Get Gentoo!
gentoo.org sites
gentoo.org Wiki Bugs Forums Packages
Planet Archives Sources
Infra Status
aboutsummaryrefslogtreecommitdiff
path: root/sci-biology/abyss
Commit message (Collapse)AuthorAgeFilesLines
* sci-biology/abyss: move the new versions to ::gentooAndrew Ammerlaan2022-01-137-217/+0
| | | | Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/abyss: add 2.3.1 release but keep patchesMartin Mokrejs2021-04-222-0/+59
| | | | | | | | 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>
* sci-biology/abyss: fix PathConsensus crashesMartin Mokrejs2021-04-145-0/+85
| | | | | | | | | | | | | | 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>
* sci-biology/abyss: version bumpMartin Mokrejs2021-04-012-2/+2
| | | | | Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: Martin Mokrejs <mmokrejs@gmail.com>
* sci-biology/abyss: version bump, fix depAndrew Ammerlaan2020-12-312-2/+2
| | | | | | | 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>
* sci-biology/abyss: EAPI 7 bumpHorea Christian2020-12-251-1/+1
| | | | | Package-Manager: Portage-3.0.12, Repoman-3.0.2 Signed-off-by: Horea Christian <chr@chymera.eu>
* sci-biology/abyss: version bumpMartin Mokrejs2020-02-202-2/+2
| | | | | Package-Manager: Portage-2.3.87, Repoman-2.3.20 Signed-off-by: Martin Mokrejs <mmokrejs@gmail.com>
* sci-biology/abyss: version bump to 2.2.3Martin Mokrejs2019-09-282-1/+1
| | | | | | | | | | | | | | 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>
* sci-biology/abyss: version bumpMartin Mokrejs2019-08-202-1/+1
| | | | | Package-Manager: Portage-2.3.71, Repoman-2.3.17 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/abyss: update LICENSE, version bumpMartin Mokrejs2019-08-152-3/+3
| | | | | | | | | | 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>
* sci-biology/abyss: Force --enable-maxk=256Martin Mokrejs2018-12-101-1/+1
| | | | | Package-Manager: Portage-2.3.52, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/abyss: version bumpMartin Mokrejs2018-12-062-2/+2
| | | | | Package-Manager: Portage-2.3.52, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/abyss: version bumpMartin Mokrejs2018-10-292-1/+1
| | | | Package-Manager: Portage-2.3.51, Repoman-2.3.10
* sci-biology/abyss: version bumpMartin Mokrejs2018-09-113-0/+73
| | | | | | | | 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
* sci-biology/abyss: removing old, 2.0.2 in main repo alreadyMartin Mokrejš2017-01-105-121/+0
|
* sci-biology/abyss: tweak for gcc-6, bug #594254 (#681)Sergei Trofimovich2016-09-232-0/+35
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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
* sci-biology/abyss: version bump, update SRC_URIMartin Mokrejš2016-07-014-0/+86
| | | | Package-Manager: portage-2.2.28
* sci-biology/abyss: moved to main treeDavid Seifert2016-04-0313-367/+0
|
* sci-biology/abyss: fix automagic haskell deps, bug #534412Sergei Trofimovich2016-04-032-4/+22
| | | | | | | | | It's a ::gentoo change a50e1769e82e28dedb16083ac9136f17f9af2297 Reported-by: Toralf Förster Bug: https://bugs.gentoo.org/534412 Package-Manager: portage-2.2.28
* metadata.xml: Set typeJustin Lecher2016-01-251-1/+1
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* metadata.xml: convert hard -> projJustin Lecher2016-01-251-1/+4
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* Drop ChangeLogs in favour of commit messagesJustin Lecher2016-01-071-17/+0
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/abyss: Bump to EAPI=5Justin Lecher2015-09-231-1/+1
| | | | | Package-Manager: portage-2.2.21 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* Convert all $Header$ to $Id$ tags as it has be done in gentoo.gitJustin Lecher2015-08-174-4/+4
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* Revert "Gentoo does https by default now"Justin Lecher2015-06-211-1/+1
| | | | This reverts commit 98718494343af4990facdefb0033471686e975a6.
* Gentoo does https by default nowJustin Lecher2015-06-211-1/+1
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/amos: bring in upstream patch to cope with secondary alignments ↵Martin Mokrejš2015-05-2314-0/+363
from 'bwa mem -M' Package-Manager: portage-2.2.18