John Marino a7ff4d0e9c biology/embassy: specify post-extraction with ${TAR} ... It's possible that EXTRACT_CMD won't be predefined in the near future in order to support distfiles in multiple formats. We know the post- extraction tool needs to be tar, so let's specify it directly. This port needs staging. It doesn't like like a quick job so I'm leaving that to the listed maintainer. Approved by: infrastructure improvements blanket Approved by: portmgr (implicit) (to skip stage check)		2014-05-29 10:47:58 +00:00
..
ariadne
artemis
avida
babel
biococoa
biojava	Unbreak	2014-03-08 16:39:01 +00:00
blast	Multiple ports: reset maintainers	2014-05-26 02:33:38 +00:00
blat	Convert b* to USES=zip	2014-03-07 15:52:40 +00:00
boinc-simap
chemeq
clustalw	Multiple ports: reset maintainers	2014-05-26 02:33:38 +00:00
consed	Replace maintainer's email address with one that seems to work	2014-05-10 18:07:52 +00:00
crux	Update the default version of GCC used in the Ports Collection from	2014-03-10 20:55:20 +00:00
embassy	biology/embassy: specify post-extraction with ${TAR}	2014-05-29 10:47:58 +00:00
emboss	Convert all :U to :tu and :L to :tl	2014-05-05 09:45:36 +00:00
fasta	- Add staging support	2014-03-24 09:01:39 +00:00
fasta3	biology/fasta3: Checked new distfile and regenerated distinfo to unbreak	2014-03-02 10:58:50 +00:00
fastdnaml
fluctuate
garlic	- Convert USE_GMAKE to USES	2014-03-13 07:41:34 +00:00
gff2ps	Add staging support	2014-03-23 17:43:41 +00:00
gmap
gperiodic	Add staging support	2014-03-23 18:09:23 +00:00
grappa
hmmer
iolib	- Update to version 1.13.5	2014-04-26 02:35:37 +00:00
jalview
lagan
lamarc
libsbml	- Update to 5.10.0	2014-05-13 07:04:17 +00:00
linux-foldingathome
mafft	- Update to 7.149	2014-05-20 19:35:30 +00:00
mapm3
migrate
molden	Catch a couple of missing convertsion to :tu/:tl	2014-05-05 11:15:53 +00:00
mopac	- Add staging support	2014-03-23 18:10:41 +00:00
mrbayes
mummer	- Convert USE_GMAKE to USES	2014-03-13 07:41:34 +00:00
muscle	Convert to USES=dos2unix	2014-05-26 06:55:07 +00:00
ncbi-toolkit	Add staging support	2014-03-23 20:50:54 +00:00
njplot
ortep3	Update the default version of GCC used in the Ports Collection from	2014-03-10 20:55:20 +00:00
p5-AcePerl
p5-Bio-ASN1-EntrezGene
p5-Bio-Das
p5-Bio-Das-Lite
p5-Bio-GFF3	- Fix PLIST	2014-03-26 14:23:09 +00:00
p5-Bio-Glite
p5-Bio-Graphics	Mark as broken unstaged perl ports	2014-04-09 09:49:02 +00:00
p5-Bio-MAGETAB	- update to 1.31	2014-05-16 13:33:02 +00:00
p5-Bio-NEXUS
p5-Bio-Phylo
p5-Bio-SCF
p5-bioperl	Mark as broken unstaged perl ports	2014-04-09 09:49:02 +00:00
p5-bioperl-run
paml	- Update to 4.8	2014-04-05 10:56:52 +00:00
phd2fasta	Replace maintainer's email address with one that seems to work	2014-05-10 18:07:52 +00:00
phrap	Replace maintainer's email address with one that seems to work	2014-05-10 18:07:52 +00:00
phred	Replace maintainer's email address with one that seems to work	2014-05-10 18:07:52 +00:00
phylip	The FreeBSD x11@ and graphics team proudly presents	2014-04-16 18:28:47 +00:00
phyml
platon	Update the default version of GCC used in the Ports Collection from	2014-03-10 20:55:20 +00:00
plink	Update the default version of GCC used in the Ports Collection from	2014-03-10 20:55:20 +00:00
plinkseq	Convert to dos2unix	2014-03-07 11:37:35 +00:00
povchem
primer3	Quote ${CC} and similar variables in MAKE_ARGS.	2014-05-20 19:32:39 +00:00
protomol	The FreeBSD x11@ and graphics team proudly presents	2014-04-16 18:28:47 +00:00
psi88	Update the default version of GCC used in the Ports Collection from	2014-03-10 20:55:20 +00:00
py-biopython	- Stage	2014-04-27 01:59:47 +00:00
pycogent	- Stage support [1]	2014-05-02 14:00:13 +00:00
pyfasta	- Update to 0.5.2	2014-04-06 04:05:43 +00:00
pymol	The FreeBSD x11@ and graphics team proudly presents	2014-04-16 18:28:47 +00:00
python-nexus
recombine
ruby-bio	Support stage	2014-04-07 13:01:26 +00:00
seaview	- Update to 4.5.1	2014-05-21 05:40:53 +00:00
seqan	Update the default version of GCC used in the Ports Collection from	2014-03-10 20:55:20 +00:00
seqio
seqtools	biology/seqtools: 4.25 -> 4.26, fix broken distinfo by upgrading	2014-05-02 19:00:04 +00:00
sim4
ssaha	biology/ssaha: undeprecate, this port fetches and builds fine.	2014-03-09 09:39:50 +00:00
t_coffee	Update the default version of GCC used in the Ports Collection from	2014-03-10 20:55:20 +00:00
tinker	- Un-break fetch stage: the name scheme of the source tarballs has changed	2014-04-22 19:28:18 +00:00
treepuzzle
treeviewx	Unbreak	2014-03-28 00:08:03 +00:00
tRNAscan-SE	Support stage	2014-05-05 10:26:15 +00:00
ugene	Update to version 1.13.1.	2014-03-07 07:39:20 +00:00
velvet	- Convert USE_GMAKE to USES	2014-03-13 07:41:34 +00:00
wise	- Add staging support	2014-03-24 10:46:35 +00:00
xmolwt	Add staging support	2014-03-24 11:06:56 +00:00
Makefile	Remove expired ports:	2014-04-18 11:17:45 +00:00