commit 0ad60f57bec0408d59349751ced4f5c7f22a3b72
Author: Horea Christian <chr@chymera.eu>
Date: Mon Jan 22 14:29:16 2024 -0500

sci-biology/SPAdes: added comment for next release

Signed-off-by: Horea Christian <chr@chymera.eu>

commit a9b2100efac435eb6fc2140c1a906d0a2758984a
Author: Horea Christian <chr@chymera.eu>
Date: Mon Jan 22 14:28:18 2024 -0500

sci-biology/SPAdes: drop 3.15.3

Signed-off-by: Horea Christian <chr@chymera.eu>

commit dd4ee9b222cf98145af87c7ca36dc3d0e40cd8c0
Author: Horea Christian <chr@chymera.eu>
Date: Mon Jan 22 12:59:43 2024 -0500

sci-biology/SPAdes: keyword 3.15.5 for ~amd64

Signed-off-by: Horea Christian <chr@chymera.eu>

commit aea1a69a5dae783cccfe1d3f513e5d090188a279
Author: Horea Christian <chr@chymera.eu>
Date: Mon Jan 22 08:01:18 2024 -0500

sci-biology/SPAdes: add 3.15.5

Signed-off-by: Horea Christian <chr@chymera.eu>

commit 8cd68194088f5c91057700f1f0def5fe733e9e19
Author: Horea Christian <chr@chymera.eu>
Date: Mon Jan 22 08:00:48 2024 -0500

sci-biology/SPAdes: unkeyword 3.15.3 for ~amd64

Signed-off-by: Horea Christian <chr@chymera.eu>

commit 54e72942b81551d47a0ebc0b1893181e1082613c
Author: Horea Christian <chr@chymera.eu>
Date: Mon Jan 22 07:57:51 2024 -0500

sci-biology/SPAdes: add github upstream metadata

Signed-off-by: Horea Christian <chr@chymera.eu>

commit f40f597ed62ebbcece98ba6ec2569f8aa09dc654
Author: Horea Christian <chr@chymera.eu>
Date: Mon Jan 22 07:55:04 2024 -0500

sci-biology/SPAdes: enable py3.11, py3.12

Signed-off-by: Horea Christian <chr@chymera.eu>

commit 57e58b916ee04062b4683b6dc2178f1ad0d1c348
Author: Horea Christian <chr@chymera.eu>
Date: Mon Jan 22 07:32:54 2024 -0500

sci-biology/SPAdes: updated cmake dependency category

Signed-off-by: Horea Christian <chr@chymera.eu>

commit 013a94d87d9a4ff23a9db6e4f02ae7d113580f2d
Author: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
Date: Thu Jan 12 12:40:54 2023 +0100

*/*: drop py3.8 and py3.9 where py3.10+ already enabled

Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>

commit 34773140d758b76b35f70f857f7b27ee06503921
Author: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
Date: Tue Jan 25 15:24:18 2022 +0100

sci-biology/SPAdes: bump to 3.15.3

Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>

commit 257e4e9f1776f2fe2e5e5a348a2f15f7baeec1ad
Author: Martin Mokrejs <mmokrejs@gmail.com>
Date: Fri Mar 5 14:34:24 2021 +0100

sci-biology/SPAdes: dropping KEYWORDS

src_install() phase does not install the files

Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Martin Mokrejs <mmokrejs@gmail.com>

commit 11e7e6552d00645d27360186f403c23dfc807099
Author: Martin Mokrejs <mmokrejs@gmail.com>
Date: Fri Mar 5 10:21:36 2021 +0100

sci-biology/SPAdes: version bump to 3.15.1

Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Martin Mokrejs <mmokrejs@gmail.com>

commit f101e36b3fa1e6d87707d5695371c14af5d365e3
Author: Andrew Ammerlaan <andrewammerlaan@riseup.net>
Date: Tue Jan 19 09:51:56 2021 +0100

sci-biology/SPAdes: version bump 3.15.0, fix fetching, add keyword

Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>

commit f3a538b68e80b3fc42af81717f48a5cbfb283f45
Author: Martin Mokrejs <mmokrejs@gmail.com>
Date: Fri May 15 21:30:28 2020 +0200

sci-biology/SPAdes: version bump to 3.14.1

This is a bug-fix release, which includes:
- Fix for read filtering tool;
- Soft and hard-filtered transcripts are now copied to the output
folder in rnaSPAdes;
- Minor fix in biosyntheticSPAdes pipeline;
- Minor fix in metaplasmidSPAdes contig output;
- Several usability fixes in `spades.py';
- Other minor bug-fixes.

Package-Manager: Portage-2.3.99, Repoman-2.3.22
Signed-off-by: Martin Mokrejs <mmokrejs@gmail.com>

commit 84bb511d7a904b2e151faa1f9224dd91a196349f
Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Mon Jan 6 18:13:56 2020 +0100

sci-biology/SPAdes: version bump

- BiosyntheticSPAdes pipeline for identifying Biosynthetic Gene Clusters (BGCs)
- Hybrid transcriptome assembly (Illumina RNA-Seq + Iso-seq / ONT RNA)
- Plasmid assembly from metagenomic datasets
- New --isolate option that improves assembly quality of standard datasets with
high coverage
- New standalone tools for read filtration based on k-mer coverage and
estimating number of unique k-mers in reads
- Improved SPAligner tool for read-to-graph alignment
- Major performance improvements and memory consumption reduction in graph
construction, simplification procedures and throughout the whole pipeline
- Several bug-fixes.

Package-Manager: Portage-2.3.84, Repoman-2.3.20
Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>

commit f7eaea4317cca5c6ca5566c05c69b604d7312bc8
Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Tue Oct 16 19:47:08 2018 +0200

sci-biology/SPAdes: version bump, drop old and buggy version

SPAdes 3.13.0
CHANGE: Switched to multi-k-mer mode in rnaSPAdes, k-mer values are detected
automatically based on read length.
CHANGE: Added manual as README.md in markdown format for github.
FIX: Updated BWA and switched to RopeBWT, which allows to handle large graphs.
FIX: Assert for path.length() > 0 in rnaSPAdes.
FIX: CQF and k-mer counting.
REMOVE: dipSPAdes module.
Package-Manager: Portage-2.3.51, Repoman-2.3.10

commit 5ef25a48bee2090fbcd6a9e92d4a8299c88edc67
Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Thu May 17 21:37:29 2018 +0200

sci-biology/SPAdes: version bump, drop old

Package-Manager: Portage-2.3.36, Repoman-2.3.9

commit 4dd7fc5f1806465684c1101c88021ab3e1993fa2
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Tue Jan 9 23:03:02 2018 +0100

sci-biology/SPAdes: version bump

Try to follow the upstream's approach to compile and install
the tool. src_compile() therefore does also src_install()
into a DESTDIR.

Package-Manager: Portage-2.3.19, Repoman-2.3.6

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 1e04d5868f177eb639f03889b59d2cba00206578
Author: Justin Lecher <jlec@gentoo.org>
Date: Sat Nov 18 21:01:49 2017 +0000

Second try to clean spaces in metadata.xml

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 c9670fe28445edf107eb51db383a7833e65056f4
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Fri Jul 28 21:13:58 2017 +0200

sci-biology/SPAdes: update comments on bundled dev-libs/boost

Package-Manager: Portage-2.3.6, Repoman-2.3.3

commit 4036ac0a6d0616ae423c7de5f5f6dfc60bd83e6f
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Sun May 14 20:48:46 2017 +0200

sci-biology/SPAdes: drop DEPENDency on boost

Upstream says SPAdes uses bundled while modified local copy.
Fix URL to new official site.

Package-Manager: Portage-2.3.5, Repoman-2.3.2

commit 7a4c5e17a64afe18b4af992e6b2df279ecd9e7e6
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Sun May 14 13:49:02 2017 +0200

sci-biology/SPAdes: install the package directly using cmake

Package-Manager: Portage-2.3.5, Repoman-2.3.2

commit a5760c4470004861915035e9baf62ae5da7e8454
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Sat May 13 23:47:11 2017 +0200

sci-biology/SPAdes: fix compile issue but drop KEYWORDS because of QA issues

Use patch from https://github.com/Homebrew/homebrew-science/pull/5616
The package install its own *.py files outside of PYTHON's site-packages/.
The "make install" procedure is flakey shellscript and there is no setup.py so we could
reuse common infrastructure for pythonic packages.
There are plenty of bundled 3rd-party apps, some of them compiling statically.

Package-Manager: Portage-2.3.5, Repoman-2.3.2

commit c3b614f81dae512b5798b74c2d9cd46952507f5c
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Sat May 13 17:08:08 2017 +0200

sci-biology/SPAdes: improve DESCRIPTION

Package-Manager: Portage-2.3.5, Repoman-2.3.2

commit e1a1e06331c449e29b30cf97df54d2f4d7b69de7
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Fri May 12 20:10:06 2017 +0200

sci-biology/SPAdes: version bump

Package-Manager: Portage-2.3.5, Repoman-2.3.2

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 8d6ea3fcf39703a49e09ad80d65f25988d54c17a
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Sun Jan 29 19:13:23 2017 +0100

sci-biology/SPAdes: install more HTML documentation

Package-Manager: Portage-2.3.3, Repoman-2.3.1

commit 8ef2d0632281aeb653b62b10b8da00f22f9cc62d
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Sun Jan 29 19:08:40 2017 +0100

sci-biology/SPAdes: version bump, remove old, src_install actually does also src_compile

Upstream contacted to split compile and install steps into separate procedures.
The Gentoo package should be probably renamed to all lowercase letters.
Hierarchy in /usr/share/spades/ is a bit awkward.

Package-Manager: Portage-2.3.3, Repoman-2.3.1

commit daeb2eded741c715ff721e2710a65663ef83621e
Author: Justin Lecher <jlec@gentoo.org>
Date: Fri Oct 28 16:23:40 2016 +0200

Bulk fix of obsolete python versions

Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit 0d4a3b17f010a8f80e089f4ea1c6f0eef9cb3eb0
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Fri Apr 8 22:04:32 2016 +0200

sci-biology/SPAdes: improve description

Package-Manager: portage-2.2.28

commit 4fa4b7a8cd446fcb898d0d25ac28d363e81861c9
Author: Justin Lecher <jlec@gentoo.org>
Date: Sun Feb 14 19:11:52 2016 +0100

Fix $Header to $Id

Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit d8a45f03438c8ac2e2b7af8787a075bae0386ce3
Author: Justin Lecher <jlec@gentoo.org>
Date: Fri Feb 12 08:52:45 2016 +0100

Fix metadata.xml for herd -> project transition

Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit 413c2c2dd02a27666281094f516976c8c7f3f357
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Wed Feb 10 16:20:19 2016 +0100

sci-biology/SPAdes: new package

Package-Manager: portage-2.2.26