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abyss
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biology/abyss: Update 2.2.3 -> 2.2.4
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2020-05-30 09:10:44 +00:00 |
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artemis
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Clean up after java/openjdk6 and java/openjdk6-jre removal
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2019-11-26 21:46:12 +00:00 |
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avida
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biology/avida: unbreak on powerpc64
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2019-10-23 16:25:10 +00:00 |
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babel
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bamtools
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devel/jsoncpp: Update 1.8.1 -> 1.9.2
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2020-01-13 21:38:35 +00:00 |
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bcftools
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math/gsl: update to 2.6
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2019-10-25 23:41:34 +00:00 |
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bedtools
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biology/bedtools: Upgrade to 2.29.2
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2019-12-19 01:04:11 +00:00 |
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bioawk
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biology/bioawk: BWK awk modified for biological data
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2020-06-05 02:45:33 +00:00 |
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biococoa
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Return theraven's ports to the pool after safekeeping his commit bit.
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2020-03-05 20:49:05 +00:00 |
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bolt-lmm
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Bump 46 ports depending on math/openblas because the after the recent math/openblas update the library name changed in openblas.
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2020-05-06 16:11:14 +00:00 |
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bowtie
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bowtie2
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Update devel/tbb to 2020.2 and bump dependent port's revisions
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2020-04-01 14:14:51 +00:00 |
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bwa
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canu
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Mark as BROKEN on powerpc64:
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2020-05-17 02:25:16 +00:00 |
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cd-hit
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cdbfasta
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checkm
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biology/checkm: Update 1.0.17 -> 1.0.18
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2019-08-19 08:25:29 +00:00 |
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clustal-omega
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clustalw
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cufflinks
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biology/cufflinks: Update 2.2.1-83 -> 2.2.1-89
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2020-03-31 06:42:22 +00:00 |
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cytoscape
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Clean up after java/openjdk6 and java/openjdk6-jre removal
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2019-11-26 21:46:12 +00:00 |
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ddocent
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diamond
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biology/diamond: Update to version 0.9.35
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2020-06-27 16:26:54 +00:00 |
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dsr-pdb
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devel/boost-*: update to 1.72.0
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2019-12-11 17:53:48 +00:00 |
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emboss
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- update libgd to 2.3.0
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2020-05-04 21:31:39 +00:00 |
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exonerate
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fasta
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Convert to UCL & cleanup pkg-message (categories a-c)
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2019-08-13 16:00:39 +00:00 |
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fasta3
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Convert to UCL & cleanup pkg-message (categories a-c)
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2019-08-13 16:00:39 +00:00 |
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fastahack
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biology/fastahack: Upgrade to 1.0.0
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2019-10-06 21:34:32 +00:00 |
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fastdnaml
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fastool
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fastp
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biology/fastp: Upgrade to 0.20.1
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2020-04-09 16:17:02 +00:00 |
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fastqc
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biology/fastqc: Upgrade to 0.11.8
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2019-09-21 02:44:54 +00:00 |
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fasttree
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fastx-toolkit
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figtree
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fluctuate
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freebayes
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garlic
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Add USES=xorg USES=gl, ports categories b
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2019-11-04 21:08:20 +00:00 |
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gatk
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biology/gatk: Update 4.1.5.0 -> 4.1.7.0
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2020-05-28 02:26:51 +00:00 |
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gcta
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Bump 46 ports depending on math/openblas because the after the recent math/openblas update the library name changed in openblas.
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2020-05-06 16:11:14 +00:00 |
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gemma
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Bump 37 ports depending on math/openblas through USES=blaslapack:openblas because after the recent math/openblas update the library name changed in openblas
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2020-05-06 16:39:12 +00:00 |
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gff2ps
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gmap
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Convert to UCL & cleanup pkg-message (categories a-c)
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2019-08-13 16:00:39 +00:00 |
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gperiodic
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- Update WWW
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2020-01-19 09:30:22 +00:00 |
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graphlan
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Deprecate a few ports
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2020-02-23 15:25:53 +00:00 |
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grappa
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groopm
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Deprecate a few ports
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2020-02-23 15:25:53 +00:00 |
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haplohseq
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Deprecate some ports using deprecated version of python
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2020-03-08 17:01:46 +00:00 |
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hhsuite
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biology/hhsuite: fix build on powerpc64 elfv2
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2020-05-11 19:33:32 +00:00 |
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hisat2
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hmmer
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biology/hmmer: update to 3.3
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2020-01-29 05:55:12 +00:00 |
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htslib
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hyphy
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biology/hyphy: Update to version 2.5.15
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2020-06-28 16:40:33 +00:00 |
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igv
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Deprecate java/openjfx8-devel consumers
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2020-03-19 09:33:13 +00:00 |
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infernal
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biology/infernal: update to 1.1.3
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2020-01-27 17:57:14 +00:00 |
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iolib
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iqtree
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biology/iqtree: Update to version 2.0.6
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2020-05-30 18:43:26 +00:00 |
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jalview
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Clean up after java/openjdk6 and java/openjdk6-jre removal
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2019-11-26 21:46:12 +00:00 |
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jellyfish
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biology/jellyfish: Patch for clang 10
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2020-03-07 19:25:54 +00:00 |
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kallisto
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kallisto: Patch for build with GCC
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2020-04-01 23:35:38 +00:00 |
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lagan
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Convert to UCL & cleanup pkg-message (categories a-c)
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2019-08-13 16:00:39 +00:00 |
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lamarc
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libbigwig
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libgtextutils
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libsbml
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Move devel/swig30 to devel/swig and update to 4.0.1
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2020-06-17 18:17:45 +00:00 |
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linux-foldingathome
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Update to 7.6.13
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2020-05-09 13:21:29 +00:00 |
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mafft
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mapm3
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migrate
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minimap2
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molden
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Add USES=xorg USES=gl, ports categories b
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2019-11-04 21:08:20 +00:00 |
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mopac
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mothur
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Update devel/gmake to 4.3.
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2020-05-09 19:24:49 +00:00 |
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mrbayes
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- Swap back from net/openmpi3 to net/openmpi
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2020-04-21 21:47:57 +00:00 |
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mummer
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muscle
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biology/muscle: unbreak in -CURRENT
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2020-01-17 16:49:03 +00:00 |
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ncbi-blast+
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Bump PORTREVISION for security/nettle shlib change
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2020-05-16 10:51:32 +00:00 |
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ncbi-cxx-toolkit
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Add USES=xorg USES=gl, ports categories b
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2019-11-04 21:08:20 +00:00 |
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ncbi-toolkit
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Bump PORTREVISION for security/nettle shlib change
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2020-05-16 10:51:32 +00:00 |
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ngs-sdk
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biology/ngs-sdk: Update 2.10.4 -> 2.10.5
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2020-04-04 20:09:00 +00:00 |
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p5-AcePerl
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p5-Bio-ASN1-EntrezGene
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Update *_DEPENDS
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2020-01-08 18:36:30 +00:00 |
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p5-Bio-Cluster
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Update *_DEPENDS
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2019-12-08 16:57:18 +00:00 |
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p5-Bio-Coordinate
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Cosmetic change
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2020-04-02 12:01:30 +00:00 |
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p5-Bio-Das
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p5-Bio-Das-Lite
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p5-Bio-DB-EMBL
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Add p5-Bio-DB-EMBL 1.7.4
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2019-12-08 16:49:19 +00:00 |
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p5-Bio-DB-NCBIHelper
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Add p5-Bio-DB-NCBIHelper 1.7.6
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2019-12-08 16:49:25 +00:00 |
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p5-Bio-FeatureIO
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Cosmetic change
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2020-04-02 12:01:35 +00:00 |
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p5-Bio-GFF3
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p5-Bio-Glite
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p5-Bio-Graphics
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p5-Bio-MAGETAB
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p5-Bio-NEXUS
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p5-Bio-Phylo
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p5-Bio-SCF
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p5-Bio-Variation
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Update to 1.7.5
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2020-01-08 18:36:35 +00:00 |
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p5-BioPerl
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Move devel/p5-IO-stringy to devel/p5-IO-Stringy and update to 2.113
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2020-06-26 11:55:23 +00:00 |
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p5-BioPerl-Run
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Remove outdated CONFLICTS: p5-bioperl-run was renamed to p5-BioPerl-Run over 3 years ago
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2020-01-08 18:36:40 +00:00 |
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p5-transdecoder
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p5-TrimGalore
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biology/p5-TrimGalore: Upgrade to 0.6.5
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2019-11-26 16:20:12 +00:00 |
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paml
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biology/paml: Update to version 4.9j
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2019-11-22 15:32:40 +00:00 |
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pbbam
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devel/boost-*: update to 1.72.0
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2019-12-11 17:53:48 +00:00 |
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pbcopper
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Mark BROKEN: fails to build
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2020-03-10 14:17:19 +00:00 |
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pbseqan
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biology/unanimity and dependencies: Flag as no longer open source
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2019-11-24 15:53:00 +00:00 |
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pear-merger
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phrap
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Sanitize COMMENT per Section 5.6 of the FreeBSD Porter's Handbook (part 1).
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2020-05-27 11:59:13 +00:00 |
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phred
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Convert to UCL & cleanup pkg-message (categories a-c)
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2019-08-13 16:00:39 +00:00 |
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phylip
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Add USES=xorg USES=gl, ports categories b
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2019-11-04 21:08:20 +00:00 |
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phyml
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- Swap back from net/openmpi3 to net/openmpi
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2020-04-21 21:51:56 +00:00 |
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picard-tools
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biology/picard-tools: CLI tools for manipulating sequencing data
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2020-06-13 13:54:47 +00:00 |
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plink
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Bump 37 ports depending on math/openblas through USES=blaslapack:openblas because after the recent math/openblas update the library name changed in openblas
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2020-05-06 16:39:12 +00:00 |
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primer3
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prodigal
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biology/prodigal: Eliminate a very old version from the portscout discovery process
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2019-10-12 15:40:21 +00:00 |
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prodigy-lig
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Unbreak bulk -a
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2020-06-13 15:05:44 +00:00 |
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protomol
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Add USES=xorg USES=gl, ports categories b
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2019-11-04 21:08:20 +00:00 |
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psi88
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py-biom-format
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Deprecate a few ports
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2020-02-23 15:25:53 +00:00 |
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py-biopython
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biology/py-biopython: Set python requirement to 3.6+
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2020-06-13 13:42:12 +00:00 |
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py-bx-python
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biology/py-bx-python: Update 0.8.8 -> 0.8.9
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2020-06-26 04:17:11 +00:00 |
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py-cutadapt
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biology/py-cutadapt: Upgrade to 2.7
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2019-11-23 14:45:53 +00:00 |
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py-dnaio
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biology/py-dnaio: Upgrade to 0.4.2
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2020-05-24 15:23:15 +00:00 |
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py-ete3
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New port: biology/py-ete3: Framework for the analysis and visualization of trees
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2020-05-16 00:13:09 +00:00 |
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py-fastTSNE
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Drop dependency on devel/openmp
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2020-03-08 21:56:36 +00:00 |
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py-Genesis-PyAPI
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py-gffutils
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biology/py-gffutils: Update 0.10 -> 0.10.1
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2020-06-16 02:10:08 +00:00 |
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py-gtfparse
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py-hits
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New port: biology/py-hits: Utilities for processing high-throughput sequencing experiments
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2020-05-16 03:11:05 +00:00 |
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py-loompy
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biology/py-loompy: Update 2.0.17 -> 3.0.6
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2020-06-16 02:26:08 +00:00 |
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py-macs2
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biology/py-macs2: Upgrade to 2.2.7.1
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2020-04-14 12:13:55 +00:00 |
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py-multiqc
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biology/py-multiqc: Upgrade to 1.8
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2019-11-26 16:25:08 +00:00 |
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py-orange3-bioinformatics
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py-orange3-single-cell
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Update Sphinx
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2020-05-11 23:51:58 +00:00 |
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py-pandas-charm
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Clean up some things
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2020-05-30 00:57:02 +00:00 |
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py-pyfaidx
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py-pysam
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biology/py-pysam: Update 0.15.4 -> 0.16.0
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2020-06-09 05:03:48 +00:00 |
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py-scikit-bio
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biology/py-scikit-bio: Fix license
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2020-05-16 02:29:20 +00:00 |
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py-xenaPython
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pyfasta
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python-nexus
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rainbow
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Update WWW
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2020-03-31 23:18:09 +00:00 |
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recombine
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Fix after gets(3) retirement using gets_s(3).
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2019-09-02 05:00:43 +00:00 |
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ruby-bio
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biology/ruby-bio: remove expired optional dependency on textproc/ruby-xmlparser
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2020-05-05 14:22:09 +00:00 |
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rubygem-bio
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samtools
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Convert to UCL & cleanup pkg-message (categories a-c)
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2019-08-13 16:00:39 +00:00 |
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scrm
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Add compiler:c++11-lang to USES to fix build on GCC-based systems:
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2020-05-15 07:30:34 +00:00 |
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seaview
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biology/seaview: Update version 5.0.3=>5.0.4
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2020-06-22 17:34:44 +00:00 |
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seqan
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seqan1
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Fix some misspelled or duplicated LICENSE_*
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2019-09-17 19:21:45 +00:00 |
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seqan-apps
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devel/boost-*: update to 1.72.0
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2019-12-11 17:53:48 +00:00 |
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seqio
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seqtk
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sim4
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slclust
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smithwaterman
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stacks
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star
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biology/star: Upgrade to 2.7.3a
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2020-04-09 12:43:03 +00:00 |
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stringtie
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biology/stringtie: fix build on GCC architectures
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2020-02-23 10:52:44 +00:00 |
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subread
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biology/subread: Read alignment, quantification and mutation discovery
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2020-06-05 01:55:49 +00:00 |
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tabixpp
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tophat
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Deprecate some ports using deprecated version of python
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2020-03-08 17:01:46 +00:00 |
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treekin
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Fix math/openblas and bump dependent ports
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2020-01-30 14:17:44 +00:00 |
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treepuzzle
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trimadap
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trimmomatic
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Clean up after java/openjdk6 and java/openjdk6-jre removal
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2019-11-26 21:46:12 +00:00 |
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tRNAscan-SE
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biology/tRNAscan-SE: update to 2.0.5
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2020-01-13 17:36:57 +00:00 |
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ugene
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biology/ugene: prepare for Qt5-5.15
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2020-05-19 18:00:02 +00:00 |
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vcflib
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vcftools
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velvet
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viennarna
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- update libgd to 2.3.0
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2020-05-04 21:31:39 +00:00 |
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vsearch
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biology/vsearch: Update to 2.15.0
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2020-06-20 14:31:59 +00:00 |
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vt
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Add compiler:c++0x to USES to fix build on GCC-based systems:
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2020-06-05 03:49:53 +00:00 |
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wise
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a-b: Add missing USES={gnome,php,sdl,xorg}
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2019-11-08 09:27:56 +00:00 |
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Makefile
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biology/picard-tools: CLI tools for manipulating sequencing data
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2020-06-13 13:54:47 +00:00 |
