mirror/freebsd-ports
1
0
Fork 0
mirror of https://git.FreeBSD.org/ports.git synced 2025-02-07 11:49:40 +00:00
Code Issues Releases Activity
freebsd-ports/biology
History
Antoine Brodin 3afa450ba3 Deprecate ports broken for more than 6 months
2015-10-25 19:35:28 +00:00
..
ariadne
6 ports categories: Remove $PTHREAD_LIBS
2015-03-24 16:01:21 +00:00
artemis
- Add empty directory to plist
2015-03-11 14:41:53 +00:00
avida
- Unbreak on PowerPC by using atomicops implementation for Linux and GCC
2015-09-02 12:29:09 +00:00
babel
Unbreak the build on PowerPC (at least) by always using va_copy() macro for
2015-09-02 10:10:06 +00:00
bcftools
New port: biology/bcftools
2015-06-05 21:01:13 +00:00
biococoa
Make all GNUstep ports install into the System domain so that the Local domain is available for stuff built from source.
2015-09-19 10:33:34 +00:00
biojava
…
blat
Update to upstream version 36
2015-01-01 18:17:53 +00:00
bwa
BWA is a program for aligning sequencing reads against a large reference
2015-09-25 18:39:36 +00:00
cd-hit
- Use compiler:openmp instead of gcc
2015-09-19 13:12:44 +00:00
cdbfasta
Fast indexing and retrieval of FASTA records from flat file data bases.
2015-09-25 18:37:24 +00:00
chemeq
…
clustalw
MASTER_SITES cleanup.
2015-05-14 10:15:04 +00:00
consed
Deprecate ports broken for more than 6 months
2015-10-25 19:35:28 +00:00
crux
Unbreak the build on PowerPC, it had nothing to do with "error in pthreads":
2015-09-02 09:23:05 +00:00
emboss
Fix packaging as a user (pkg already takes care of credentials)
2015-03-18 21:52:19 +00:00
fasta
- Do not falsely advertise that PowerPC build runs out of space and fails
2015-09-02 10:35:25 +00:00
fasta3
- Update to 36.3.8
2015-10-16 13:31:10 +00:00
fastdnaml
Cleanup plist
2014-10-20 07:10:48 +00:00
fastool
Simple and quick FastQ and FastA tool for file reading and conversion.
2015-09-25 18:35:14 +00:00
fasttree
FastTree infers approximately-maximum-likelihood phylogenetic trees from
2015-09-25 18:34:29 +00:00
fastx-toolkit
The FASTX-Toolkit is a collection of command line tools for Short-Reads
2015-09-25 18:33:18 +00:00
fluctuate
Remove $FreeBSD$ from patches files in categories a-j.
2015-05-22 13:34:20 +00:00
garlic
Cleanup plist
2014-10-20 07:10:48 +00:00
gff2ps
Convert ports to use the options helpers in categories [abc]*, and minor fixes.
2015-08-19 13:29:59 +00:00
gmap
…
gperiodic
…
grappa
biology/grappa: define license (GPLv2)
2015-09-25 18:55:08 +00:00
hmmer
- Remove deprecated option
2015-04-02 15:41:31 +00:00
htslib
Update ports in the [bcd]* categories to not use GH_COMMIT.
2015-05-06 15:16:53 +00:00
iolib
- Update to 1.14.4
2015-10-07 00:26:33 +00:00
jalview
Remove $FreeBSD$ from patches files in categories a-j.
2015-05-22 13:34:20 +00:00
lagan
- Fix shebangs
2015-06-11 10:17:24 +00:00
lamarc
Remove ansi version fo wxGTK 2.8 and only keep the unicode version
2015-09-16 19:51:26 +00:00
libgtextutils
Gordon's text utilities.
2015-09-25 18:31:28 +00:00
libsbml
- Add LICENSE_FILE
2015-10-14 23:51:20 +00:00
linux-foldingathome
Cleanup plist
2014-12-20 17:27:08 +00:00
mafft
Use BROKEN helpers
2015-06-27 14:30:19 +00:00
mapm3
…
migrate
- Update options
2015-06-28 15:30:41 +00:00
molden
…
mopac
- Upadate biology/mopac to version 1.15
2014-12-16 22:10:23 +00:00
mrbayes
…
mummer
Fix build on mips by properly respecting compiler and flags
2015-08-05 12:18:41 +00:00
muscle
…
ncbi-blast+
- Unbreak
2015-05-04 06:08:59 +00:00
ncbi-toolkit
Cleanup plist
2014-10-20 07:10:48 +00:00
njplot
Deprecate ports broken for more than 6 months
2015-10-25 19:35:28 +00:00
ortep3
Deprecate ports broken for more than 6 months
2015-10-25 19:35:28 +00:00
p5-AcePerl
Make it so that the default Perl is always called perl5.
2015-09-14 12:19:48 +00:00
p5-Bio-ASN1-EntrezGene
Start removing MASTER_SITE_SUBDIR=CPAN:username where possible. The
2015-06-24 15:16:23 +00:00
p5-Bio-Das
Change the way Perl modules are installed, update the default Perl to 5.18.
2014-11-26 13:08:24 +00:00
p5-Bio-Das-Lite
Remove TEST dependency on p5-Test-Simple when the version in core is
2015-02-26 16:54:41 +00:00
p5-Bio-GFF3
Make it so that the default Perl is always called perl5.
2015-09-14 12:19:48 +00:00
p5-Bio-Glite
Change the way Perl modules are installed, update the default Perl to 5.18.
2014-11-26 13:08:24 +00:00
p5-Bio-Graphics
Make it so that the default Perl is always called perl5.
2015-09-14 12:19:48 +00:00
p5-Bio-MAGETAB
Some OCD cleanups on some of the perl@ ports.
2015-03-12 23:00:02 +00:00
p5-Bio-NEXUS
Make it so that the default Perl is always called perl5.
2015-09-14 12:19:48 +00:00
p5-Bio-Phylo
- Update to 0.58
2014-12-07 04:41:47 +00:00
p5-Bio-SCF
Change the way Perl modules are installed, update the default Perl to 5.18.
2014-11-26 13:08:24 +00:00
p5-bioperl
Make it so that the default Perl is always called perl5.
2015-09-14 12:19:48 +00:00
p5-bioperl-run
For the new USE_GITHUB with only GH_TAGNAME set default DISTNAME to
2015-03-20 20:07:50 +00:00
paml
Update biology/paml to 4.8a and unbreak.
2015-04-10 15:39:01 +00:00
phrap
- Fix various distinfo errors
2014-10-16 08:55:30 +00:00
phred
…
phylip
Unbreak
2015-07-28 17:52:11 +00:00
phyml
Convert to USES=autoreconf
2014-12-28 19:14:13 +00:00
platon
Convert ports to use the options helpers in categories [abc]*, and minor fixes.
2015-08-19 13:29:59 +00:00
plink
…
plinkseq
- Update to 0.10
2014-10-12 03:16:10 +00:00
povchem
Deprecate ports broken for more than 6 months
2015-10-25 19:35:28 +00:00
primer3
…
protomol
Convert ports to use the options helpers in categories [abc]*, and minor fixes.
2015-08-19 13:29:59 +00:00
psi88
- Strip binaries
2015-06-03 17:27:08 +00:00
py-biopython
Update to 1.65.
2015-08-05 10:32:31 +00:00
pycogent
- Convert ports from benchmarks/ and biology/ to new USES=python
2014-10-19 07:38:11 +00:00
pyfasta
- Convert ports from benchmarks/ and biology/ to new USES=python
2014-10-19 07:38:11 +00:00
python-nexus
- Convert ports from benchmarks/ and biology/ to new USES=python
2014-10-19 07:38:11 +00:00
recombine
…
ruby-bio
- Fix typo
2015-10-10 23:15:16 +00:00
samtools
Update ports in the [bcd]* categories to not use GH_COMMIT.
2015-05-06 15:16:53 +00:00
seaview
biology/seaview: Update version 4.5.4.7=>4.5.4.8
2015-10-20 11:51:32 +00:00
seqan
biology/segan: Limit GCC to 4.8 while waiting for update
2015-03-21 11:53:27 +00:00
seqio
…
seqtools
biology/seqtools: 4.35 -> 4.36
2015-08-08 11:22:24 +00:00
sim4
…
ssaha
Cleanup plist
2014-12-20 17:27:08 +00:00
t_coffee
MASTER_SITES cleanup.
2015-05-14 10:15:04 +00:00
tinker
Convert ports to use the options helpers in categories [abc]*, and minor fixes.
2015-08-19 13:29:59 +00:00
treepuzzle
…
treeviewx
- Pet portlint
2015-10-14 23:50:11 +00:00
tRNAscan-SE
…
ugene
biology/ugene: qt4-linguist -> qt4-linguisttools
2015-08-18 20:02:45 +00:00
velvet
Designatate 4 ports as unsafe for parallel building
2015-01-19 17:43:57 +00:00
wise
Cleanup plist
2014-12-20 17:27:08 +00:00
xmolwt
Fix previous commit.
2015-08-19 13:41:51 +00:00
Makefile
BWA is a program for aligning sequencing reads against a large reference
2015-09-25 18:39:36 +00:00