| .. |
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abyss
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biology/abyss: Add PORTSCOUT line
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2021-03-14 05:17:40 +00:00 |
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ad2vcf
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biology/ad2vcf: Add allelic depth info from a SAM stream to a VCF file
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2021-03-23 15:15:00 +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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For ports on riscv64 that fail the same (or similar ways) to aarch64, mark
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2021-01-02 01:46:08 +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/htslib: Update to 1.12
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2021-03-20 17:14:32 +00:00 |
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bedtools
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biology/bedtools: Upgrade to 2.30.0
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2021-01-24 18:25:39 +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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Update a few GNUstep ports:
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2021-02-14 23:21:02 +00:00 |
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biolibc
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biology/biolibc: Low-level high-performance bioinformatics library
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2021-03-21 15:10:17 +00:00 |
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bioparser
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biology/bioparser: Update 3.0.12 -> 3.0.12-2
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2021-02-03 19:08:28 +00:00 |
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biosoup
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New port: biology/biosoup: Collection of C++ header-only data structures for bioinformatics
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2021-01-19 09:01:41 +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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Introduce devel/onetbb and mark devel/tbb as legacy
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2021-02-19 15:14:46 +00:00 |
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bwa
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biology/bwa: fix build on powerpc64le
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2021-03-02 15:01:55 +00:00 |
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canu
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biology/canu: Drop dependency on gcc
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2021-01-11 16:51:15 +00:00 |
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cd-hit
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biology/cd-hit: Drop dependency on gcc
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2021-01-11 16:55:15 +00:00 |
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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 2.0.8
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2021-03-11 12:41:20 +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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edlib
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Fix build on GCC-based systems by adding compiler:c++14-lang to USES:
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2021-01-20 02:31:33 +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: Update to 0.11.9
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2021-02-04 15:56:33 +00:00 |
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fasttree
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biology/fasttree: Drop dependency on gcc
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2021-01-11 16:58:13 +00:00 |
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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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For ports on riscv64 that fail the same (or similar ways) to aarch64, mark
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2021-01-02 01:46:08 +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 fetch
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2021-03-13 18:55:14 +00:00 |
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gcta
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biology/gcta: Drop dependency on gcc
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2021-01-11 17:09:37 +00:00 |
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gemma
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biology/gemma: Upgrade to 0.98.3
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2021-01-02 22:05:58 +00:00 |
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generand
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biology/generand: Update to 0.1.2
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2021-03-20 14:31:48 +00:00 |
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gff2ps
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Fix spelling mistakes, typos, poor wording, hyphenation, jargonisms,
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2021-03-22 10:17:43 +00:00 |
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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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haplohseq
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biology/haplohseq: Fix example scripts for python 3
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2021-01-23 19:31:49 +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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biology/hmmer: disable on powerpc64le and powerpcspe
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2021-03-10 16:09:46 +00:00 |
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htslib
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biology/htslib: Update to 1.12
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2021-03-20 17:14:32 +00:00 |
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hyphy
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biology/hyphy: Update to 2.5.29
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2021-02-25 01:39:51 +00:00 |
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igv
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biology/igv: Update 2.8.13 -> 2.9.4
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2021-03-28 16:41:33 +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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biology/iqtree: Remove USES=compiler:openmp, fix amd64 clang++ build
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2021-01-12 18:12:12 +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: Add -lz for pending hdf5 upgrade
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2021-01-26 01:34:20 +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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biology/libbigwig: Update 0.4.4 -> 0.4.6
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2021-03-06 00:16:34 +00:00 |
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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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Mark BROKEN on riscv64 the same as armv*:
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2021-01-19 02:26:53 +00:00 |
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minimap2
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molden
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biology/molden: Fix build with gfortran10
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2021-03-29 21:51:03 +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+: Drop dependency on gcc
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2021-01-11 17:17:35 +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 2.10.9 -> 2.11.0
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2021-03-20 06:39:38 +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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For ports on riscv64 that fail the same (or similar ways) to aarch64, mark
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2021-01-02 01:46:08 +00:00 |
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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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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: Upgrade to 1.76
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2021-01-08 22:44:13 +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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Update USES=python: math/py-pandas 1.2.0 requires Python 3.7+
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2021-01-30 13:29:58 +00:00 |
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py-biopython
|
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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biology/py-bx-python: Update 0.8.9 -> 0.8.10
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2021-02-27 03:55:36 +00:00 |
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py-cutadapt
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Unbreak INDEX
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2021-03-06 21:18:14 +00:00 |
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py-dnaio
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biology/py-cutadapt: Update to 3.2
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2021-02-02 20:39:09 +00:00 |
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py-ete3
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PyQt5: Update PyQt5 to 5.15.4 and py-qtbuilder to 1.9.1
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2021-03-16 09:29:53 +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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Update USES=python: math/py-pandas 1.2.0 requires Python 3.7+
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2021-01-30 13:29:58 +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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Update USES=python: math/py-pandas 1.2.0 requires Python 3.7+
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2021-01-30 13:29:58 +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: Update to 1.10
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2021-03-20 14:25:48 +00:00 |
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py-orange3-bioinformatics
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Mark ports recursively depending on Python 2.7 for expiration on June 23.
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2021-03-24 13:34:35 +00:00 |
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py-orange3-single-cell
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Mark ports recursively depending on Python 2.7 for expiration on June 23.
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2021-03-24 13:34:35 +00:00 |
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py-pandas-charm
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Update USES=python: math/py-pandas 1.2.0 requires Python 3.7+
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2021-01-30 13:29:58 +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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biology/py-scikit-bio: fix build on powerpc64
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2021-03-09 10:38:33 +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
|
Update WWW
|
2020-03-31 23:18:09 +00:00 |
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rampler
|
Add compiler:c++11-lang to USES to fix build on GCC-based systems:
|
2021-01-20 02:30:13 +00:00 |
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recombine
|
Fix after gets(3) retirement using gets_s(3).
|
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
|
2020-05-05 14:22:09 +00:00 |
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rubygem-bio
|
Update to 2.0.1
|
2020-07-24 07:49:43 +00:00 |
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rubygem-bio-executables
|
Add rubygem-bio-executables 1.0.0
|
2020-07-24 07:08:00 +00:00 |
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rubygem-bio-old-biofetch-emulator
|
Add rubygem-bio-old-biofetch-emulator 1.0.0
|
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
|
2020-07-24 07:08:11 +00:00 |
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samtools
|
biology/htslib: Update to 1.12
|
2021-03-20 17:14:32 +00:00 |
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scrm
|
Add compiler:c++11-lang to USES to fix build on GCC-based systems:
|
2020-05-15 07:30:34 +00:00 |
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seaview
|
Mark BROKEN in 13/14 (via latest llvm update).
|
2021-02-17 21:59:47 +00:00 |
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seqan
|
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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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seqan1
|
Fix some misspelled or duplicated LICENSE_*
|
2019-09-17 19:21:45 +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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spoa
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biology/spoa: fix build on non-x86
|
2021-03-04 19:18:53 +00:00 |
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stacks
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biology/stacks: Drop dependency on gcc
|
2021-01-11 17:27:30 +00:00 |
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star
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biology/star: Drop dependency on gcc
|
2021-01-11 17:39:52 +00:00 |
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stringtie
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biology/stringtie: fix build on GCC architectures
|
2020-02-23 10:52:44 +00:00 |
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subread
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biology/subread: Update to 2.0.2
|
2021-03-30 15:30:27 +00:00 |
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tabixpp
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biology/tabixpp: fix build on GCC architectures
|
2020-11-23 16:13:15 +00:00 |
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treekin
|
Fix math/openblas and bump dependent ports
|
2020-01-30 14:17:44 +00:00 |
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treepuzzle
|
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trimadap
|
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trimmomatic
|
Clean up after java/openjdk6 and java/openjdk6-jre removal
|
2019-11-26 21:46:12 +00:00 |
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tRNAscan-SE
|
biology/tRNAscan-SE: update to 2.0.5
|
2020-01-13 17:36:57 +00:00 |
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ugene
|
- Update Unipro UGENE to version 38.0
|
2021-03-23 14:20:49 +00:00 |
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vcf-split
|
biology/vcf-split: Split a multi-sample VCF into single-sample VCFs
|
2021-03-21 15:17:27 +00:00 |
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vcf2hap
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biology/vcf2hap: Generate .hap file from VCF for haplohseq
|
2021-03-23 16:32:29 +00:00 |
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vcflib
|
biology/vcflib: fix build on powerpc64le
|
2021-03-28 16:39:24 +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
|
2020-12-06 20:14:53 +00:00 |
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vsearch
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biology/vsearch: Update to 2.16.0
|
2021-03-24 18:43:42 +00:00 |
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vt
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biology/vt: Fix build with htslib 1.11
|
2020-11-09 00:35:58 +00:00 |
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wise
|
a-b: Add missing USES={gnome,php,sdl,xorg}
|
2019-11-08 09:27:56 +00:00 |
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Makefile
|
biology/vcf2hap: Generate .hap file from VCF for haplohseq
|
2021-03-23 16:32:29 +00:00 |
