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mirror of https://git.FreeBSD.org/ports.git synced 2024-12-11 02:50:24 +00:00
freebsd-ports/biology
2017-07-22 11:01:38 +00:00
..
ariadne
artemis - Fix shebangs 2017-04-21 16:28:25 +00:00
avida Mark some ports failing on power64. In cases where the error message 2017-05-13 03:35:51 +00:00
babel
bcftools Update math/gsl to 2.4 2017-07-03 20:38:11 +00:00
bedtools Mark some ports failing on armv6, for errors classified as "clang". 2017-05-27 15:07:11 +00:00
biococoa
biojava Deprecate ports BROKEN for more than 6 months 2017-07-22 11:01:38 +00:00
blat - Update WWW 2017-06-10 09:01:19 +00:00
bowtie - Fix shebangs 2017-04-22 09:25:44 +00:00
bowtie2 Update devel/tbb to 2017.5 2017-03-07 12:44:41 +00:00
bwa Mark some ports failing on armv6, for errors classified as "???". 2017-05-26 20:02:44 +00:00
cd-hit Bump PORTREVISIONs for ports depending on the canonical version of GCC and 2017-04-01 15:23:30 +00:00
cdbfasta Update WWW: SF redirects to https://sourceforge.net/projects/<PROJECT_NAME>/ 2017-01-20 20:33:30 +00:00
chemeq biology/chemeq: fix build on GCC (taken from dports) 2016-12-18 04:22:26 +00:00
clustalw
consed - Replace Mk/bsd.linux-apps.mk and Mk/bsd.linux-rpm.mk with 2016-09-05 19:23:42 +00:00
crux Mark some ports failing on armv6, for errors classified as "???". 2017-05-26 20:02:44 +00:00
diamond biology/diamond: Update to version 0.9.9 2017-07-03 19:12:18 +00:00
emboss
fasta ${RM} already has -f. 2016-10-21 12:51:40 +00:00
fasta3
fastdnaml
fastool Never set WRKSRC when using USE_GITHUB. 2017-01-03 18:12:13 +00:00
fasttree Bump PORTREVISIONs for ports depending on the canonical version of GCC and 2017-04-01 15:23:30 +00:00
fastx-toolkit
fluctuate
garlic
gff2ps
gmap Mark some ports failing on power64. In cases where the error message 2017-05-13 03:35:51 +00:00
gperiodic Remove libintl.so.9 compatibility link that was added in r374303 to 2016-12-08 19:52:19 +00:00
grappa
hmmer Begin deorbit burn of ia64. We have not attempted to build packages for 2017-06-25 00:29:09 +00:00
htslib Use USES=pathfix where applicable. 2016-10-21 15:21:13 +00:00
iolib Mark some ports failing on power64. In cases where the error message 2017-05-13 03:35:51 +00:00
jalview
jellyfish Bump PORTREVISIONs for ports depending on the canonical version of GCC and 2017-04-01 15:23:30 +00:00
lagan
lamarc biology/lamarc: Fix build on DF (taken from dports) 2016-12-18 04:34:33 +00:00
libgtextutils Use USES=pathfix where applicable. 2016-10-21 15:21:13 +00:00
libsbml - Update to 5.15.0 2017-05-18 02:22:18 +00:00
linux-foldingathome - Replace Mk/bsd.linux-apps.mk and Mk/bsd.linux-rpm.mk with 2016-09-05 19:23:42 +00:00
mafft
mapm3
migrate
molden Chase next distfile update. Upstream contacted whether we would be allowed to host a distfile copy. 2017-07-13 21:56:29 +00:00
mopac Bump PORTREVISIONs for ports depending on the canonical version of GCC and 2017-04-01 15:23:30 +00:00
mrbayes Update devel/readline to 7.0 patch 3 2017-06-27 13:46:53 +00:00
mummer
muscle Mark various leaf ports broken on aarch64, and, where appropriate, other 2016-11-11 09:31:02 +00:00
ncbi-blast+ Bump PORTREVISIONs for ports depending on the canonical version of GCC and 2017-04-01 15:23:30 +00:00
ncbi-toolkit Remove libjpeg.so.11 compatibility link that was added in r374303 to 2016-12-08 16:39:11 +00:00
njplot biology/njplot: Add site in MASTER_SITES because package builders are 2016-11-28 15:19:42 +00:00
p5-AcePerl Move -fPIC to where Linux puts it so it is limited to a single library. 2017-02-13 22:43:58 +00:00
p5-Bio-ASN1-EntrezGene - Add LICENSE 2016-12-18 15:25:13 +00:00
p5-Bio-Coordinate - Add p5-Bio-Coordinate 1.007001 2016-12-19 15:54:39 +00:00
p5-Bio-Das - Add LICENSE 2016-12-18 15:25:18 +00:00
p5-Bio-Das-Lite
p5-Bio-GFF3
p5-Bio-Glite
p5-Bio-Graphics Remove outdated PERL_LEVEL check 2017-06-01 23:50:28 +00:00
p5-Bio-MAGETAB
p5-Bio-NEXUS
p5-Bio-Phylo - Add LICENSE_FILE 2016-12-18 15:25:22 +00:00
p5-Bio-SCF
p5-BioPerl Remove outdated PERL_LEVEL check 2017-06-01 23:50:33 +00:00
p5-BioPerl-Run Bump PORTREVISION for ports affected by the fix the last commit. 2017-01-31 16:21:45 +00:00
p5-transdecoder Never set WRKSRC when using USE_GITHUB. 2017-01-03 18:12:13 +00:00
paml Cleanup no longer needed CHMOD usage after r424898. 2016-11-02 22:45:14 +00:00
phrap
phred
phylip
phyml Update WWW 2017-05-30 15:22:06 +00:00
plink Bump PORTREVISIONs for ports depending on the canonical version of GCC and 2017-04-01 15:23:30 +00:00
plinkseq Mark some ports failing on power64. In cases where the error message 2017-05-13 03:35:51 +00:00
primer3
protomol Revision bump of all ports with USE_GL after consolidation of mesa-libs 2017-05-23 05:03:14 +00:00
psi88 Bump PORTREVISIONs for ports depending on the canonical version of GCC and 2017-04-01 15:23:30 +00:00
py-biom-format biology/py-biom-format: Update to version 2.1.6 2017-04-29 13:59:15 +00:00
py-biopython - Update to 1.69 2017-05-03 12:39:28 +00:00
py-bx-python bx-python is a python library and associated set of scripts to allow for rapid 2017-05-06 06:07:03 +00:00
py-pysam - Update to 0.11.2.2 2017-06-10 02:03:39 +00:00
pycogent
pyfasta
python-nexus - Update to 1.42 2017-03-01 07:00:37 +00:00
recombine
ruby-bio - Update to 1.5.1 2017-05-07 15:44:34 +00:00
rubygem-bio Update to 1.5.1 2017-02-06 23:03:17 +00:00
samtools
seaview biology/seaview: Update version 4.6.1=>4.6.2 2017-07-21 17:33:10 +00:00
seqan - Update biology/seqan and bilogy/seqan-apps to version 2.2.0 [1] 2016-09-14 19:38:58 +00:00
seqan1
seqan-apps It is possible that r441426 will fix the build problem on armv6. Give 2017-05-21 23:37:34 +00:00
seqio
seqtools Mark some ports failing on power64. In cases where the error message 2017-05-21 21:55:08 +00:00
sim4
slclust Update WWW: SF redirects to https://sourceforge.net/projects/<PROJECT_NAME>/ 2017-01-20 20:33:30 +00:00
ssaha Bump PORTREVISIONs for ports depending on the canonical version of GCC and 2017-04-01 15:23:30 +00:00
t_coffee Bump PORTREVISIONs for ports depending on the canonical version of GCC and 2017-04-01 15:23:30 +00:00
tinker Bump PORTREVISIONs for ports depending on the canonical version of GCC and 2017-04-01 15:23:30 +00:00
treepuzzle
trimmomatic
tRNAscan-SE
ugene Revision bump of all ports with USE_GL after consolidation of mesa-libs 2017-05-23 05:03:14 +00:00
vcftools Assume "pkg-config zlib" works after 9.x reached EOL 2017-01-03 17:06:49 +00:00
velvet
wise Remove libintl.so.9 compatibility link that was added in r374303 to 2016-12-08 19:52:19 +00:00
xmolwt Remove libintl.so.9 compatibility link that was added in r374303 to 2016-12-08 19:52:19 +00:00
Makefile bx-python is a python library and associated set of scripts to allow for rapid 2017-05-06 06:07:03 +00:00