commit ecafe6de617cdf6c61a300eafffca973aeac428b
Author: Lucas Mitrak <lucas@lucasmitrak.com>
Date: Wed Aug 4 20:54:17 2021 -0400

sci-biology/SEECER: EAPI bump, patch, remove files, fix build system

* EAPI bump
* Remove "rename_jellyfish_binary.patch" from ebuild which does nothing
* Add a patch that increases the max sequence length
* Add a patch that removes CXXFLAGS, CFLAGS, LDFLAGS
* Add tc-check-openmp so the ebuild fails without OpenMP support
* Remove copying a new replace_ids.cc file which is now a patch
* Delete all object files
* Delete packaged seqan
* Add eautoreconf to recreate the build system
* Add system seqan include path and CXXFLAGS to econf

Currently, sci-biology/SEECER will not compile due to object files
remaining in the package. This was fixed by deleting all object files
and so forcing them to be rebuilt. The packaged seqan was deleted as
well so the system's seqan is used. In order to achieve this, the
system's seqan include path was passed into econf as
"/usr/include/seqan". The user's CXXFLAGS were passed into econf also.
The patch SEECER-remove-flags.patch removes any other CXXFLAGS, CFLAGS,
and LDFLAGS present in configure.ac and Makefile.am.
Since configure.ac and Makefile.am were updated, the build system was
recreated using eautoreconf -i to account for this. The -i was needed
because the "compile" file is missing, so it had to be added. The patch
SEECER-increase-max-sequence-length.patch increases the max sequence
length from 256 to 10000. This patch was made from an updated
replace_ids.cc downloaded from an archived upstream mail list
that is no longer available online [1]. The previous revision ebuild
included this same replace_ids.cc file; however, despite it appearing
as a text file, it was actually a gzipped file with an incorrect
extension. In addition, this gzipped file was copied into the src/
directory when the replace_ids.cc file is in the pipeline/ directory.
The patch file "rename_jellyfish_binary.patch" also did nothing
but modify a comment so it was removed as well. In addition,
a tc-check-openmp was added so the ebuild fails without OpenMP support.
OpenMP cannot be added as a use flag or a configure enable flag because
gomp is always enabled and the source code assumes the system has OpenMP
installed. Finally, the EAPI was bumped.

[1] URL Split into three parts for the sake of the commit message:
https://web.archive.org/web/20150911132231/
http://seecer-rna-read-error-correction-mailing-list.21961.x6.nabble.com
/Segmentation-fault-in-step-4-td41.html

Closes: https://bugs.gentoo.org/755776
Package-Manager: Portage-3.0.20, Repoman-3.0.2
Signed-off-by: Lucas Mitrak <lucas@lucasmitrak.com>
Closes: https://github.com/gentoo/sci/pull/1105
Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>

commit 1a5bc27fa079f59ddf98753103c24b11c8301ce3
Author: Andrew Ammerlaan <andrewammerlaan@riseup.net>
Date: Fri Mar 5 16:51:56 2021 +0100

sci-biology/SEECER: EAPI bump

Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>

commit 2778b51209c924509c1dfcdf68d505b78f7654a1
Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Sat Apr 21 21:07:06 2018 +0200

sci-biology/jellyfish: SLOT jellyfish to support concurrent ver.

This renames the resulting binaries, pkg-config file contents, headers, and all
packages currently depending on sci-biology/jellyfish.

sci-biology/quorum: SLOT jellyfish to support concurrent ver.
sci-biology/Rcorrector: SLOT jellyfish to support concurrent ver.
sci-biology/SEECER: SLOT jellyfish to support concurrent ver.
sci-biology/amos: SLOT jellyfish to support concurrent ver.
sci-biology/kraken: SLOT jellyfish to support concurrent ver.
sci-biology/wgs-assembler: SLOT jellyfish to support concurrent ver.

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 aab87747b89b64107677056a3d4874d8f5ee7bbf
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Tue Nov 21 17:11:28 2017 +0100

sci-biology/SEECER: execute jellyfish1 instead of jellyfish

Also I wrote a few cleanup patches to expose THREADS
variable and cleanup the code.

Package-Manager: Portage-2.3.14, Repoman-2.3.6

commit 6283a774209756751880212d783863da56b9f80e
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Tue Nov 21 15:15:55 2017 +0100

sci-biology/SEECER: 'patch -p1' and not 'patch -p0' is used

Package-Manager: Portage-2.3.14, Repoman-2.3.6

commit a6b2257d10e785afb2c8045af72d4eb24ceaa55f
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Tue Nov 21 15:06:46 2017 +0100

sci-biology/SEECER: drop trailing .ori from filenames

Package-Manager: Portage-2.3.14, Repoman-2.3.6

commit 8c3e0095958a9efae40423c93b9b6480152d32b1
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Tue Nov 21 15:03:47 2017 +0100

sci-biology/SEECER: remove stale .swp files from mschulz

Package-Manager: Portage-2.3.14, Repoman-2.3.6

commit a3a57382876fcf7675ad8865da9a4fc18122d5ac
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Tue Nov 21 14:50:40 2017 +0100

sci-biology/SEECER: adjust paths to work with patch -p1

With bump to EAPI=6 the patch does not apply anymore
due to extraneous 'SEECER-0.1.3/SEECER/'.

Package-Manager: Portage-2.3.14, Repoman-2.3.6

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 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 c38274779a20385ad70d5c2aa2dac34d8525868d
Author: Justin Lecher <jlec@gentoo.org>
Date: Sun Jan 29 13:44:25 2017 +0000

sci-biology/SEECER: QA fixes

Bump to6 EAPI
drop non active code
add missing slot operator

Package-Manager: Portage-2.3.3, Repoman-2.3.1
Signed-off-by: Justin Lecher <jlec@gentoo.org>

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 e1d13a2f0d3827367a8e5b10813a1dafbcbd46ae
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Sun Nov 15 19:42:06 2015 +0100

sci-biology/SEECER: add einfo() message that default kmer size 17 is suboptimal

Package-Manager: portage-2.2.18

commit 6af16cbc76de1d4d8a1726e81880cfccb28adbb6
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Fri Nov 13 20:03:02 2015 +0100

sci-biology/SEECER: patch crappy shellscripts to at leats die on error; require jellyfish-1.1.11

Package-Manager: portage-2.2.18

commit c10c56b06fbaf0b0127db70aa6ad7b7910694d2e
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Fri Nov 13 18:26:00 2015 +0100

sci-biology/SEECER: remove hardcoded paths

Package-Manager: portage-2.2.18

commit d9df37217fca3b4f9de03d13f3891c9267f5f191
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Thu Nov 12 01:31:36 2015 +0100

sci-biology/SEECER: install also the main program wrapper

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 d4e2d5a53d73f9a69ca36fbd54fff4ac161398bb
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Thu Apr 30 23:59:43 2015 +0200

sci-biology/SEECER: added upstream 'patch'; do more proper install process

Package-Manager: portage-2.2.18

commit 495d790cea315b38978ec1d8738f7dd961c118a3
Author: Justin Lecher <jlec@gentoo.org>
Date: Sat Jan 10 15:13:39 2015 +0100

sci-biology/SEECER: Fix license

Package-Manager: portage-2.2.15

commit 048f49ddebd47dfe85fdffad7ec869913a6ccec7
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Wed Jan 7 23:30:38 2015 +0100

Initial ebuild