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freebsd-ports/biology
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Yuri Victorovich 0ddfd47db4 biology/molden: Unbreak: fix the problem that it can't find libgcc_s.so from gcc 
Add $(LDFLAGS) to makefile.
While here, add USES=gl.

Approved by:	portmgr
2018-11-07 00:03:34 +00:00
..
artemis
avida biology/avida: Fix build with Clang 6 2018-08-25 03:22:18 +00:00
babel
bamtools
bcftools biology/bcftools: update to 1.9 2018-08-02 19:30:57 +00:00
bedtools Fix build on gcc-based archs by updating USES. 2018-09-22 05:30:31 +00:00
biococoa Update Objective-C LLVM version to 6.0. 2018-09-26 15:23:37 +00:00
bowtie biology/bowtie: Patch for gcc8 and clean up 2018-11-03 23:24:29 +00:00
bowtie2 Update devel/tbb to version 2019.1 and bump dependent ports' revisions 2018-10-11 14:47:13 +00:00
bwa
canu biology/canu: Upgrade to 1.8, add experimental SLURM integration 2018-11-04 14:29:02 +00:00
cd-hit Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +00:00
cdbfasta
chemeq
clustal-omega
clustalw
clustalx
consed
cytoscape biology/cytoscape: Fix license 2018-08-12 06:29:51 +00:00
ddocent
diamond
emboss
exonerate New port: biology/exonerate: Generic tool for sequence alignment 2018-07-13 07:02:16 +00:00
fasta
fasta3
fastahack
fastdnaml
fastool
fastqc
fasttree Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +00:00
fastx-toolkit
fluctuate
freebayes Upgrade these ports to USES=compiler:c++11-lang to fix build on gcc-based 2018-09-18 09:28:34 +00:00
garlic
gff2ps
gmap
gperiodic
grappa
hmmer
htslib biology/htslib: update to 1.9 2018-08-02 19:27:13 +00:00
hyphy biology/hyphy: Update to version 2.3.14.16 2018-10-20 12:21:15 +00:00
igv biology/igv: Update 2.4.10 -> 2.4.15 2018-11-04 22:55:24 +00:00
infernal Allow building on powerpc64. 2018-09-27 23:02:56 +00:00
iolib Remove the incorrect typedefs to fix build on tier-2. 2018-11-05 19:45:23 +00:00
iqtree biology/iqtree: Update to version 1.6.8 2018-10-28 22:00:18 +00:00
jalview
jellyfish Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +00:00
kallisto Update science/hdf5 to 1.10.2 2018-09-05 22:05:23 +00:00
lagan
lamarc biology/lamarc: Fix build with Clang 6 2018-08-25 03:13:37 +00:00
libgtextutils
libsbml biology/libsbml: Fix build with Clang 6 2018-08-25 03:31:43 +00:00
linux-foldingathome biology/linux-foldingathome: reset maintainer by request 2018-07-27 02:19:43 +00:00
mafft
mapm3
migrate
molden biology/molden: Unbreak: fix the problem that it can't find libgcc_s.so from gcc 2018-11-07 00:03:34 +00:00
mopac Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +00:00
mrbayes
mummer
muscle
ncbi-blast+ Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +00:00
ncbi-cxx-toolkit New port: biology/ncbi-cxx-toolkit: NCBI C++ Toolkit 2018-10-08 07:54:49 +00:00
ncbi-toolkit Fix build failure with base GCC because of double typedefs. 2018-11-05 19:47:42 +00:00
ngs-sdk biology/ngs-sdk: Update 2.9.2 -> 2.9.3 2018-10-18 21:38:21 +00:00
njplot
p5-AcePerl Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-ASN1-EntrezGene Update to 1.73 2018-10-10 10:23:10 +00:00
p5-Bio-Coordinate Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-Das Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-Das-Lite Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-FeatureIO Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-GFF3 Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-Glite Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-Graphics Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-MAGETAB Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-NEXUS Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-Phylo Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-SCF Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-BioPerl Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-BioPerl-Run Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-transdecoder biology/p5-transdecoder: Upgrade to 5.4.0 2018-10-23 12:51:20 +00:00
p5-TrimGalore
paml
pbbam More precisely specify USES=compiler to fix build on gcc-based 2018-09-18 08:14:23 +00:00
pbcopper More precisely specify USES=compiler to fix build on gcc-based 2018-09-18 08:14:23 +00:00
pbseqan
pear-merger
phrap Add DOCS options to ports that should have one. 2018-09-10 13:14:50 +00:00
phred Add DOCS options to ports that should have one. 2018-09-10 13:14:50 +00:00
phylip
phyml Change 4 ports from net/mpich2 to net/mpich 2018-09-22 18:00:24 +00:00
plinkseq
primer3 biology/primer3: Fix build with Clang 6 2018-08-25 03:35:46 +00:00
protomol biology/protomol: Fix doubled USES overwriting the old value 2018-08-25 03:47:25 +00:00
psi88 Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +00:00
py-biom-format biology/py-biom-format: Update to version 2.1.7 2018-10-06 15:28:01 +00:00
py-biopython - Update to 1.72 2018-08-24 00:12:38 +00:00
py-bx-python biology/py-bx-python: Update 0.8.1 -> 0.8.2 2018-08-26 09:50:41 +00:00
py-cutadapt biology/py-cutadapt: Upgrade to 1.18 2018-09-20 14:10:52 +00:00
py-Genesis-PyAPI
py-gffutils New port: biology/py-gffutils: Work with GFF and GTF files in a flexible database framework 2018-10-19 02:06:53 +00:00
py-gtfparse New port: biology/py-gtfparse: Parsing tools for GTF (gene transfer format) files 2018-10-19 02:03:40 +00:00
py-loompy biology/py-loompy: Update 2.0.15 -> 2.0.16 2018-10-30 05:57:43 +00:00
py-macs2
py-orange3-bioinformatics biology/py-orange3-bioinformatics: Update 3.2.0 -> 3.2.2 2018-10-14 03:22:49 +00:00
py-orange3-single-cell biology/py-orange3-single-cell: Update 0.8.1 -> 0.8.2 2018-10-17 07:31:34 +00:00
py-pyfaidx biology/py-pyfaidx: Update 0.5.5.1 -> 0.5.5.2 2018-10-28 04:34:14 +00:00
py-pysam biology/py-pysam: Update 0.15.0 -> 0.15.1 2018-09-17 17:40:28 +00:00
pycogent
pyfasta
python-nexus - Update to 1.63 2018-09-22 08:54:58 +00:00
rainbow
recombine
ruby-bio
rubygem-bio Update to 1.5.2 2018-09-21 18:08:24 +00:00
samtools biology/samtools: update to 1.9 2018-08-02 19:28:36 +00:00
seaview biology/seaview: Fix build with Clang 6 2018-09-08 09:01:35 +00:00
seqan
seqan1
seqan-apps devel/boost-*: update to 1.68.0 2018-08-09 06:58:30 +00:00
seqio
seqtk
seqtools
sim4
slclust
smithwaterman
stacks Fix build with tier-2 arches. 2018-10-28 08:58:00 +00:00
stringtie
t_coffee Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +00:00
tabixpp
treepuzzle
trimadap
trimmomatic
tRNAscan-SE - Unbreak by adding missing pkg-plist 2018-09-28 00:12:48 +00:00
ugene Update to 1.31.0 2018-09-02 20:47:15 +00:00
unanimity More precisely specify USES=compiler to fix build on gcc-based 2018-09-18 08:14:23 +00:00
vcflib
vcftools biology/vcftools: Update to 0.1.16, a security release 2018-08-04 01:29:29 +00:00
velvet
wise
xmolwt Deprecate most glib12 consumers 2018-10-12 09:19:04 +00:00
Makefile New port: biology/py-gffutils: Work with GFF and GTF files in a flexible database framework 2018-10-19 02:06:53 +00:00