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freebsd-ports/biology
History
Tijl Coosemans 564a799c71 Convert all USE_FORTRAN=yes to "USES=fortran, USE_GCC=yes". In most cases 
USE_GCC=yes has been omitted though.

Remove USE_FORTRAN handling from bsd.port.mk and bsd.gcc.mk.

Minor cleanups in some ports like USE_GMAKE, NOPORTDOCS,...

Exp-run:	bdrewery
Approved by:	portmgr (bdrewery)
2014-02-16 17:15:31 +00:00
..
ariadne
…
artemis
Support stage
2014-01-20 23:06:48 +00:00
avida
…
babel
Support stage
2014-01-15 22:44:13 +00:00
biococoa
…
biojava
According to the Porter's Handbook (5.12.2.3.) default options must be added to
2014-02-10 13:54:26 +00:00
blast
Convert biology to MDOCS and MEXAMPLES
2014-01-03 15:46:52 +00:00
blat
…
boinc-simap
Drop maintainership BOINC ports, old machine running them gave up.
2014-02-04 17:54:29 +00:00
chemeq
Stage support
2014-01-18 15:55:42 +00:00
clustalw
- Fix build with clang/libc++.
2013-12-20 15:29:07 +00:00
consed
According to the Porter's Handbook (5.12.2.3.) default options must be added to
2014-02-10 13:54:26 +00:00
crux
Convert all USE_FORTRAN=yes to "USES=fortran, USE_GCC=yes". In most cases
2014-02-16 17:15:31 +00:00
embassy
Reduce over inclusion of bsd.port.mk
2014-01-15 22:48:32 +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
Reduce over inclusion of bsd.port.mk
2014-01-15 22:50:18 +00:00
fasta3
Mark as broken: Invalid checksum, seems like the software was rerolled
2014-01-03 19:46:05 +00:00
fastdnaml
Support staging
2014-02-16 11:32:43 +00:00
finchtv
According to the Porter's Handbook (5.12.2.3.) default options must be added to
2014-02-10 13:54:26 +00:00
fluctuate
Support staging
2014-02-16 11:35:00 +00:00
garlic
…
genpak
According to the Porter's Handbook (5.12.2.3.) default options must be added to
2014-02-10 13:54:26 +00:00
gff2ps
…
gmap
…
gperiodic
…
grappa
- Respect CC/CFLAGS
2013-12-20 13:27:13 +00:00
hmmer
Stage support
2013-12-30 18:08:14 +00:00
iolib
Support stage
2014-01-20 17:02:11 +00:00
jalview
Fix properties on pkg-plist
2014-01-21 23:18:05 +00:00
lagan
…
lamarc
- rename AL2 to APACHE20 in Mk/bsd.licenses.db.mk
2013-12-30 20:55:18 +00:00
libgenome
biology/libgenome: Fix build on dragonfly
2014-02-05 23:47:48 +00:00
libsbml
Reduce over inclusion of bsd.port.mk
2014-01-15 22:50:50 +00:00
linux-foldingathome
…
mafft
Convert biology to MDOCS and MEXAMPLES
2014-01-03 15:46:52 +00:00
mapm3
- Fix build with clang
2014-01-12 19:07:28 +00:00
migrate
- Stagify; cleanup Makefile and reorder the knobs a bit
2014-01-29 12:08:29 +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
According to the Porter's Handbook (5.12.2.3.) default options must be added to
2014-02-10 13:54:26 +00:00
muscle
…
ncbi-toolkit
…
njplot
According to the Porter's Handbook (5.12.2.3.) default options must be added to
2014-02-10 13:54:26 +00:00
ortep3
USES=fortran, fix LDFLAGS, staging.
2013-12-17 21:24:17 +00:00
p5-AcePerl
- Stage support
2014-02-10 06:56:52 +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
- fix pkg-plist
2014-01-30 07:34:25 +00:00
p5-Bio-GFF3
- Update to 1.9
2014-01-23 03:28:37 +00:00
p5-Bio-Glite
- support stage
2014-01-05 12:07:20 +00:00
p5-Bio-Graphics
…
p5-Bio-MAGETAB
…
p5-Bio-NEXUS
- Stage support
2014-01-31 12:47:06 +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
According to the Porter's Handbook (5.12.2.3.) default options must be added to
2014-02-10 13:54:26 +00:00
p5-bioperl-run
According to the Porter's Handbook (5.12.2.3.) default options must be added to
2014-02-10 13:54:26 +00:00
paml
According to the Porter's Handbook (5.12.2.3.) default options must be added to
2014-02-10 13:54:26 +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
…
phyml
- Stage support
2014-01-31 12:32:55 +00:00
platon
Version 2013.12.12, USES=fortran, staging.
2013-12-17 21:55:24 +00:00
plink
Convert all USE_FORTRAN=yes to "USES=fortran, USE_GCC=yes". In most cases
2014-02-16 17:15:31 +00:00
plinkseq
- Stage support
2014-01-31 12:33:11 +00:00
povchem
…
primer3
…
protomol
Reduce over inclusion of bsd.port.mk
2014-01-15 22:51:26 +00:00
psi88
USES=fortran, staging, miscellaneous cleanups.
2013-12-18 16:23:08 +00:00
py-biopython
Python cleanup:
2014-01-13 21:00:02 +00:00
pycogent
…
pyfasta
- Convert to PYDISTUTILS_AUTOPLIST
2014-01-31 12:31:24 +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
- Convert to PYDISTUTILS_AUTOPLIST
2014-01-31 12:30:39 +00:00
rasmol
…
recombine
- Support staging
2014-02-16 11:39:42 +00:00
ruby-bio
Reduce over inclusion of bsd.port.mk
2014-01-15 22:52:28 +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
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seqio
Support staging
2014-02-16 11:42:09 +00:00
seqtools
Fix old makeplist bug.
2014-02-12 14:03:25 +00:00
sim4
Support staging
2014-02-16 11:43:07 +00:00
ssaha
Deprecate ports unmaintained for which distillator is not able to find public distfiles
2014-02-07 18:50:30 +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
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treeviewx
Stage support
2013-12-30 18:27:32 +00:00
tRNAscan-SE
biology/tRNAscan-SE: Fix hardcoded perl path
2014-02-05 23:44:50 +00:00
ugene
Unbreak the fetch: one of the documentation PDF files was rerolled.
2014-01-30 13:38:26 +00:00
velvet
According to the Porter's Handbook (5.12.2.3.) default options must be added to
2014-02-10 13:54:26 +00:00
wise
biology/wise: Add dragonfly support
2014-02-05 23:42:06 +00:00
xmolwt
…
Makefile
…