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abyss
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biology/abyss: Update 2.2.4 -> 2.2.5
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2020-09-27 06:59:05 +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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Bump devel/jsoncpp consumers after r540853.
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2020-06-30 17:46:18 +00:00 |
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bcftools
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biology/bcftools: Upgrade to 1.11
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2020-11-05 20:34:03 +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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Canonicalize powerpc64le CXXFLAGS to be the same as powerpc64.
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2020-09-27 07:41:33 +00:00 |
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bowtie
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biology/bowtie: Unbreak build with GCC 10
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2020-07-04 10:46:08 +00:00 |
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bowtie2
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biology/bowtie2: Upgrade to 2.4.2
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2020-11-07 13:47:41 +00:00 |
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bwa
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biology/bwa: fix build on recent current
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2020-08-28 11:17:13 +00:00 |
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canu
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biology/canu: Upgrade to 2.1
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2020-09-14 22:27:37 +00:00 |
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cd-hit
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cdbfasta
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checkm
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scipy 1.5.4 is only compatible with python 3.6+
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2020-12-24 09:03:39 +00:00 |
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clustal-omega
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clustalw
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cufflinks
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- Upgrade math/eigen3 to 3.3.8;
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2020-12-12 17:04:37 +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 2.0.6
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2020-12-20 20:21:41 +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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fasta3
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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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Add education virtual category
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2020-11-20 07:16:06 +00:00 |
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fluctuate
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freebayes
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Fix build with -fno-common
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2020-09-21 18:14:57 +00:00 |
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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: Fix build
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2020-09-08 19:25:36 +00:00 |
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gcta
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- Upgrade math/eigen3 to 3.3.8;
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2020-12-12 17:04:37 +00:00 |
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gemma
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- Upgrade math/eigen3 to 3.3.8;
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2020-12-12 17:04:37 +00:00 |
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gff2ps
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gmap
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biology/gmap: enable on powerpc64le
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2020-10-09 13:23:12 +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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biology/graphlan: Remove the 2.7 limitation on python because it's no longer needed
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2020-08-14 04:59:29 +00:00 |
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grappa
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Extend expiration of ports broken with -fno-common
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2020-08-30 09:47:49 +00:00 |
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groopm
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scipy 1.5.4 is only compatible with python 3.6+
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2020-12-24 09:03:39 +00:00 |
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hhsuite
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biology/hhsuite: Update 3.2.0 -> 3.3.0
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2020-08-27 04:28:24 +00:00 |
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hisat2
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hmmer
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Also enable on powerpc64le.
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2020-09-24 20:29:35 +00:00 |
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htslib
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biology/htslib: Upgrade to 1.11.0
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2020-11-05 20:30:50 +00:00 |
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hyphy
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biology/hyphy: Update to version 2.5.24
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2020-12-20 20:21:52 +00:00 |
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igv
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biology/igv: Fix fetch by fixing a small left-over mistake
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2020-11-30 17:29:48 +00:00 |
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infernal
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Also enable on powerpc64le.
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2020-09-24 20:38:59 +00:00 |
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iolib
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iqtree
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- Upgrade math/eigen3 to 3.3.8;
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2020-12-12 17:04:37 +00:00 |
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jalview
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Restrict to Java 8, since this doesn't compile with Java 11
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2020-12-26 23:01:20 +00:00 |
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jellyfish
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biology/htslib: Upgrade to 1.10.2
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2020-08-03 17:40:04 +00:00 |
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kallisto
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biology/kallisto: Revert to 0.46.1
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2020-08-03 15:45:21 +00:00 |
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lagan
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Extend expiration of ports broken with -fno-common
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2020-08-30 09:47:49 +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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Set CMAKE options explicitly
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2020-12-20 15:23:50 +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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biology/mapm3: Reformat patches.
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2020-09-04 12:24:23 +00:00 |
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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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biology/mothur: fix build on powerpc64le
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2020-10-19 10:30:11 +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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biology/mummer: fix build on powerpc64 elfv2 and powerpc64le
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2020-10-25 23:03:14 +00:00 |
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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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biology/ncbi-blast+: Upgrade to 2.11.0
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2020-11-16 18:25:03 +00:00 |
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ncbi-cxx-toolkit
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biology/ncbi-cxx-toolkit: Fix build on 13
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2020-09-27 04:57:44 +00:00 |
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ncbi-toolkit
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Chase security/p11-kit update
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2020-08-30 03:10:23 +00:00 |
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ngs-sdk
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biology/ngs-sdk: Update 2.10.5 -> 2.10.9
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2020-12-17 20:12:12 +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: fix the build with LLVM 11
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2020-08-20 17:07:03 +00:00 |
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pbbam
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biology/htslib: Upgrade to 1.10.2
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2020-08-03 17:40:04 +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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phylip
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Extend expiration of ports broken with -fno-common
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2020-08-30 09:47:49 +00:00 |
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phyml
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biology/phyml: fix build on recent current
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2020-08-29 08:34:27 +00:00 |
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picard-tools
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biology/picard-tools: Remove extraneous file
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2020-08-30 14:06:54 +00:00 |
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plink
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Allow building on powerpc64le.
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2020-09-27 07:44:15 +00:00 |
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pooler
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biology/pooler: Optimise DNA sequencing primer-set combinations
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2020-11-15 18:50:17 +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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biology/psi88: Unbreak build with GCC 10
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2020-07-04 12:15:58 +00:00 |
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py-biom-format
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biology/py-biom-format: Fix fetch and relax scipy requirement
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2020-09-26 09:10:37 +00:00 |
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py-biopython
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biology/py-biopython: Upgrade to 1.78
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2020-10-16 19:12:43 +00:00 |
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py-bx-python
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Drop python 2.7 support from a few ports
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2020-12-28 23:02:12 +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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Update PyQt5 to 5.15.2, sip to 5.5.0, py-qtbuilder to 1.6.0 and py-qt5-sip to 12.8.1
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2020-12-15 17:56:00 +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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Drop python 2.7 support from a few ports
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2020-12-28 23:02:12 +00:00 |
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py-gffutils
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Unbreak bulk -a
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2020-07-14 07:59:28 +00:00 |
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py-gtfparse
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Drop python 2.7 support from a few ports
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2020-12-28 23:02:12 +00:00 |
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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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Unbreak bulk -a
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2020-09-19 14:15:42 +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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Drop python 2.7 support from a few ports
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2020-12-28 23:02:12 +00:00 |
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py-pyfaidx
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Drop python 2.7 support from a few ports
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2020-12-28 23:02:12 +00:00 |
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py-pysam
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Drop python 2.7 support from a few ports
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2020-12-28 23:02:12 +00:00 |
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py-scikit-bio
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Add education virtual category
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2020-11-20 07:16:06 +00:00 |
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py-xenaPython
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Drop python 2.7 support from a few ports
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2020-12-28 23:02:12 +00:00 |
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pyfasta
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Drop python 2.7 support from a few ports
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2020-12-28 23:02:12 +00:00 |
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python-nexus
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Drop python 2.7 support from a few ports
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2020-12-28 23:02:12 +00:00 |
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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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Update to 2.0.1
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2020-07-24 07:49:43 +00:00 |
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rubygem-bio-executables
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Add rubygem-bio-executables 1.0.0
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2020-07-24 07:08:00 +00:00 |
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rubygem-bio-old-biofetch-emulator
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Add rubygem-bio-old-biofetch-emulator 1.0.0
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2020-07-24 07:08:05 +00:00 |
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rubygem-bio-shell
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Add rubygem-bio-shell 1.0.0
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2020-07-24 07:08:11 +00:00 |
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samtools
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biology/samtools: Upgrade to 1.11
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2020-11-05 20:32:39 +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: Add -fcommon for clang 11
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2020-09-18 00:57:35 +00:00 |
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tabixpp
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biology/tabixpp: fix build on GCC architectures
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2020-11-23 16:13:15 +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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- Update Unipro UGENE port to version 37.0
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2020-12-31 13:43:09 +00:00 |
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vcflib
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biology/htslib: Upgrade to 1.10.2
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2020-08-03 17:40:04 +00:00 |
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vcftools
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velvet
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viennarna
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biology/viennarna: Update 2.4.16 -> 2.4.17
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2020-12-06 20:14:53 +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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biology/vt: Fix build with htslib 1.11
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2020-11-09 00:35:58 +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/pooler: Optimise DNA sequencing primer-set combinations
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2020-11-15 18:50:17 +00:00 |
8f46816990