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freebsd-ports/biology
History
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 Support stage 2014-01-20 23:06:48 +00:00
avida
babel Support stage 2014-01-15 22:44:13 +00:00
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 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 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 Support staging 2014-02-16 11:32:43 +00:00
fluctuate Support staging 2014-02-16 11:35:00 +00:00
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 - Respect CC/CFLAGS 2013-12-20 13:27:13 +00:00
hmmer Stage support 2013-12-30 18:08:14 +00:00
iolib - Update to version 1.13.5 2014-04-26 02:35:37 +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
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 - 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 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 Support stage 2013-12-10 17:54:12 +00:00
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 Remove trailing whitespaces from category biology 2014-02-21 13:35:26 +00:00
ortep3 Update the default version of GCC used in the Ports Collection from 2014-03-10 20:55:20 +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 - Fix PLIST 2014-03-26 14:23:09 +00:00
p5-Bio-Glite - support stage 2014-01-05 12:07:20 +00:00
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 - 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 Mark as broken unstaged perl ports 2014-04-09 09:49:02 +00:00
p5-bioperl-run Remove trailing whitespaces from category biology 2014-02-21 13:35:26 +00:00
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 - Stage support 2014-01-31 12:32:55 +00:00
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 - Convert to PYDISTUTILS_AUTOPLIST 2014-01-31 12:30:39 +00:00
recombine - Support staging 2014-02-16 11:39:42 +00:00
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 Support staging 2014-02-16 11:42:09 +00:00
seqtools biology/seqtools: 4.25 -> 4.26, fix broken distinfo by upgrading 2014-05-02 19:00:04 +00:00
sim4 Support staging 2014-02-16 11:43:07 +00:00
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