirectory with bundled GAL-0.2.1
Package-Manager: portage-2.2.28
commit e1714efc4d71beec0428f59ae0fa6ec7b166bd0a
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Mon Apr 11 21:43:14 2016 +0200
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
commit 057a98c5e6346d6696fcc7b0ec8fefc9e826245f
Author: Justin Lecher <jlec@gentoo.org>
Date: Mon Jan 25 09:53:09 2016 +0100
metadata.xml: Set type
Signed-off-by: Justin Lecher <jlec@gentoo.org>
commit b9d823e1ea1018d1356a0c18a083eab4d5ea6d8d
Author: Justin Lecher <jlec@gentoo.org>
Date: Mon Jan 25 09:50:12 2016 +0100
metadata.xml: convert hard -> proj
Signed-off-by: Justin Lecher <jlec@gentoo.org>
commit 2ef24e800910be3786e23a31a0217ba0f38659f8
Author: Justin Lecher <jlec@gentoo.org>
Date: Thu Jan 7 15:10:39 2016 +0100
Drop ChangeLogs in favour of commit messages
Signed-off-by: Justin Lecher <jlec@gentoo.org>
commit 947409e4f7403ac77e7207b0d685a1b47e4edcfd
Author: Marius Brehler <marbre@linux.sungazer.de>
Date: Tue Jan 5 09:55:15 2016 +0100
sci-biology/trinityrnaseq: Add missing die
Package-Manager: portage-2.2.26
commit 34d8b8ffbcae869875b972bf8fba46b9d75d9fb5
Author: Marius Brehler <marbre@linux.sungazer.de>
Date: Tue Jan 5 09:53:30 2016 +0100
sci-biology/trinityrnaseq: Drop KEYWORDS (depends on masked package)
Package-Manager: portage-2.2.26
commit 9942cc6d89af0ff581857128d04cd32071880686
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Thu Dec 31 22:21:05 2015 +0100
sci-biology/trinityrnaseq: do not install bundled GAL but DEPEND on it via external package as sci-biology/GAL
commit e1a9394386238099ece40fe0e8d7f805c23b679d
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Sat Nov 21 00:54:55 2015 +0100
sci-biology/trinityrnaseq: version bump but dropping KEYWORDS because we relocate *.pm file into vendor_perl and all 'use blah' calls to trinity-provided perl modules need to be changed to 'use trinityrnaseq::blah', or PERL5INC modified?
Package-Manager: portage-2.2.18
commit 6271f0c55cbb6af7fe88ae1ec9d7dbdedd562565
Author: Justin Lecher <jlec@gentoo.org>
Date: Mon Aug 17 08:53:12 2015 +0200
Convert all $Header$ to $Id$ tags as it has be done in gentoo.git
Signed-off-by: Justin Lecher <jlec@gentoo.org>
commit a891336052fb27fd9f3f82e33c30f0984f50ea54
Author: Justin Lecher <jlec@gentoo.org>
Date: Sun Jun 21 12:25:27 2015 +0200
Revert "Gentoo does https by default now"
This reverts commit 98718494343af4990facdefb0033471686e975a6.
commit 98718494343af4990facdefb0033471686e975a6
Author: Justin Lecher <jlec@gentoo.org>
Date: Sun Jun 21 12:14:25 2015 +0200
Gentoo does https by default now
Signed-off-by: Justin Lecher <jlec@gentoo.org>
commit e765f59ec430f319abf20fb38cd5c887179de9ef
Author: Justin Lecher <jlec@gentoo.org>
Date: Sat Jun 6 12:13:18 2015 +0200
sci-biology/trinityrnaseq: Add github to remote-id in metadata.xml
Package-Manager: portage-2.2.20
commit fa3f2a761a2d68aee8b6ad302b9c0903a69f2d70
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Sat May 2 18:14:37 2015 +0200
sci-biology/trinityrnaseq: added missing quotes
Package-Manager: portage-2.2.18
commit 5b84166e0195cbf63e9954986da0798f35ad0aee
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Fri May 1 00:45:08 2015 +0200
sci-biology/trinityrnaseq: added a note and removed broken symlink upon installation
Package-Manager: portage-2.2.18
commit cd5ffe2b8f606c841206f700c8718f5c3b7fda9e
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Thu Apr 30 12:52:33 2015 +0200
sci-biology/trinityrnaseq: version bump; dropped patches because target file is gone; ideally should depend on <sci-biology/samtools-1.1 but lets see what are the real requirements
Package-Manager: portage-2.2.18
commit 5d1cf37ff6399cd2ad05dd51f23f67a24f94ae2e
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Thu Apr 30 11:25:42 2015 +0200
sci-biology/trinityrnaseq: new package (with last release on sourceforge)
Package-Manager: portage-2.2.18
Author: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
Date: Tue Jan 25 11:19:22 2022 +0100
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@gentoo.org>
commit 2d72ece0d970ae520b1b54a2d0a32d814e78042a
Author: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
Date: Thu Dec 16 11:38:27 2021 +0100
sci-biology/trinityrnaseq: drop UnusedInherits
Package-Manager: Portage-3.0.28, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
commit 1f05480bb02af520c73801fd11cc200432e973e5
Author: Andrew Ammerlaan <andrewammerlaan@riseup.net>
Date: Thu Mar 18 19:51:09 2021 +0100
sci-biology/trinityrnaseq: use perl_domodule
Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
commit 451b8632c92318dc8aec4ec7b625a968c30a28be
Author: Andrew Ammerlaan <andrewammerlaan@riseup.net>
Date: Mon Feb 1 10:13:31 2021 +0100
sci-biology/trinityrnaseq: version bump 2.11.0
no keywords, because dep GAL is missing them
Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
commit 307a9995cc3b29bd9726ad7ade53132c7c08f7fa
Author: Justin Lecher <jlec@gentoo.org>
Date: Sat Oct 27 21:03:05 2018 +0100
Sort keywords
Signed-off-by: Justin Lecher <jlec@gentoo.org>
commit aef6b7cc29677f3720adb39bebdc124ab6f64aa7
Author: Justin Lecher <jlec@gentoo.org>
Date: Sat Oct 27 20:45:04 2018 +0100
Sort keywords
Signed-off-by: Justin Lecher <jlec@gentoo.org>
commit f06b6ae4856f27f991bccd3f6d5a6231869a7991
Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Sat Apr 21 20:56:02 2018 +0200
sci-biology/trinityrnaseq: rename patch filename
Package-Manager: Portage-2.3.28, Repoman-2.3.9
commit 2dffd7378f16086d11d32432d30d0325d40d3238
Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Sat Apr 21 20:53:23 2018 +0200
sci-biology/trinityrnaseq: version bump (no KEYWORDS set)
The perl include paths are not matching the paths in *.pm files
all *.pm need to be patched so that they could be placed into
site_perl subdirectory.
In brief, the package still does not support installation into
a site-wide directory. users are supposed to executed off the
unpacked tarball directly.
Package-Manager: Portage-2.3.28, Repoman-2.3.9
commit 3072d10e6c4f21185d53e4728d0fa0fad58537e7
Author: Justin Lecher <jlec@gentoo.org>
Date: Sun Dec 10 22:20:38 2017 +0000
Update Manifests to new hashes
Signed-off-by: Justin Lecher <jlec@gentoo.org>
commit bce61aa3e4fe85fe411df858eb30ebe72a3a8f88
Author: Justin Lecher <jlec@gentoo.org>
Date: Sat Nov 18 20:39:44 2017 +0000
Consistently ident with tabs
Signed-off-by: Justin Lecher <jlec@gentoo.org>
commit 3199ec7737e923dc19479e5de7b31bb583071931
Author: Justin Lecher <jlec@gentoo.org>
Date: Sun Apr 30 11:12:48 2017 +0100
Cleanup remote IDs
Signed-off-by: Justin Lecher <jlec@gentoo.org>
commit f69e73182fc7cdc6c600a72fceb88ae1626db25d
Author: Justin Lecher <jlec@gentoo.org>
Date: Sat Feb 25 16:50:59 2017 +0000
Drop leftover from CVS in HEADER
Signed-off-by: Justin Lecher <jlec@gentoo.org>
commit 7a150bd50eb5360ef6f9e35f42838ba58f32a4d7
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Tue Jan 10 02:04:11 2017 +0100
sci-biology/trinityrnaseq: slightly relax required version numbers
Package-Manager: Portage-2.3.3, Repoman-2.3.1
commit bbb461d3b960a06f3725deec10fd3d3c2e87f45b
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Wed Dec 7 18:51:31 2016 +0100
sci-biology/trinityrnaseq: upstream removes fasta_tool script in future versions
Package-Manager: portage-2.3.2
commit e827560c61549b25f628da85a51de6261012868b
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Thu Dec 1 16:57:16 2016 +0100
sci-biology/trinityrnaseq: do not install fasta_tool which belongs to sci-biology/GAL
Package-Manager: portage-2.3.2
commit 1f9880950c49a6543a08ca5d285e32b7fb4c4e91
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Mon Apr 11 21:54:33 2016 +0200
sci-biology/trinityrnaseq: use 'rm -rf' when deleting a subdirectory with bundled GAL-0.2.1
Package-Manager: portage-2.2.28
commit e1714efc4d71beec0428f59ae0fa6ec7b166bd0a
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Mon Apr 11 21:43:14 2016 +0200
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
commit 057a98c5e6346d6696fcc7b0ec8fefc9e826245f
Author: Justin Lecher <jlec@gentoo.org>
Date: Mon Jan 25 09:53:09 2016 +0100
metadata.xml: Set type
Signed-off-by: Justin Lecher <jlec@gentoo.org>
commit b9d823e1ea1018d1356a0c18a083eab4d5ea6d8d
Author: Justin Lecher <jlec@gentoo.org>
Date: Mon Jan 25 09:50:12 2016 +0100
metadata.xml: convert hard -> proj
Signed-off-by: Justin Lecher <jlec@gentoo.org>
commit 2ef24e800910be3786e23a31a0217ba0f38659f8
Author: Justin Lecher <jlec@gentoo.org>
Date: Thu Jan 7 15:10:39 2016 +0100
Drop ChangeLogs in favour of commit messages
Signed-off-by: Justin Lecher <jlec@gentoo.org>
commit 947409e4f7403ac77e7207b0d685a1b47e4edcfd
Author: Marius Brehler <marbre@linux.sungazer.de>
Date: Tue Jan 5 09:55:15 2016 +0100
sci-biology/trinityrnaseq: Add missing die
Package-Manager: portage-2.2.26
commit 34d8b8ffbcae869875b972bf8fba46b9d75d9fb5
Author: Marius Brehler <marbre@linux.sungazer.de>
Date: Tue Jan 5 09:53:30 2016 +0100
sci-biology/trinityrnaseq: Drop KEYWORDS (depends on masked package)
Package-Manager: portage-2.2.26
commit 9942cc6d89af0ff581857128d04cd32071880686
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Thu Dec 31 22:21:05 2015 +0100
sci-biology/trinityrnaseq: do not install bundled GAL but DEPEND on it via external package as sci-biology/GAL
commit e1a9394386238099ece40fe0e8d7f805c23b679d
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Sat Nov 21 00:54:55 2015 +0100
sci-biology/trinityrnaseq: version bump but dropping KEYWORDS because we relocate *.pm file into vendor_perl and all 'use blah' calls to trinity-provided perl modules need to be changed to 'use trinityrnaseq::blah', or PERL5INC modified?
Package-Manager: portage-2.2.18
commit 6271f0c55cbb6af7fe88ae1ec9d7dbdedd562565
Author: Justin Lecher <jlec@gentoo.org>
Date: Mon Aug 17 08:53:12 2015 +0200
Convert all $Header$ to $Id$ tags as it has be done in gentoo.git
Signed-off-by: Justin Lecher <jlec@gentoo.org>
commit a891336052fb27fd9f3f82e33c30f0984f50ea54
Author: Justin Lecher <jlec@gentoo.org>
Date: Sun Jun 21 12:25:27 2015 +0200
Revert "Gentoo does https by default now"
This reverts commit 98718494343af4990facdefb0033471686e975a6.
commit 98718494343af4990facdefb0033471686e975a6
Author: Justin Lecher <jlec@gentoo.org>
Date: Sun Jun 21 12:14:25 2015 +0200
Gentoo does https by default now
Signed-off-by: Justin Lecher <jlec@gentoo.org>
commit e765f59ec430f319abf20fb38cd5c887179de9ef
Author: Justin Lecher <jlec@gentoo.org>
Date: Sat Jun 6 12:13:18 2015 +0200
sci-biology/trinityrnaseq: Add github to remote-id in metadata.xml
Package-Manager: portage-2.2.20
commit fa3f2a761a2d68aee8b6ad302b9c0903a69f2d70
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Sat May 2 18:14:37 2015 +0200
sci-biology/trinityrnaseq: added missing quotes
Package-Manager: portage-2.2.18
commit 5b84166e0195cbf63e9954986da0798f35ad0aee
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Fri May 1 00:45:08 2015 +0200
sci-biology/trinityrnaseq: added a note and removed broken symlink upon installation
Package-Manager: portage-2.2.18
commit cd5ffe2b8f606c841206f700c8718f5c3b7fda9e
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Thu Apr 30 12:52:33 2015 +0200
sci-biology/trinityrnaseq: version bump; dropped patches because target file is gone; ideally should depend on <sci-biology/samtools-1.1 but lets see what are the real requirements
Package-Manager: portage-2.2.18
commit 5d1cf37ff6399cd2ad05dd51f23f67a24f94ae2e
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Thu Apr 30 11:25:42 2015 +0200
sci-biology/trinityrnaseq: new package (with last release on sourceforge)
Package-Manager: portage-2.2.18