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* sci-biology/trimmomatic: unkeyword 0.39 for ~x86Andrew Ammerlaan2024-10-201-1/+1
| | | | Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/cutadapt: new package, add 4.9Alexey Shvetsov2024-09-293-0/+41
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* dev-python/bedtools: move from sci-biology, version bump 0.10.0Michael Schubert2024-07-194-103/+0
| | | | | | Signed-off-by: Michael Schubert <mschu.dev@gmail.com> Closes: https://github.com/gentoo/sci/pull/1285 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-bioloy/gffutils: version bump 0.13; fix testsMichael Schubert2024-07-194-47/+33
| | | | | Signed-off-by: Michael Schubert <mschu.dev@gmail.com> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* dev-python/pyfaidx: version bump 0.8.1.1Michael Schubert2024-07-194-64/+0
| | | | | Signed-off-by: Michael Schubert <mschu.dev@gmail.com> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/bx-python: version bump 0.12.0, enable testsMichael Schubert2024-07-187-111/+51
| | | | | | Signed-off-by: Michael Schubert <mschu.dev@gmail.com> Closes: https://github.com/gentoo/sci/pull/1287 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/multiqc: version bump 1.23Michael Schubert2024-07-112-1/+1
| | | | | | Signed-off-by: Michael Schubert <mschu.dev@gmail.com> Closes: https://github.com/gentoo/sci/pull/1281 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/multiqc: version bump 1.22.2Michael Schubert2024-06-193-41/+43
| | | | | | Signed-off-by: Michael Schubert <mschu.dev@gmail.com> Closes: https://github.com/gentoo/sci/pull/1277 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/imagej: ant-core deprecatedIsrael Hernandez2024-06-172-2/+0
| | | | | | | | | | | | | | Signed-off-by: IAHMCOL <IAHMCOL@thejabberwocky.net> This commit removes dev-java/ant-core from dependencies This has been deprecated, and it gets automatically used with ant2 Latest updates had depclean dev-java/ant-core, and the packages still builds after dependency removal see: https://packages.gentoo.org/packages/dev-java/ant-core Closes: https://github.com/gentoo/sci/pull/1275 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/imagej: add 1.54i, drop 1.54hIsrael Hernandez2024-06-103-10/+10
| | | | | | | | | | | Signed-off-by: IAHMCOL <IAHMCOL@thejabberwocky.net> * This PR bumps imagej to version 1.54i * This PR, also, redirects the icon to the new URL. Old URL hosted on the nih became disabled Closes: https://github.com/gentoo/sci/pull/1272 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/afni: add 24.1.15, 24.1.16Horea Christian2024-06-064-0/+282
| | | | Signed-off-by: Horea Christian <chr@chymera.eu>
* sci-biology/afni: drop 24.0.04-r1, 24.0.08-r1, 24.0.08-r2Horea Christian2024-05-304-349/+0
| | | | Signed-off-by: Horea Christian <chr@chymera.eu>
* sci-biology/afni: correct version annotationHorea Christian2024-05-291-0/+125
| | | | Signed-off-by: Horea Christian <chr@chymera.eu>
* sci-biology/afni: env variable for AFNI dataHorea Christian2024-05-282-0/+125
| | | | Signed-off-by: Horea Christian <chr@chymera.eu>
* sci-biology/afni-datasets: new package, add 20240503Horea Christian2024-05-283-0/+33
| | | | Signed-off-by: Horea Christian <chr@chymera.eu>
* sci-biology/afni: update DESCRIPTION, HOMEPAGEHorea Christian2024-05-242-12/+12
| | | | Signed-off-by: Horea Christian <chr@chymera.eu>
* sci-biology/VelvetOptimiser: fix dependency on perlAndrew Ammerlaan2024-05-221-1/+1
| | | | Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/nilearn: updated dependency nameHorea Christian2024-05-222-2/+2
| | | | Signed-off-by: Horea Christian <chr@chymera.eu>
* */*: drop sourceforge mirrorAndrew Ammerlaan2024-05-073-3/+3
| | | | Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/neuroconv: dependency revbumpHorea Christian2024-04-021-2/+3
| | | | Signed-off-by: Horea Christian <chr@chymera.eu>
* sci-biology/afni: removed deprecated depsHorea Christian2024-03-222-2/+0
| | | | Signed-off-by: Horea Christian <chr@chymera.eu>
* sci-biology/neuroconv: version bump, treecleanHorea Christian2024-03-213-58/+7
| | | | Signed-off-by: Horea Christian <chr@chymera.eu>
* sci-biology/fsl: updated C++ versionHorea Christian2024-02-291-2/+2
| | | | Signed-off-by: Horea Christian <chr@chymera.eu>
* sci-biology/deeptools: dropped ~x86, added PEP517Horea Christian2024-02-282-4/+6
| | | | Signed-off-by: Horea Christian <chr@chymera.eu>
* sci-biology/behaviopy: treecleanHorea Christian2024-02-283-69/+0
| | | | Signed-off-by: Horea Christian <chr@chymera.eu>
* sci-biology/afni: drop 20.1.16, 20.3.03, 22.0.21Horea Christian2024-02-285-235/+0
| | | | Signed-off-by: Horea Christian <chr@chymera.eu>
* sci-biology/afni: add 24.0.04, 24.0.08Horea Christian2024-02-285-0/+272
| | | | Signed-off-by: Horea Christian <chr@chymera.eu>
* sci-biology/libBigWig: add 0.4.7Alexander Puck Neuwirth2024-02-192-0/+32
| | | | | | Signed-off-by: Alexander Puck Neuwirth <alexander@neuwirth-informatik.de> Co-authored-by: Andrew Nowa Ammerlaan <andrewammerlaan@gentoo.org> Closes: https://github.com/gentoo/sci/pull/1241
* sci-biology/samri: updated sckikit-image package categoryHorea Christian2024-02-153-3/+3
| | | | Signed-off-by: Horea Christian <chr@chymera.eu>
* sci-biology/multiqc: add ebuildMichael Schubert2024-01-303-0/+53
| | | | | | Signed-off-by: Michael Schubert <mschu.dev@gmail.com> Closes: https://github.com/gentoo/sci/pull/1223 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/fastp: add ebuildmschubertv2024-01-303-0/+32
| | | | | | Signed-off-by: Michael Schubert <mschu.dev@gmail.com> Closes: https://github.com/gentoo/sci/pull/1225 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/neuroconv: updated dependencyHorea Christian2024-01-251-0/+1
| | | | Signed-off-by: Horea Christian <chr@chymera.eu>
* sci-biology/neuroconv: add 0.4.6Horea Christian2024-01-252-0/+59
| | | | Signed-off-by: Horea Christian <chr@chymera.eu>
* sci-biology/SPAdes: added comment for next releaseHorea Christian2024-01-221-0/+2
| | | | Signed-off-by: Horea Christian <chr@chymera.eu>
* sci-biology/SPAdes: drop 3.15.3Horea Christian2024-01-222-42/+0
| | | | Signed-off-by: Horea Christian <chr@chymera.eu>
* sci-biology/SPAdes: keyword 3.15.5 for ~amd64Horea Christian2024-01-222-3/+54
| | | | Signed-off-by: Horea Christian <chr@chymera.eu>
* sci-biology/SPAdes: add 3.15.5Horea Christian2024-01-222-0/+42
| | | | Signed-off-by: Horea Christian <chr@chymera.eu>
* sci-biology/SPAdes: unkeyword 3.15.3 for ~amd64Horea Christian2024-01-221-1/+3
| | | | Signed-off-by: Horea Christian <chr@chymera.eu>
* sci-biology/SPAdes: add github upstream metadataHorea Christian2024-01-221-4/+7
| | | | Signed-off-by: Horea Christian <chr@chymera.eu>
* sci-biology/SPAdes: enable py3.11, py3.12Horea Christian2024-01-221-1/+1
| | | | Signed-off-by: Horea Christian <chr@chymera.eu>
* sci-biology/SPAdes: updated cmake dependency categoryHorea Christian2024-01-221-1/+1
| | | | Signed-off-by: Horea Christian <chr@chymera.eu>
* sci-biology/sra-tools: remove unused patch(es)Michael Mair-Keimberger2023-12-313-165/+0
| | | | | Signed-off-by: Michael Mair-Keimberger <mmk@levelnine.at> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/nilearn: remove unused patchMichael Mair-Keimberger2023-12-311-39/+0
| | | | | Signed-off-by: Michael Mair-Keimberger <mmk@levelnine.at> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/gffcompare: remove unused patch(es)Michael Mair-Keimberger2023-12-311-79/+0
| | | | | Signed-off-by: Michael Mair-Keimberger <mmk@levelnine.at> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/fsl: remove unused patchesMichael Mair-Keimberger2023-12-314-241/+0
| | | | | Signed-off-by: Michael Mair-Keimberger <mmk@levelnine.at> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/cluster: remove unused patch(es)Michael Mair-Keimberger2023-12-311-30/+0
| | | | | Signed-off-by: Michael Mair-Keimberger <mmk@levelnine.at> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/ants: remove unused patchMichael Mair-Keimberger2023-12-311-13/+0
| | | | | Signed-off-by: Michael Mair-Keimberger <mmk@levelnine.at> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/imagej: revbump 1.54hAndrew Ammerlaan2023-12-201-0/+0
| | | | Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/imagej: drop 1.54gIsrael Hernandez2023-12-202-121/+0
| | | | | | Signed-off-by: IAHMCOL <IAHMCOL@thejabberwocky.net> Closes: https://github.com/gentoo/sci/pull/1227 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/imagej: bump version imagej sources and pluginsIsrael Hernandez2023-12-204-8/+6
| | | | | | | | * ImageJ version bump 1.53t to 1.54g from NIH sources * plugins version bump 153 to 154 Signed-off-by: IAHMCOL <IAHMCOL@thejabberwocky.net> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>