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* sci-biology/SEECER: EAPI bump, patch, remove files, fix build systemLucas Mitrak2021-08-053-0/+140
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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>
* sci-biology/SEECER: EAPI bumpAndrew Ammerlaan2021-03-051-6/+3
| | | | | Package-Manager: Portage-3.0.16, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/jellyfish: SLOT jellyfish to support concurrent ver. {1,2}Martin Mokrejs2018-04-213-4/+4
| | | | | | | | | | | | | | 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. {1,2} sci-biology/Rcorrector: SLOT jellyfish to support concurrent ver. {1,2} sci-biology/SEECER: SLOT jellyfish to support concurrent ver. {1,2} sci-biology/amos: SLOT jellyfish to support concurrent ver. {1,2} sci-biology/kraken: SLOT jellyfish to support concurrent ver. {1,2} sci-biology/wgs-assembler: SLOT jellyfish to support concurrent ver. {1,2} Package-Manager: Portage-2.3.28, Repoman-2.3.9
* Update Manifests to new hashesJustin Lecher2017-12-101-2/+2
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/SEECER: execute jellyfish1 instead of jellyfishMartin Mokrejš2017-11-214-2/+130
| | | | | | | 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
* sci-biology/SEECER: 'patch -p1' and not 'patch -p0' is usedMartin Mokrejš2017-11-211-4/+4
| | | | Package-Manager: Portage-2.3.14, Repoman-2.3.6
* sci-biology/SEECER: drop trailing .ori from filenamesMartin Mokrejš2017-11-211-2/+2
| | | | Package-Manager: Portage-2.3.14, Repoman-2.3.6
* sci-biology/SEECER: remove stale .swp files from mschulzMartin Mokrejš2017-11-211-0/+1
| | | | Package-Manager: Portage-2.3.14, Repoman-2.3.6
* sci-biology/SEECER: adjust paths to work with patch -p1Martin Mokrejš2017-11-211-4/+4
| | | | | | | 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
* Consistently ident with tabsJustin Lecher2017-11-181-8/+8
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* Drop leftover from CVS in HEADERJustin Lecher2017-02-251-1/+0
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/SEECER: QA fixesJustin Lecher2017-01-292-13/+12
| | | | | | | | | 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>
* metadata.xml: Set typeJustin Lecher2016-01-251-2/+2
| | | | 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 Lecher2016-01-071-39/+0
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/SEECER: add einfo() message that default kmer size 17 is suboptimalMartin Mokrejš2015-11-152-2/+16
| | | | Package-Manager: portage-2.2.18
* sci-biology/SEECER: patch crappy shellscripts to at leats die on error; ↵Martin Mokrejš2015-11-133-7/+48
| | | | | | require jellyfish-1.1.11 Package-Manager: portage-2.2.18
* sci-biology/SEECER: remove hardcoded pathsMartin Mokrejš2015-11-133-0/+59
| | | | Package-Manager: portage-2.2.18
* sci-biology/SEECER: install also the main program wrapperMartin Mokrejš2015-11-122-1/+5
| | | | Package-Manager: portage-2.2.18
* Convert all $Header$ to $Id$ tags as it has be done in gentoo.gitJustin Lecher2015-08-172-2/+2
| | | | 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/SEECER: added upstream 'patch'; do more proper install processMartin Mokrejš2015-04-305-36/+42
| | | | Package-Manager: portage-2.2.18
* sci-biology/SEECER: Fix licenseJustin Lecher2015-01-102-4/+8
| | | | Package-Manager: portage-2.2.15
* Initial ebuildMartin Mokrejš2015-01-074-0/+54