freebsd-ports/biology
Rene Ladan b6cb229310 Remove deprecated ports:
2020-08-15 archivers/py-backports.lzma: Uses deprecated version of python
2020-08-15 archivers/py-bup: Uses deprecated version of python
2020-08-15 archivers/py-librtfcomp: Uses deprecated version of python
2020-08-15 audio/blop-lv2: Uses deprecated version of python
2020-08-15 audio/bs2b-lv2: Uses deprecated version of python
2020-08-15 audio/py-gmusicproxy: Uses deprecated version of python
2020-08-15 audio/py-karaoke: Uses deprecated version of python
2020-08-15 audio/py-openal: Uses deprecated version of python
2020-08-15 audio/py-py-jack: Uses deprecated version of python
2020-08-15 audio/py-xmms2: Uses deprecated version of python
2020-08-15 audio/triceratops-lv2: Uses deprecated version of python
2020-08-15 biology/py-biom-format: Uses deprecated version of python
2020-08-15 comms/py-bulksms: Uses deprecated version of python
2020-08-15 comms/py-gammu: Uses deprecated version of python
2020-08-15 databases/py-geoalchemy: Uses deprecated version of python
2020-08-15 databases/py-htsql-mysql: Uses deprecated version of python
2020-08-15 databases/py-htsql-pgsql: Uses deprecated version of python
2020-08-15 databases/py-mysql2pgsql: Uses deprecated version of python
2020-08-15 databases/py-oursql: Uses deprecated version of python
2020-08-15 databases/py-pyPgSQL: Uses deprecated version of python
2020-08-15 databases/py-pyhs: Uses deprecated version of python
2020-08-15 databases/py-pytc: Uses deprecated version of python
2020-08-15 databases/py-riak: Uses deprecated version of python
2020-08-15 databases/py-umemcache: Uses deprecated version of python
2020-08-15 devel/py-Breve: Uses deprecated version of python
2020-08-15 devel/py-PyODE: Uses deprecated version of python
2020-08-15 devel/py-akismet: Uses deprecated version of python
2020-08-15 devel/py-aspects: Uses deprecated version of python
2020-08-15 devel/py-backports.tempfile: Uses deprecated version of python
2020-08-15 devel/py-backports.weakref: Uses deprecated version of python
2020-08-15 devel/py-cfgparse: Uses deprecated version of python
2020-08-15 devel/py-ciphon: Uses deprecated version of python
2020-08-15 devel/py-cjson: Uses deprecated version of python
2020-08-15 devel/py-clonedigger: Uses deprecated version of python
2020-08-15 devel/py-cuisine: Uses deprecated version of python
2020-08-15 devel/py-deliciousapi: Uses deprecated version of python
2020-08-15 devel/py-dialog: Uses deprecated version of python
2020-08-15 devel/py-efl: Uses deprecated version of python
2020-08-15 devel/py-ezpyinline: Uses deprecated version of python
2020-08-15 devel/py-fsm: Uses deprecated version of python
2020-08-15 devel/py-gdbgui: Uses deprecated version of python
2020-08-15 devel/py-gearman: Uses deprecated version of python
2020-08-15 devel/py-generate: Uses deprecated version of python
2020-08-15 devel/py-geotypes: Uses deprecated version of python
2020-08-15 devel/py-gitosis: Uses deprecated version of python
2020-08-15 devel/py-google-apputils: Uses deprecated version of python
2020-08-15 devel/py-hghooks: Uses deprecated version of python
2020-08-15 devel/py-instant: Uses deprecated version of python
2020-08-15 devel/py-jcc: Uses deprecated version of python
2020-08-15 devel/py-json-py: Uses deprecated version of python
2020-08-15 devel/py-json-sempai: Uses deprecated version of python
2020-08-15 devel/py-jsonlib: Uses deprecated version of python
2020-08-15 devel/py-jsonlib2: Uses deprecated version of python
2020-08-15 devel/py-jsonrpclib: Uses deprecated version of python
2020-08-15 devel/py-kayako: Uses deprecated version of python
2020-08-15 devel/py-kid: Uses deprecated version of python
2020-08-15 devel/py-kjbuckets: Uses deprecated version of python
2020-08-15 devel/py-kqueue: Uses deprecated version of python
2020-08-15 devel/py-log4py: Uses deprecated version of python
2020-08-15 devel/py-mwlib.ext: Uses deprecated version of python
2020-08-15 devel/py-mx-experimental: Uses deprecated version of python
2020-08-15 devel/py-option_merge: Uses deprecated version of python
2020-08-15 devel/py-prioritized_methods: Uses deprecated version of python
2020-08-15 devel/py-protocols: Uses deprecated version of python
2020-08-15 devel/py-ptrace: Uses deprecated version of python
2020-08-15 devel/py-pydoop: Uses deprecated version of python
2020-08-15 devel/py-pyke: Uses deprecated version of python
2020-08-15 devel/py-pymtbl: Uses deprecated version of python
2020-08-15 devel/py-pyshapelib: Uses deprecated version of python
2020-08-15 devel/py-pytemplate: Uses deprecated version of python
2020-08-15 devel/py-python2-pythondialog: Uses deprecated version of python
2020-08-15 devel/py-pyutil: Uses deprecated version of python
2020-08-15 devel/py-pyvalid: Uses deprecated version of python
2020-08-15 devel/py-pyxml2obj: Uses deprecated version of python
2020-08-15 devel/py-qpid: Uses deprecated version of python
2020-08-15 devel/py-repoze.what-pylons: Uses deprecated version of python
2020-08-15 devel/py-repoze.who-friendlyform: Uses deprecated version of python
2020-08-15 devel/py-robotframework-ride: Uses deprecated version of python
2020-08-15 devel/py-ruamel.ordereddict: Uses deprecated version of python
2020-08-15 devel/py-sanetime: Uses deprecated version of python
2020-08-15 devel/py-selectors34: Uses deprecated version of python
2020-08-15 devel/py-sqlcc: Uses deprecated version of python
2020-08-15 devel/py-statgrab: Uses deprecated version of python
2020-08-15 devel/py-tconfpy: Uses deprecated version of python
2020-08-15 devel/py-terminable_thread: Uses deprecated version of python
2020-08-15 devel/py-trace2html: Uses deprecated version of python
2020-08-15 devel/py-tvrage: Uses deprecated version of python
2020-08-15 devel/py-tw.forms: Uses deprecated version of python
2020-08-15 devel/py-uncompyle2: Uses deprecated version of python
2020-08-15 devel/py-yum-metadata-parser: Uses deprecated version of python
2020-08-15 devel/rubygem-warden127: No longer needed
2020-08-15 dns/py-dnschain: Uses deprecated version of python
2020-08-15 dns/py-idnkit2: Uses deprecated version of python
2020-08-15 games/colobot: Uses deprecated version of python
2020-08-15 games/endgame-singularity: Uses deprecated version of python
2020-08-15 games/katawa-shoujo: Uses deprecated version of RenPy
2020-08-15 games/pyfa: Uses deprecated version of python
2020-08-15 games/renpy6: Uses deprecated version of python
2020-08-15 games/solarwolf: Uses deprecated version of python
2020-08-15 games/thudboard: Uses deprecated version of python
2020-08-15 graphics/djvusmooth: Uses deprecated version of python
2020-08-15 graphics/py-glewpy: Uses deprecated version of python
2020-08-15 graphics/py-openexr: Uses deprecated version of python
2020-08-15 graphics/py-poppler: Uses deprecated version of python
2020-08-15 graphics/py-pygooglechart: Uses deprecated version of python
2020-08-15 graphics/py-sane: Uses deprecated version of python
2020-08-15 graphics/py-stltools: Uses deprecated version of python
2020-08-15 graphics/sk1: Uses deprecated version of python
2020-08-15 japanese/py-mecab: Uses deprecated version of python
2020-08-15 japanese/py-tegaki-gtk: Uses deprecated version of python
2020-08-15 lang/py-mx-base: Uses deprecated version of python
2020-08-15 mail/mailpile: Uses deprecated version of python
2020-08-15 math/py-ffc: Uses deprecated version of python
2020-08-15 math/py-fiat: Uses deprecated version of python
2020-08-15 math/py-nzmath: Uses deprecated version of python
2020-08-15 math/py-pymc: Uses deprecated version of python
2020-08-15 math/py-ufl: Uses deprecated version of python
2020-08-15 misc/py-socli: Uses deprecated version of python
2020-08-15 misc/py-yolk: Uses deprecated version of python
2020-08-15 multimedia/py-flvlib: Uses deprecated version of python
2020-08-15 net/py-gspreadsheet: Uses deprecated version of python
2020-08-15 net/py-libnet: Uses deprecated version of python
2020-08-15 net/py-netlib: Uses deprecated version of python
2020-08-15 net/py-pynmsg: Uses deprecated version of python
2020-08-15 net/py-rainbowstream: Uses deprecated version of python
2020-08-15 net/py-wolframalpha: Uses deprecated version of python
2020-08-15 net-im/empathy: Uses deprecated version of python
2020-08-15 net-im/farsight2: Uses deprecated version of python
2020-08-15 net-im/py-xmpppy: Uses deprecated version of python
2020-08-15 net-im/telepathy-farsight: Uses deprecated version of python
2020-08-15 net-im/telepathy-python: Uses deprecated version of python
2020-08-15 net-im/telepathy-rakia: Uses deprecated version of python
2020-08-15 net-mgmt/py-pynsca: Uses deprecated version of python
2020-08-15 net-mgmt/py-yapsnmp: Uses deprecated version of python
2020-08-15 net-p2p/py-py2play: Uses deprecated version of python
2020-08-15 news/py-yenc: Uses deprecated version of python
2020-08-15 print/py-pyscript: Uses deprecated version of python
2020-08-15 print/py-stapler: Uses deprecated version of python
2020-08-15 print/py-trml2pdf: Uses deprecated version of python
2020-08-15 science/py-PyQuante: Uses deprecated version of python
2020-08-15 science/py-mlpy: Uses deprecated version of python
2020-08-15 science/py-ws2300: Uses deprecated version of python
2020-08-15 security/py-PF: Uses deprecated version of python
2020-08-15 security/py-cracklib: Uses deprecated version of python
2020-08-15 security/py-fteproxy: Uses deprecated version of python
2020-08-15 security/py-onetime: Uses deprecated version of python
2020-08-15 security/py-pydeep: Uses deprecated version of python
2020-08-15 security/py-slowaes: Uses deprecated version of python
2020-08-15 security/py-sslstrip: Uses deprecated version of python
2020-08-15 security/py-volatility: Uses deprecated version of python
2020-08-15 sysutils/py-analyzemft: Uses deprecated version of python
2020-08-15 sysutils/py-cdmi: Uses deprecated version of python
2020-08-15 sysutils/py-ezjailremote: Uses deprecated version of python
2020-08-15 sysutils/py-gmailfs-fuse: Uses deprecated version of python
2020-08-15 sysutils/py-ploy_ec2: Uses deprecated version of python
2020-08-15 sysutils/py-ploy_fabric: Uses deprecated version of python
2020-08-15 sysutils/py-scriptine: Uses deprecated version of python
2020-08-15 sysutils/py-superlance: Uses deprecated version of python
2020-08-15 textproc/py-bugzillatools: Uses deprecated version of python
2020-08-15 textproc/py-elib.intl: Uses deprecated version of python
2020-08-15 textproc/py-errorhandler: Uses deprecated version of python
2020-08-15 textproc/py-hyperestraier-python: Uses deprecated version of python
2020-08-15 textproc/py-pyes: Uses deprecated version of python
2020-08-15 textproc/py-pyhwp: Uses deprecated version of python
2020-08-15 textproc/py-sphinx_numfig: Uses deprecated version of python
2020-08-15 www/py-HTMLgen: Uses deprecated version of python
2020-08-15 www/py-albatross: Uses deprecated version of python
2020-08-15 www/py-amf: Uses deprecated version of python
2020-08-15 www/py-apachelog: Uses deprecated version of python
2020-08-15 www/py-aws-requests-auth: Uses deprecated version of python
2020-08-15 www/py-clientform: Uses deprecated version of python
2020-08-15 www/py-django-appmedia: Uses deprecated version of python
2020-08-15 www/py-django-evolution: Uses deprecated version of python
2020-08-15 www/py-fedex: Uses deprecated version of python
2020-08-15 www/py-formalchemy: Uses deprecated version of python
2020-08-15 www/py-frappe-bench: Uses deprecated version of python
2020-08-15 www/py-funkload: Uses deprecated version of python
2020-08-15 www/py-goobook: Uses deprecated version of python
2020-08-15 www/py-poster: Uses deprecated version of python
2020-08-15 www/py-pyquery: Uses deprecated version of python
2020-08-15 www/py-pysearch: Uses deprecated version of python
2020-08-15 www/py-pywebdav: Uses deprecated version of python
2020-08-15 www/py-slimmer: Uses deprecated version of python
2020-08-15 www/py-surl: Uses deprecated version of python
2020-08-15 www/py-tmdb3: Uses deprecated version of python
2020-08-15 www/py-trello: Uses deprecated version of python
2020-08-15 www/py-uliweb: Uses deprecated version of python
2020-08-15 www/py-wsgiauth: Uses deprecated version of python
2020-08-15 x11-toolkits/py-wax: Uses deprecated version of python
2020-08-15 x11-toolkits/py-wxPython-common: Uses deprecated version of python
2020-08-15 x11-toolkits/py-wxPython28-common: Uses deprecated version of python
2020-08-15 10:50:58 +00:00
..
abyss Chanse update of devel/libffi 2020-07-04 18:11:42 +00:00
artemis Clean up after java/openjdk6 and java/openjdk6-jre removal 2019-11-26 21:46:12 +00:00
avida biology/avida: unbreak on powerpc64 2019-10-23 16:25:10 +00:00
babel
bamtools Bump devel/jsoncpp consumers after r540853. 2020-06-30 17:46:18 +00:00
bcftools biology/bcftools: Upgrade to 1.10.2 2020-08-03 18:16:54 +00:00
bedtools biology/bedtools: Upgrade to 2.29.2 2019-12-19 01:04:11 +00:00
bioawk biology/bioawk: BWK awk modified for biological data 2020-06-05 02:45:33 +00:00
biococoa Return theraven's ports to the pool after safekeeping his commit bit. 2020-03-05 20:49:05 +00:00
bolt-lmm Bump 46 ports depending on math/openblas because the after the recent math/openblas update the library name changed in openblas. 2020-05-06 16:11:14 +00:00
bowtie biology/bowtie: Unbreak build with GCC 10 2020-07-04 10:46:08 +00:00
bowtie2 Update devel/tbb to 2020.3 and bump dependent ports' revisions 2020-07-17 10:12:25 +00:00
bwa
canu Mark as BROKEN on powerpc64: 2020-05-17 02:25:16 +00:00
cd-hit
cdbfasta
checkm
clustal-omega
clustalw
cufflinks biology/htslib: Upgrade to 1.10.2 2020-08-03 17:40:04 +00:00
cytoscape Clean up after java/openjdk6 and java/openjdk6-jre removal 2019-11-26 21:46:12 +00:00
ddocent
diamond biology/diamond: Update to version 2.0.2 2020-08-07 11:20:11 +00:00
dsr-pdb devel/boost-*: update to 1.72.0 2019-12-11 17:53:48 +00:00
emboss - update libgd to 2.3.0 2020-05-04 21:31:39 +00:00
exonerate
fasta
fasta3
fastahack
fastdnaml
fastool
fastp biology/fastp: Upgrade to 0.20.1 2020-04-09 16:17:02 +00:00
fastqc
fasttree
fastx-toolkit
figtree
fluctuate
freebayes
garlic Add USES=xorg USES=gl, ports categories b 2019-11-04 21:08:20 +00:00
gatk biology/gatk: Update 4.1.7.0 -> 4.1.8.0 2020-07-09 00:40:56 +00:00
gcta Bump 46 ports depending on math/openblas because the after the recent math/openblas update the library name changed in openblas. 2020-05-06 16:11:14 +00:00
gemma Bump 37 ports depending on math/openblas through USES=blaslapack:openblas because after the recent math/openblas update the library name changed in openblas 2020-05-06 16:39:12 +00:00
gff2ps
gmap
gperiodic - Update WWW 2020-01-19 09:30:22 +00:00
graphlan biology/graphlan: Remove the 2.7 limitation on python because it's no longer needed 2020-08-14 04:59:29 +00:00
grappa
groopm biology/groopm: Remove python's 2.7 restriction placed here by mistake 2020-08-13 19:19:23 +00:00
haplohseq Deprecate some ports using deprecated version of python 2020-03-08 17:01:46 +00:00
hhsuite biology/hhsuite: fix build on powerpc64 elfv2 2020-05-11 19:33:32 +00:00
hisat2
hmmer biology/hmmer: update to 3.3 2020-01-29 05:55:12 +00:00
htslib biology/htslib: Upgrade to 1.10.2 2020-08-03 17:40:04 +00:00
hyphy biology/hyphy: Update to version 2.5.15 2020-06-28 16:40:33 +00:00
igv Deprecate java/openjfx8-devel consumers 2020-03-19 09:33:13 +00:00
infernal biology/infernal: update to 1.1.3 2020-01-27 17:57:14 +00:00
iolib
iqtree biology/iqtree: Update to version 2.0.6 2020-05-30 18:43:26 +00:00
jalview Clean up after java/openjdk6 and java/openjdk6-jre removal 2019-11-26 21:46:12 +00:00
jellyfish biology/htslib: Upgrade to 1.10.2 2020-08-03 17:40:04 +00:00
kallisto biology/kallisto: Revert to 0.46.1 2020-08-03 15:45:21 +00:00
lagan
lamarc
libbigwig
libgtextutils
libsbml Move devel/swig30 to devel/swig and update to 4.0.1 2020-06-17 18:17:45 +00:00
linux-foldingathome Update to 7.6.13 2020-05-09 13:21:29 +00:00
mafft
mapm3
migrate
minimap2
molden Add USES=xorg USES=gl, ports categories b 2019-11-04 21:08:20 +00:00
mopac
mothur Update devel/gmake to 4.3. 2020-05-09 19:24:49 +00:00
mrbayes - Swap back from net/openmpi3 to net/openmpi 2020-04-21 21:47:57 +00:00
mummer
muscle biology/muscle: unbreak in -CURRENT 2020-01-17 16:49:03 +00:00
ncbi-blast+ Bump PORTREVISION for security/nettle shlib change 2020-05-16 10:51:32 +00:00
ncbi-cxx-toolkit Add USES=xorg USES=gl, ports categories b 2019-11-04 21:08:20 +00:00
ncbi-toolkit Bump PORTREVISION for security/nettle shlib change 2020-05-16 10:51:32 +00:00
ngs-sdk biology/ngs-sdk: Update 2.10.4 -> 2.10.5 2020-04-04 20:09:00 +00:00
p5-AcePerl
p5-Bio-ASN1-EntrezGene Update *_DEPENDS 2020-01-08 18:36:30 +00:00
p5-Bio-Cluster Update *_DEPENDS 2019-12-08 16:57:18 +00:00
p5-Bio-Coordinate Cosmetic change 2020-04-02 12:01:30 +00:00
p5-Bio-Das
p5-Bio-Das-Lite
p5-Bio-DB-EMBL Add p5-Bio-DB-EMBL 1.7.4 2019-12-08 16:49:19 +00:00
p5-Bio-DB-NCBIHelper Add p5-Bio-DB-NCBIHelper 1.7.6 2019-12-08 16:49:25 +00:00
p5-Bio-FeatureIO Cosmetic change 2020-04-02 12:01:35 +00:00
p5-Bio-GFF3
p5-Bio-Glite
p5-Bio-Graphics
p5-Bio-MAGETAB
p5-Bio-NEXUS
p5-Bio-Phylo
p5-Bio-SCF
p5-Bio-Variation Update to 1.7.5 2020-01-08 18:36:35 +00:00
p5-BioPerl Move devel/p5-IO-stringy to devel/p5-IO-Stringy and update to 2.113 2020-06-26 11:55:23 +00:00
p5-BioPerl-Run Remove outdated CONFLICTS: p5-bioperl-run was renamed to p5-BioPerl-Run over 3 years ago 2020-01-08 18:36:40 +00:00
p5-transdecoder
p5-TrimGalore biology/p5-TrimGalore: Upgrade to 0.6.5 2019-11-26 16:20:12 +00:00
paml biology/paml: Update to version 4.9j 2019-11-22 15:32:40 +00:00
pbbam biology/htslib: Upgrade to 1.10.2 2020-08-03 17:40:04 +00:00
pbcopper Deprecate ports broken for more than 6 months 2020-07-26 07:32:00 +00:00
pbseqan biology/unanimity and dependencies: Flag as no longer open source 2019-11-24 15:53:00 +00:00
pear-merger
phrap Sanitize COMMENT per Section 5.6 of the FreeBSD Porter's Handbook (part 1). 2020-05-27 11:59:13 +00:00
phred
phylip Add USES=xorg USES=gl, ports categories b 2019-11-04 21:08:20 +00:00
phyml biology/phyml: update to 3.3.20200621 2020-07-10 09:45:48 +00:00
picard-tools biology/picard-tools: CLI tools for manipulating sequencing data 2020-06-13 13:54:47 +00:00
plink Bump 37 ports depending on math/openblas through USES=blaslapack:openblas because after the recent math/openblas update the library name changed in openblas 2020-05-06 16:39:12 +00:00
primer3
prodigal
prodigy-lig Unbreak bulk -a 2020-06-13 15:05:44 +00:00
protomol Add USES=xorg USES=gl, ports categories b 2019-11-04 21:08:20 +00:00
psi88 biology/psi88: Unbreak build with GCC 10 2020-07-04 12:15:58 +00:00
py-biopython biology/py-biopython: Set python requirement to 3.6+ 2020-06-13 13:42:12 +00:00
py-bx-python biology/py-bx-python: Update 0.8.8 -> 0.8.9 2020-06-26 04:17:11 +00:00
py-cutadapt biology/py-cutadapt: Upgrade to 2.7 2019-11-23 14:45:53 +00:00
py-dnaio biology/py-dnaio: Upgrade to 0.4.2 2020-05-24 15:23:15 +00:00
py-ete3 New port: biology/py-ete3: Framework for the analysis and visualization of trees 2020-05-16 00:13:09 +00:00
py-fastTSNE Drop dependency on devel/openmp 2020-03-08 21:56:36 +00:00
py-Genesis-PyAPI
py-gffutils Unbreak bulk -a 2020-07-14 07:59:28 +00:00
py-gtfparse biology/py-gtfparse: Update 1.2.0 -> 1.2.1 2020-08-07 04:13:00 +00:00
py-hits New port: biology/py-hits: Utilities for processing high-throughput sequencing experiments 2020-05-16 03:11:05 +00:00
py-loompy biology/py-loompy: Update 2.0.17 -> 3.0.6 2020-06-16 02:26:08 +00:00
py-macs2 biology/py-macs2: Upgrade to 2.2.7.1 2020-04-14 12:13:55 +00:00
py-multiqc biology/py-multiqc: Upgrade to 1.8 2019-11-26 16:25:08 +00:00
py-orange3-bioinformatics
py-orange3-single-cell Update Sphinx 2020-05-11 23:51:58 +00:00
py-pandas-charm Clean up some things 2020-05-30 00:57:02 +00:00
py-pyfaidx
py-pysam biology/py-pysam: Update 0.15.4 -> 0.16.0 2020-06-09 05:03:48 +00:00
py-scikit-bio biology/py-scikit-bio: Fix license 2020-05-16 02:29:20 +00:00
py-xenaPython
pyfasta
python-nexus
rainbow Update WWW 2020-03-31 23:18:09 +00:00
recombine
ruby-bio biology/ruby-bio: remove expired optional dependency on textproc/ruby-xmlparser 2020-05-05 14:22:09 +00:00
rubygem-bio Update to 2.0.1 2020-07-24 07:49:43 +00:00
rubygem-bio-executables Add rubygem-bio-executables 1.0.0 2020-07-24 07:08:00 +00:00
rubygem-bio-old-biofetch-emulator Add rubygem-bio-old-biofetch-emulator 1.0.0 2020-07-24 07:08:05 +00:00
rubygem-bio-shell Add rubygem-bio-shell 1.0.0 2020-07-24 07:08:11 +00:00
samtools biology/samtools: Upgrade to 1.10 2020-08-03 18:22:06 +00:00
scrm Add compiler:c++11-lang to USES to fix build on GCC-based systems: 2020-05-15 07:30:34 +00:00
seaview biology/seaview: Update version 5.0.3=>5.0.4 2020-06-22 17:34:44 +00:00
seqan
seqan1
seqan-apps devel/boost-*: update to 1.72.0 2019-12-11 17:53:48 +00:00
seqio
seqtk
sim4
slclust
smithwaterman
stacks
star biology/star: Upgrade to 2.7.3a 2020-04-09 12:43:03 +00:00
stringtie biology/stringtie: fix build on GCC architectures 2020-02-23 10:52:44 +00:00
subread biology/subread: Read alignment, quantification and mutation discovery 2020-06-05 01:55:49 +00:00
tabixpp biology/htslib: Upgrade to 1.10.2 2020-08-03 17:40:04 +00:00
tophat Deprecate some ports using deprecated version of python 2020-03-08 17:01:46 +00:00
treekin Fix math/openblas and bump dependent ports 2020-01-30 14:17:44 +00:00
treepuzzle
trimadap
trimmomatic Clean up after java/openjdk6 and java/openjdk6-jre removal 2019-11-26 21:46:12 +00:00
tRNAscan-SE biology/tRNAscan-SE: update to 2.0.5 2020-01-13 17:36:57 +00:00
ugene biology/ugene: prepare for Qt5-5.15 2020-05-19 18:00:02 +00:00
vcflib biology/htslib: Upgrade to 1.10.2 2020-08-03 17:40:04 +00:00
vcftools
velvet
viennarna - update libgd to 2.3.0 2020-05-04 21:31:39 +00:00
vsearch biology/vsearch: Update to 2.15.0 2020-06-20 14:31:59 +00:00
vt biology/vt: Patch to work with htslib 1.10.2 2020-08-03 17:42:32 +00:00
wise a-b: Add missing USES={gnome,php,sdl,xorg} 2019-11-08 09:27:56 +00:00
Makefile Remove deprecated ports: 2020-08-15 10:50:58 +00:00