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freebsd-ports/biology
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Andrej Zverev f09fca2358 - add stage support 
Approved by:	portmgr (blanket infrastructure)
2014-01-06 09:57:19 +00:00
..
ariadne
Stage support
2013-11-12 21:54:36 +00:00
artemis
Add NO_STAGE all over the place in preparation for the staging support (cat: biology)
2013-09-20 15:55:44 +00:00
avida
- Fix build with clang
2013-11-27 16:07:51 +00:00
babel
Add NO_STAGE all over the place in preparation for the staging support (cat: biology)
2013-09-20 15:55:44 +00:00
biococoa
Update BioCocoa to the latest release.
2013-10-08 18:34:45 +00:00
biojava
Convert biology to MDOCS and MEXAMPLES
2014-01-03 15:46:52 +00:00
blast
Convert biology to MDOCS and MEXAMPLES
2014-01-03 15:46:52 +00:00
blat
Add stage support
2013-11-12 22:02:02 +00:00
boinc-simap
The hmmer binary was renamed upstream to indicate that it is now an
2013-12-29 10:41:50 +00:00
chemeq
Add NO_STAGE all over the place in preparation for the staging support (cat: biology)
2013-09-20 15:55:44 +00:00
clustalw
- Fix build with clang/libc++.
2013-12-20 15:29:07 +00:00
consed
Convert biology to MDOCS and MEXAMPLES
2014-01-03 15:46:52 +00:00
crux
In preparation for making libtool generate libraries with a sane name, fix all
2013-12-11 14:43:51 +00:00
embassy
In preparation for making libtool generate libraries with a sane name, fix all
2013-12-11 14:43:51 +00:00
emboss
In preparation for making libtool generate libraries with a sane name, fix all
2013-12-11 14:43:51 +00:00
fasta
Add NO_STAGE all over the place in preparation for the staging support (cat: biology)
2013-09-20 15:55:44 +00:00
fasta3
Mark as broken: Invalid checksum, seems like the software was rerolled
2014-01-03 19:46:05 +00:00
fastdnaml
Add NO_STAGE all over the place in preparation for the staging support (cat: biology)
2013-09-20 15:55:44 +00:00
finchtv
Convert biology to MDOCS and MEXAMPLES
2014-01-03 15:46:52 +00:00
fluctuate
Add NO_STAGE all over the place in preparation for the staging support (cat: biology)
2013-09-20 15:55:44 +00:00
garlic
Add NO_STAGE all over the place in preparation for the staging support (cat: biology)
2013-09-20 15:55:44 +00:00
genpak
Respect PORT_OPTIONS:MDOCS
2013-12-09 01:28:41 +00:00
gff2ps
Add NO_STAGE all over the place in preparation for the staging support (cat: biology)
2013-09-20 15:55:44 +00:00
gmap
Support stage
2013-12-10 17:21:46 +00:00
gperiodic
- Remove manual creation and removal of share/applications, as it's now in the mtree (categories starting with [bce])
2013-10-22 13:57:35 +00:00
grappa
- Respect CC/CFLAGS
2013-12-20 13:27:13 +00:00
hmmer
Stage support
2013-12-30 18:08:14 +00:00
iolib
In preparation for making libtool generate libraries with a sane name, fix all
2013-12-11 14:43:51 +00:00
jalview
Add NO_STAGE all over the place in preparation for the staging support (cat: biology)
2013-09-20 15:55:44 +00:00
lagan
- Fix build
2013-11-27 13:16:47 +00:00
lamarc
- rename AL2 to APACHE20 in Mk/bsd.licenses.db.mk
2013-12-30 20:55:18 +00:00
libgenome
Add NO_STAGE all over the place in preparation for the staging support (cat: biology)
2013-09-20 15:55:44 +00:00
libsbml
In preparation for making libtool generate libraries with a sane name, fix all
2013-12-11 14:43:51 +00:00
linux-foldingathome
Add NO_STAGE all over the place in preparation for the staging support (cat: biology)
2013-09-20 15:55:44 +00:00
mafft
Convert biology to MDOCS and MEXAMPLES
2014-01-03 15:46:52 +00:00
mapm3
Add NO_STAGE all over the place in preparation for the staging support (cat: biology)
2013-09-20 15:55:44 +00:00
migrate
Add NO_STAGE all over the place in preparation for the staging support (cat: biology)
2013-09-20 15:55:44 +00:00
molden
- USES=fortran gmake.
2013-12-29 14:30:20 +00:00
mopac
In preparation for making libtool generate libraries with a sane name, fix all
2013-12-11 14:43:51 +00:00
mrbayes
Support stage
2013-12-10 17:54:12 +00:00
mummer
Convert biology to MDOCS and MEXAMPLES
2014-01-03 15:46:52 +00:00
muscle
Add NO_STAGE all over the place in preparation for the staging support (cat: biology)
2013-09-20 15:55:44 +00:00
ncbi-toolkit
Add NO_STAGE all over the place in preparation for the staging support (cat: biology)
2013-09-20 15:55:44 +00:00
njplot
Convert biology to MDOCS and MEXAMPLES
2014-01-03 15:46:52 +00:00
ortep3
USES=fortran, fix LDFLAGS, staging.
2013-12-17 21:24:17 +00:00
p5-AcePerl
Add NO_STAGE all over the place in preparation for the staging support (cat: biology)
2013-09-20 15:55:44 +00:00
p5-Bio-ASN1-EntrezGene
- add stage support
2014-01-06 09:57:19 +00:00
p5-Bio-Das
- support stage
2014-01-05 12:07:20 +00:00
p5-Bio-Das-Lite
Add NO_STAGE all over the place in preparation for the staging support (cat: biology)
2013-09-20 15:55:44 +00:00
p5-Bio-GFF3
- Update to 1.8
2013-11-02 19:55:32 +00:00
p5-Bio-Glite
- support stage
2014-01-05 12:07:20 +00:00
p5-Bio-Graphics
Add NO_STAGE all over the place in preparation for the staging support (cat: biology)
2013-09-20 15:55:44 +00:00
p5-Bio-MAGETAB
- Update to 1.28
2013-11-28 15:05:08 +00:00
p5-Bio-NEXUS
Add NO_STAGE all over the place in preparation for the staging support (cat: biology)
2013-09-20 15:55:44 +00:00
p5-Bio-Phylo
- support stage
2014-01-05 12:07:20 +00:00
p5-Bio-SCF
- add stage support
2014-01-06 09:44:19 +00:00
p5-bioperl
Convert biology to MDOCS and MEXAMPLES
2014-01-03 15:46:52 +00:00
p5-bioperl-run
Convert biology to MDOCS and MEXAMPLES
2014-01-03 15:46:52 +00:00
paml
Convert biology to MDOCS and MEXAMPLES
2014-01-03 15:46:52 +00:00
phd2fasta
Convert biology to MDOCS and MEXAMPLES
2014-01-03 15:46:52 +00:00
phrap
Convert biology to MDOCS and MEXAMPLES
2014-01-03 15:46:52 +00:00
phred
Convert biology to MDOCS and MEXAMPLES
2014-01-03 15:46:52 +00:00
phylip
Add NO_STAGE all over the place in preparation for the staging support (cat: biology)
2013-09-20 15:55:44 +00:00
phyml
Add NO_STAGE all over the place in preparation for the staging support (cat: biology)
2013-09-20 15:55:44 +00:00
platon
Version 2013.12.12, USES=fortran, staging.
2013-12-17 21:55:24 +00:00
plink
Fix the build with more standards-compliant compilers such as GCC 4.7. [1]
2013-12-13 09:34:40 +00:00
plinkseq
In preparation for making libtool generate libraries with a sane name, fix all
2013-12-11 14:43:51 +00:00
povchem
Convert to USES=dos2unix
2013-11-18 13:45:44 +00:00
primer3
Add NO_STAGE all over the place in preparation for the staging support (cat: biology)
2013-09-20 15:55:44 +00:00
protomol
In preparation for making libtool generate libraries with a sane name, fix all
2013-12-11 14:43:51 +00:00
psi88
USES=fortran, staging, miscellaneous cleanups.
2013-12-18 16:23:08 +00:00
py-biopython
Update to libmpc version 1.0.1 which brings the following fixes:
2013-10-26 00:52:33 +00:00
pycogent
Update to libmpc version 1.0.1 which brings the following fixes:
2013-10-26 00:52:33 +00:00
pyfasta
Update to libmpc version 1.0.1 which brings the following fixes:
2013-10-26 00:52:33 +00:00
pymol
In preparation for making libtool generate libraries with a sane name, fix all
2013-12-11 14:43:51 +00:00
python-nexus
Add NO_STAGE all over the place in preparation for the staging support (cat: biology)
2013-09-20 15:55:44 +00:00
rasmol
Add NO_STAGE all over the place in preparation for the staging support (cat: biology)
2013-09-20 15:55:44 +00:00
recombine
Add NO_STAGE all over the place in preparation for the staging support (cat: biology)
2013-09-20 15:55:44 +00:00
ruby-bio
Add NO_STAGE all over the place in preparation for the staging support (cat: biology)
2013-09-20 15:55:44 +00:00
seaview
In preparation for making libtool generate libraries with a sane name, fix all
2013-12-11 14:43:51 +00:00
seqan
Update to libmpc version 1.0.1 which brings the following fixes:
2013-10-26 00:52:33 +00:00
seqio
Add NO_STAGE all over the place in preparation for the staging support (cat: biology)
2013-09-20 15:55:44 +00:00
seqtools
biology/seqtools: update to 4.24
2013-12-24 17:23:23 +00:00
sim4
Add NO_STAGE all over the place in preparation for the staging support (cat: biology)
2013-09-20 15:55:44 +00:00
ssaha
Add NO_STAGE all over the place in preparation for the staging support (cat: biology)
2013-09-20 15:55:44 +00:00
t_coffee
USES=fortran, staging.
2013-12-18 17:24:51 +00:00
tinker
- biology/tinker: USES=fortran, staging.
2013-12-18 18:27:04 +00:00
treepuzzle
- Remove NO_STAGE as these have been tested to be safe
2013-09-25 00:54:08 +00:00
treeviewx
Stage support
2013-12-30 18:27:32 +00:00
tRNAscan-SE
Add NO_STAGE all over the place in preparation for the staging support (cat: biology)
2013-09-20 15:55:44 +00:00
ugene
- Install official UGENE documentation (PDF)
2013-11-01 15:20:28 +00:00
velvet
Convert biology to MDOCS and MEXAMPLES
2014-01-03 15:46:52 +00:00
wise
Add NO_STAGE all over the place in preparation for the staging support (cat: biology)
2013-09-20 15:55:44 +00:00
xmolwt
Add NO_STAGE all over the place in preparation for the staging support (cat: biology)
2013-09-20 15:55:44 +00:00
Makefile
biology/seqtools: Tools for visualising sequence alignments
2013-11-10 11:01:02 +00:00