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2021-02-14Update a few GNUstep ports:Neel Chauhan1-1/+1
2021-02-05biology/py-multiqc: Update to 1.9Jason W. Bacon2-6/+7
2021-02-04biology/fastqc: Update to 0.11.9Jason W. Bacon2-4/+4
2021-02-03biology/bioparser: Update 3.0.12 -> 3.0.12-2Yuri Victorovich3-17/+17
2021-02-02biology/py-cutadapt: Update to 3.2Jason W. Bacon4-12/+12
2021-01-30biology/bowtie2: Reverse switch to devel/onetbbJason W. Bacon1-2/+2
2021-01-30biology/bowtie2: Switch to devel/onetbbJason W. Bacon1-1/+2
2021-01-30biology/vsearch: Update to 2.15.2Jason W. Bacon3-10/+11
2021-01-30Update USES=python: math/py-pandas 1.2.0 requires Python 3.7+Sunpoet Po-Chuan Hsieh5-5/+5
2021-01-27biology/hyphy: Update to version 2.5.27Joseph Mingrone2-4/+4
2021-01-26biology/kallisto: Add -lz for pending hdf5 upgradeJason W. Bacon1-1/+2
2021-01-24biology/bedtools: Upgrade to 2.30.0Jason W. Bacon6-34/+46
2021-01-23biology/haplohseq: Fix example scripts for python 3Jason W. Bacon6-43/+81
2021-01-22biology/bedtools: License changed upstreamJason W. Bacon1-1/+1
2021-01-22biology/gatk: Add the WITH_LARGE_FILES option.Yuri Victorovich1-0/+30
2021-01-21biology/gatk: Update 4.1.8.1 -> 4.1.9.0Yuri Victorovich2-6/+6
2021-01-20Fix build on GCC-based systems by adding compiler:c++14-lang to USES:Mark Linimon1-1/+1
2021-01-20Add compiler:c++11-lang to USES to fix build on GCC-based systems:Mark Linimon1-1/+1
2021-01-19biology/bioparser: Cosmetic changesYuri Victorovich1-9/+9
2021-01-19New port: biology/rampler: Standalone module for sampling genomic sequencesYuri Victorovich5-0/+66
2021-01-19New port: biology/edlib: Fast C++ library for sequence alignment using edit d...Yuri Victorovich5-0/+40
2021-01-19New port: biology/spoa: C++ implementation of the partial order alignment (PO...Yuri Victorovich6-0/+166
2021-01-19New port: biology/biosoup: Collection of C++ header-only data structures for ...Yuri Victorovich4-0/+46
2021-01-19New port: biology/bioparser: C++ header only parsing library for several form...Yuri Victorovich4-0/+49
2021-01-19Mark BROKEN on riscv64 the same as on aarch64.Mark Linimon1-2/+3
2021-01-19Mark BROKEN on riscv64 the same as armv*:Mark Linimon1-0/+1
2021-01-16biology/vsearch: enable on powerpc64lePiotr Kubaj1-1/+1
2021-01-15biology/hyphy: Update to version 2.5.26Joseph Mingrone2-5/+4
2021-01-15biology/haplohseq: Restrict to python3Jason W. Bacon2-2/+1
2021-01-14Hook haplohseq to the buildAntoine Brodin1-0/+1
2021-01-14biology/haplohseq: Resurrect and fix python2 dependencyJason W. Bacon13-0/+308
2021-01-14Remove PY_SPHINX from ports using Python 3Danilo G. Baio1-1/+1
2021-01-12biology/iqtree: Remove USES=compiler:openmp, fix amd64 clang++ buildJoseph Mingrone2-2/+14
2021-01-11biology/hyphy: Remove USES=compiler:openmpJoseph Mingrone1-1/+2
2021-01-11biology/star: Drop dependency on gccJason W. Bacon2-15/+15
2021-01-11biology/stacks: Drop dependency on gccJason W. Bacon1-4/+4
2021-01-11biology/ncbi-blast+: Drop dependency on gccJason W. Bacon2-4/+26
2021-01-11biology/gcta: Drop dependency on gccJason W. Bacon1-10/+4
2021-01-11biology/fasttree: Drop dependency on gccJason W. Bacon1-3/+1
2021-01-11biology/cd-hit: Drop dependency on gccJason W. Bacon1-2/+2
2021-01-11biology/canu: Drop dependency on gccJason W. Bacon1-9/+3
2021-01-11biology/py-biom-format: Update to version 2.1.10Joseph Mingrone2-5/+4
2021-01-11biology/hyphy: Update to version 2.5.25Joseph Mingrone2-4/+4
2021-01-08biology/pooler: Upgrade to 1.76Jason W. Bacon2-4/+4
2021-01-02biology/gemma: Upgrade to 0.98.3Jason W. Bacon3-20/+4
2021-01-02For ports on riscv64 that fail the same (or similar ways) to aarch64, markMark Linimon6-0/+6
2020-12-31- Update Unipro UGENE port to version 37.0Alexey Dokuchaev13-248/+56
2020-12-28Drop python 2.7 support from a few portsAntoine Brodin9-9/+9
2020-12-26Restrict to Java 8, since this doesn't compile with Java 11Greg Lewis1-0/+1
2020-12-24scipy 1.5.4 is only compatible with python 3.6+Antoine Brodin2-2/+2
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