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freebsd-ports/biology
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John Marino 35bfc60170 Add new port biology/ncbi-blast 
PR:		190854
Submitted by:	Jason Bacon

The Basic Local Alignment Search Tool (BLAST) finds regions of local
similarity between sequences. The program compares nucleotide or protein
sequences to sequence databases and calculates the statistical
significance of matches. BLAST can be used to infer functional and
evolutionary relationships between sequences as well as help identify
members of gene families.
2014-10-06 20:16:35 +00:00
..
ariadne Convert a bunch of EXTRACT_SUFX=... into USES=tar:... 2014-07-29 19:11:51 +00:00
artemis Support stage 2014-01-20 23:06:48 +00:00
avida
babel Rename biology/ patch-xy patches to reflect the files they modify. 2014-07-28 14:22:16 +00:00
biococoa Update the default version of GCC in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
biojava - add stage support 2014-06-01 10:37:22 +00:00
blat Put HOME in MAKE_ARGS to handle pverride of HOME in MAKE_ENV from bsd.port.mk 2014-06-25 08:55:55 +00:00
boinc-simap biology/boinc-simap: Deprecate, project shutting down on 2015-01-01 2014-09-19 23:05:44 +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 update ports: 2014-08-23 18:04:58 +00:00
crux Update the default version of GCC in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
emboss Remove indefinite articles and trailing periods from COMMENT, plus 2014-06-09 11:21:52 +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 biology/garlic: Stage properly to unbreak 2014-07-17 10:13:06 +00:00
gff2ps Add staging support 2014-03-23 17:43:41 +00:00
gmap Fix MASTER_SITES 2014-09-05 09:25:45 +00:00
gperiodic Add staging support 2014-03-23 18:09:23 +00:00
grappa
hmmer Add DOCS to OPTIONS_DEFINE to ports that check for PORT_OPTIONS:MDOCS. 2014-07-15 14:54:54 +00:00
iolib - I forgot to svn add a new patch 2014-05-31 18:03:08 +00:00
jalview Fix properties on pkg-plist 2014-01-21 23:18:05 +00:00
lagan
lamarc
libsbml - Update to 5.10.2 2014-08-10 06:21:53 +00:00
linux-foldingathome Stagify. 2014-07-06 16:05:34 +00:00
mafft Convert a bunch of EXTRACT_SUFX=... into USES=tar:... 2014-07-29 19:11:51 +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 Update the default version of GCC in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
mopac - Switch to USES=libtool, drop .la files 2014-08-06 16:05:49 +00:00
mrbayes Fix build on -current by un-clobbering LDFLAGS. Also, don't 2014-08-15 16:37:37 +00:00
mummer biology/mummer: Use OPSYS with OSVERSION 2014-07-19 22:00:16 +00:00
muscle Update to 3.8.31. 2014-06-17 21:36:06 +00:00
ncbi-blast Add new port biology/ncbi-blast 2014-10-06 20:16:35 +00:00
ncbi-toolkit Add staging support 2014-03-23 20:50:54 +00:00
njplot - add stage support 2014-06-01 11:26:39 +00:00
ortep3 Update the default version of GCC in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
p5-AcePerl Fix build. Hopefully it doesn't break the app. 2014-08-22 00:33:16 +00:00
p5-Bio-ASN1-EntrezGene Convert a bunch of EXTRACT_SUFX=... into USES=tar:... 2014-07-29 19:11:51 +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 Really fix. 2014-07-25 23:08:58 +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 Remove all the bootstrap files (.bs) from the plists. 2014-06-10 12:14:12 +00:00
p5-bioperl biology/p5-bioperl: fix pkg-descr sidenote link 2014-08-04 04:32:38 +00:00
p5-bioperl-run biology/p5-bioperl-run: 1.6.1 -> 1.6.901, unbreak, stagify 2014-08-04 08:54:10 +00:00
paml Convert a bunch of EXTRACT_SUFX=... into USES=tar:... 2014-07-29 19:11:51 +00:00
phrap update ports: 2014-08-23 18:04:58 +00:00
phred update ports: 2014-08-23 18:04:58 +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 in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
plink Update the default version of GCC in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
plinkseq - Update to 2.6.0 2014-10-04 15:12:44 +00:00
povchem Rename biology/ patch-xy patches to reflect the files they modify. 2014-07-28 14:22:16 +00:00
primer3 Quote ${CC} and similar variables in MAKE_ARGS. 2014-05-20 19:32:39 +00:00
protomol Update the default version of GCC in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
psi88 Update the default version of GCC in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
py-biopython Update the default version of GCC in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
pycogent Update the default version of GCC in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
pyfasta Update the default version of GCC in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
python-nexus Remove indefinite articles and trailing periods from COMMENT, plus 2014-06-09 11:21:52 +00:00
recombine - Support staging 2014-02-16 11:39:42 +00:00
ruby-bio - any version for RUN_DEPENDS 2014-09-21 13:44:58 +00:00
seaview Update the default version of GCC in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
seqan Update the default version of GCC in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
seqio Support staging 2014-02-16 11:42:09 +00:00
seqtools USES=execinfo 2014-08-04 23:06:21 +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 in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
tinker Update the default version of GCC in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
treepuzzle
treeviewx Update the default version of GCC in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
tRNAscan-SE Convert a bunch of EXTRACT_SUFX=... into USES=tar:... 2014-07-29 19:11:51 +00:00
ugene Update the default version of GCC in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
velvet Convert a bunch of EXTRACT_SUFX=... into USES=tar:... 2014-07-29 19:11:51 +00:00
wise - Add staging support 2014-03-24 10:46:35 +00:00
xmolwt devel/glib12 x11-toolkits/gtk12: 2014-09-13 15:11:27 +00:00
Makefile Add new port biology/ncbi-blast 2014-10-06 20:16:35 +00:00