sci-biology/abyss
Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
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commit 6c252245a4ab18f5d211723f9078682dfa06bd00
Author: Martin Mokrejs <mmokrejs@gmail.com>
Date: Thu Apr 22 09:23:16 2021 +0200
sci-biology/abyss: add 2.3.1 release but keep patches
The PathConsensus crash fixes were not included by upstream,
keep them.
Package-Manager: Portage-3.0.18, Repoman-3.0.3
Signed-off-by: Martin Mokrejs <mmokrejs@gmail.com>
commit f22bb3be4e8f283831edc5f4c38a839442355644
Author: Martin Mokrejs <mmokrejs@gmail.com>
Date: Wed Apr 14 15:07:12 2021 +0200
sci-biology/abyss: fix PathConsensus crashes
Fixes: https://github.com/bcgsc/abyss/issues/267
Fix crashes of PathConsensus during long-scaffolding
step per @sjackman suggestions.
Add back 2.2.5 version which does not have yet the
RResolver which addition broke the paired de Bruijn
graph assembly approach and since that only the
Bloom filter-based approach works in 2.3.0.
Package-Manager: Portage-3.0.18, Repoman-3.0.3
Signed-off-by: Martin Mokrejs <mmokrejs@gmail.com>
commit 85d646372a278f85c05c5c7c717b9e94fa967ddc
Author: Martin Mokrejs <mmokrejs@gmail.com>
Date: Thu Apr 1 22:11:06 2021 +0200
sci-biology/abyss: version bump
Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Martin Mokrejs <mmokrejs@gmail.com>
commit 45d35292cee5f5b1f1f9c17d8fc343bdd99e7088
Author: Andrew Ammerlaan <andrewammerlaan@riseup.net>
Date: Thu Dec 31 17:22:46 2020 +0100
sci-biology/abyss: version bump, fix dep
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
Closes: https://github.com/gentoo/sci/pull/1022
Signed-off-by: Aisha Tammy <gentoo@aisha.cc>
commit c7e35e6a3ba60f35a787c02b1472c867ed3e1e3f
Author: Horea Christian <chr@chymera.eu>
Date: Fri Dec 25 05:21:55 2020 -0500
sci-biology/abyss: EAPI 7 bump
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Horea Christian <chr@chymera.eu>
commit 05629a9dc997950a1bf3dfa002307decc492e4b7
Author: Martin Mokrejs <mmokrejs@gmail.com>
Date: Thu Feb 20 16:15:16 2020 +0100
sci-biology/abyss: version bump
Package-Manager: Portage-2.3.87, Repoman-2.3.20
Signed-off-by: Martin Mokrejs <mmokrejs@gmail.com>
commit 08f6cb388ea7db562f4f6a32e9cef76dfd62caff
Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Sat Sep 28 15:05:52 2019 +0200
sci-biology/abyss: version bump to 2.2.3
Release version 2.2.3
Revert memory consumption of Bloom filters to pre 2.2.0 behaviour.
ABySS will now share the specified memory among all Bloom filters
instead of just the counting Bloom filter.
Fix gcc-9 compilation warnings
Release version 2.2.2
Fix abyss-overlap for 32-bit systems
Package-Manager: Portage-2.3.75, Repoman-2.3.17
Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
commit 982e84f44b14e71d4bae96aab4d246a3f0ec0f6f
Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Tue Aug 20 15:22:28 2019 +0200
sci-biology/abyss: version bump
Package-Manager: Portage-2.3.71, Repoman-2.3.17
Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
commit 581b836c34e32d3e201b8cfc7a4377514d16e2e3
Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Thu Aug 15 09:51:31 2019 +0200
sci-biology/abyss: update LICENSE, version bump
Upstream released abyss 3 years ago under GPL-3, now also another
part of the code is under GPL-3.
https://github.com/bcgsc/abyss/issues/295
Package-Manager: Portage-2.3.69, Repoman-2.3.16
Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
commit 9eeb095bd6468b0ab9ac265d730eaf458afae83a
Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Mon Dec 10 14:28:09 2018 +0100
sci-biology/abyss: Force --enable-maxk=256
Package-Manager: Portage-2.3.52, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
commit f0b1356038ad8ed9fcfd12298dd5e92749bc6a87
Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Thu Dec 6 11:59:50 2018 +0100
sci-biology/abyss: version bump
Package-Manager: Portage-2.3.52, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
commit 0e4eaa3b33984588d0d57ca68b0ea877c461c6ab
Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Mon Oct 29 14:56:23 2018 +0100
sci-biology/abyss: version bump
Package-Manager: Portage-2.3.51, Repoman-2.3.10
commit e09e5ec884dd0210694529c19b81fab9c48a76bc
Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Tue Sep 11 23:54:18 2018 +0200
sci-biology/abyss: version bump
An improved version with sealer using OpenMP+OpenMPI now.
https://github.com/bcgsc/abyss/releases/tag/2.1.1
Package-Manager: Portage-2.3.48, Repoman-2.3.10
commit 1ee6452972e294f0825ef450ec0f53cda42cb65f
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Tue Jan 10 01:20:33 2017 +0100
sci-biology/abyss: removing old, 2.0.2 in main repo already
commit b81e4c632efa6b2d53c8750b84deb2b315c86dd0
Author: Sergei Trofimovich <slyfox@inbox.ru>
Date: Fri Sep 23 14:16:56 2016 +0100
sci-biology/abyss: tweak for gcc-6, bug #594254 (#681)
Build failed as:
```
In file included from AssemblyAlgorithms.cpp:4:0:
../DataLayer/FastaReader.h: In member function ‘FastaReader::operator void*() const’:
../DataLayer/FastaReader.h:49:35: error: cannot convert ‘std::istream {aka std::basic_istream<char>}’ to ‘void*’ ...
operator void*() const { return m_in; }
^~~~
```
In the following source:
```c++
static bool existFile(const char* f)
{
ifstream file(f);
return file;
}
```
c++98 provides file->operator void*()
c++11 provides file->explicit operator bool()
Hence the failure on c++11.
The change adds explicit casts around istream.
Reported-by: Toralf Förster
Bug: https://bugs.gentoo.org/594254
Package-Manager: portage-2.3.0
commit 76c8aa5fabb5f1ae43d4fdf831bcf94b7e6e09a6
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Fri Jul 1 00:02:59 2016 +0200
sci-biology/abyss: version bump, update SRC_URI
Package-Manager: portage-2.2.28
commit 9c102d9aebd555a1db337e89911a198ba8274b55
Author: David Seifert <soap@gentoo.org>
Date: Sun Apr 3 20:04:28 2016 +0200
sci-biology/abyss: moved to main tree
commit f1f6c31bb308f59777bb396827099ec71b4b35a1
Author: Sergei Trofimovich <siarheit@google.com>
Date: Sun Apr 3 16:34:21 2016 +0100
sci-biology/abyss: fix automagic haskell deps, bug #534412
It's a ::gentoo change a50e1769e82e28dedb16083ac9136f17f9af2297
Reported-by: Toralf Förster
Bug: https://bugs.gentoo.org/534412
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 060a770920f2cd21994b2ff0efa7d263c3c70493
Author: Justin Lecher <jlec@gentoo.org>
Date: Wed Sep 23 14:08:24 2015 +0200
sci-biology/abyss: Bump to EAPI=5
Package-Manager: portage-2.2.21
Signed-off-by: Justin Lecher <jlec@gentoo.org>
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 4c3880bfe25f6b81461523e3f1f38b43614d51b9
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Sat May 23 23:51:58 2015 +0200
sci-biology/amos: bring in upstream patch to cope with secondary alignments from 'bwa mem -M'
Package-Manager: portage-2.2.18
Author: Martin Mokrejs <mmokrejs@gmail.com>
Date: Thu Apr 22 09:23:16 2021 +0200
sci-biology/abyss: add 2.3.1 release but keep patches
The PathConsensus crash fixes were not included by upstream,
keep them.
Package-Manager: Portage-3.0.18, Repoman-3.0.3
Signed-off-by: Martin Mokrejs <mmokrejs@gmail.com>
commit f22bb3be4e8f283831edc5f4c38a839442355644
Author: Martin Mokrejs <mmokrejs@gmail.com>
Date: Wed Apr 14 15:07:12 2021 +0200
sci-biology/abyss: fix PathConsensus crashes
Fixes: https://github.com/bcgsc/abyss/issues/267
Fix crashes of PathConsensus during long-scaffolding
step per @sjackman suggestions.
Add back 2.2.5 version which does not have yet the
RResolver which addition broke the paired de Bruijn
graph assembly approach and since that only the
Bloom filter-based approach works in 2.3.0.
Package-Manager: Portage-3.0.18, Repoman-3.0.3
Signed-off-by: Martin Mokrejs <mmokrejs@gmail.com>
commit 85d646372a278f85c05c5c7c717b9e94fa967ddc
Author: Martin Mokrejs <mmokrejs@gmail.com>
Date: Thu Apr 1 22:11:06 2021 +0200
sci-biology/abyss: version bump
Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Martin Mokrejs <mmokrejs@gmail.com>
commit 45d35292cee5f5b1f1f9c17d8fc343bdd99e7088
Author: Andrew Ammerlaan <andrewammerlaan@riseup.net>
Date: Thu Dec 31 17:22:46 2020 +0100
sci-biology/abyss: version bump, fix dep
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
Closes: https://github.com/gentoo/sci/pull/1022
Signed-off-by: Aisha Tammy <gentoo@aisha.cc>
commit c7e35e6a3ba60f35a787c02b1472c867ed3e1e3f
Author: Horea Christian <chr@chymera.eu>
Date: Fri Dec 25 05:21:55 2020 -0500
sci-biology/abyss: EAPI 7 bump
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Horea Christian <chr@chymera.eu>
commit 05629a9dc997950a1bf3dfa002307decc492e4b7
Author: Martin Mokrejs <mmokrejs@gmail.com>
Date: Thu Feb 20 16:15:16 2020 +0100
sci-biology/abyss: version bump
Package-Manager: Portage-2.3.87, Repoman-2.3.20
Signed-off-by: Martin Mokrejs <mmokrejs@gmail.com>
commit 08f6cb388ea7db562f4f6a32e9cef76dfd62caff
Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Sat Sep 28 15:05:52 2019 +0200
sci-biology/abyss: version bump to 2.2.3
Release version 2.2.3
Revert memory consumption of Bloom filters to pre 2.2.0 behaviour.
ABySS will now share the specified memory among all Bloom filters
instead of just the counting Bloom filter.
Fix gcc-9 compilation warnings
Release version 2.2.2
Fix abyss-overlap for 32-bit systems
Package-Manager: Portage-2.3.75, Repoman-2.3.17
Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
commit 982e84f44b14e71d4bae96aab4d246a3f0ec0f6f
Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Tue Aug 20 15:22:28 2019 +0200
sci-biology/abyss: version bump
Package-Manager: Portage-2.3.71, Repoman-2.3.17
Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
commit 581b836c34e32d3e201b8cfc7a4377514d16e2e3
Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Thu Aug 15 09:51:31 2019 +0200
sci-biology/abyss: update LICENSE, version bump
Upstream released abyss 3 years ago under GPL-3, now also another
part of the code is under GPL-3.
https://github.com/bcgsc/abyss/issues/295
Package-Manager: Portage-2.3.69, Repoman-2.3.16
Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
commit 9eeb095bd6468b0ab9ac265d730eaf458afae83a
Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Mon Dec 10 14:28:09 2018 +0100
sci-biology/abyss: Force --enable-maxk=256
Package-Manager: Portage-2.3.52, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
commit f0b1356038ad8ed9fcfd12298dd5e92749bc6a87
Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Thu Dec 6 11:59:50 2018 +0100
sci-biology/abyss: version bump
Package-Manager: Portage-2.3.52, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
commit 0e4eaa3b33984588d0d57ca68b0ea877c461c6ab
Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Mon Oct 29 14:56:23 2018 +0100
sci-biology/abyss: version bump
Package-Manager: Portage-2.3.51, Repoman-2.3.10
commit e09e5ec884dd0210694529c19b81fab9c48a76bc
Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Tue Sep 11 23:54:18 2018 +0200
sci-biology/abyss: version bump
An improved version with sealer using OpenMP+OpenMPI now.
https://github.com/bcgsc/abyss/releases/tag/2.1.1
Package-Manager: Portage-2.3.48, Repoman-2.3.10
commit 1ee6452972e294f0825ef450ec0f53cda42cb65f
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Tue Jan 10 01:20:33 2017 +0100
sci-biology/abyss: removing old, 2.0.2 in main repo already
commit b81e4c632efa6b2d53c8750b84deb2b315c86dd0
Author: Sergei Trofimovich <slyfox@inbox.ru>
Date: Fri Sep 23 14:16:56 2016 +0100
sci-biology/abyss: tweak for gcc-6, bug #594254 (#681)
Build failed as:
```
In file included from AssemblyAlgorithms.cpp:4:0:
../DataLayer/FastaReader.h: In member function ‘FastaReader::operator void*() const’:
../DataLayer/FastaReader.h:49:35: error: cannot convert ‘std::istream {aka std::basic_istream<char>}’ to ‘void*’ ...
operator void*() const { return m_in; }
^~~~
```
In the following source:
```c++
static bool existFile(const char* f)
{
ifstream file(f);
return file;
}
```
c++98 provides file->operator void*()
c++11 provides file->explicit operator bool()
Hence the failure on c++11.
The change adds explicit casts around istream.
Reported-by: Toralf Förster
Bug: https://bugs.gentoo.org/594254
Package-Manager: portage-2.3.0
commit 76c8aa5fabb5f1ae43d4fdf831bcf94b7e6e09a6
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Fri Jul 1 00:02:59 2016 +0200
sci-biology/abyss: version bump, update SRC_URI
Package-Manager: portage-2.2.28
commit 9c102d9aebd555a1db337e89911a198ba8274b55
Author: David Seifert <soap@gentoo.org>
Date: Sun Apr 3 20:04:28 2016 +0200
sci-biology/abyss: moved to main tree
commit f1f6c31bb308f59777bb396827099ec71b4b35a1
Author: Sergei Trofimovich <siarheit@google.com>
Date: Sun Apr 3 16:34:21 2016 +0100
sci-biology/abyss: fix automagic haskell deps, bug #534412
It's a ::gentoo change a50e1769e82e28dedb16083ac9136f17f9af2297
Reported-by: Toralf Förster
Bug: https://bugs.gentoo.org/534412
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 060a770920f2cd21994b2ff0efa7d263c3c70493
Author: Justin Lecher <jlec@gentoo.org>
Date: Wed Sep 23 14:08:24 2015 +0200
sci-biology/abyss: Bump to EAPI=5
Package-Manager: portage-2.2.21
Signed-off-by: Justin Lecher <jlec@gentoo.org>
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 4c3880bfe25f6b81461523e3f1f38b43614d51b9
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Sat May 23 23:51:58 2015 +0200
sci-biology/amos: bring in upstream patch to cope with secondary alignments from 'bwa mem -M'
Package-Manager: portage-2.2.18