Alexey Dokuchaev 9dc680d0e8 - Update to version 1.13.0 and improve FreeBSD support; it also builds ... pretty cleanly with GCC v4.2, v4.6, and Clang (modulo a few warnings) - Sadly, do not use PORTDOCS: since DOCSDIR is set to be inside DATADIR, and will get appended to PLIST after @dirrm %%DATADIR%%, which upsets sanity checking tools; instead, list the docs explicitly in DISTFILES and add them to pkg-plist (guarded by %%PORTDOCS%%) Tested on: i386 (only)		2014-01-16 17:17:15 +00:00
..
ariadne
artemis
avida	- Fix build with clang	2013-11-27 16:07:51 +00:00
babel	Support stage	2014-01-15 22:44:13 +00:00
biococoa
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
boinc-simap	The hmmer binary was renamed upstream to indicate that it is now an	2013-12-29 10:41:50 +00:00
chemeq
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	Python cleanup:	2014-01-13 21:00:02 +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
finchtv	Convert biology to MDOCS and MEXAMPLES	2014-01-03 15:46:52 +00:00
fluctuate
garlic
genpak	Respect PORT_OPTIONS:MDOCS	2013-12-09 01:28:41 +00:00
gff2ps
gmap	Support stage	2013-12-10 17:21:46 +00:00
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	In preparation for making libtool generate libraries with a sane name, fix all	2013-12-11 14:43:51 +00:00
jalview
lagan
lamarc	- rename AL2 to APACHE20 in Mk/bsd.licenses.db.mk	2013-12-30 20:55:18 +00:00
libgenome
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
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
ncbi-toolkit
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
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
p5-Bio-GFF3
p5-Bio-Glite	- support stage	2014-01-05 12:07:20 +00:00
p5-Bio-Graphics
p5-Bio-MAGETAB	- Update to 1.28	2013-11-28 15:05:08 +00:00
p5-Bio-NEXUS
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
phyml
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
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	Python cleanup:	2014-01-13 21:00:02 +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
rasmol
recombine
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
seqio
seqtools	biology/seqtools: update to 4.24	2013-12-24 17:23:23 +00:00
sim4
ssaha
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
treeviewx	Stage support	2013-12-30 18:27:32 +00:00
tRNAscan-SE
ugene	- Update to version 1.13.0 and improve FreeBSD support; it also builds	2014-01-16 17:17:15 +00:00
velvet	Convert biology to MDOCS and MEXAMPLES	2014-01-03 15:46:52 +00:00
wise
xmolwt
Makefile