freebsd-ports/biology
David Chisnall 3f627ab4ce Move Objective-C ports to the v2 GNUstep ABI.
* Bump the LLVM revision used for GNUstep to 7, the minimum to support
   the new ABI.
 * GNUstep-back does not work with lld, so mark it to use Gold (BFD LD
   doesn't seem able to link Objective-C things).
 * Turn off some annoying debug logs in GNUstep back, which generate
   several messages per second when you move the mouse.  These should
   never have been enabled in a release build anyway.
 * Downgrade Cenon to 4.0.2.  This was the last version to actually work
   with GNUstep (the later ones use XCode >= 5 .xib files, which GNUstep
   can't parse).
 * Update gorm to git head. The current release doesn't work with the
   new Objective-C ABI, but -head has the patches to fix it.
 * Update PikoPixel and add it to the gnustep-app meta-package.
 * Update the three core GNUstep packages to the latest release.
 * Update gnumail and pantomime to the latest release and fix a linking
   error with the new ABI.
 * Update GNUstep FTP to the latest version.

Reviewed by:	bapt (previous version)
2019-02-03 15:37:58 +00:00
..
artemis
avida Change cmake default behaviour to outsource. 2018-12-25 20:25:39 +00:00
babel
bamtools Change cmake default behaviour to outsource. 2018-12-25 20:25:39 +00:00
bcftools
bedtools
biococoa Move Objective-C ports to the v2 GNUstep ABI. 2019-02-03 15:37:58 +00:00
bowtie
bowtie2
bwa
canu
cd-hit
cdbfasta
checkm
chemeq
clustal-omega
clustalw
clustalx
consed
cytoscape
ddocent
diamond biology/diamond: Update to version 0.9.24 2018-12-31 19:00:00 +00:00
dsr-pdb New port: biology/dsr-pdb: Simple C++ PDB reader (reads the protein description format) 2019-01-29 07:56:30 +00:00
emboss
exonerate
fasta
fasta3
fastahack
fastdnaml
fastool
fastqc
fasttree
fastx-toolkit
fluctuate
freebayes
garlic
gatk
gff2ps
gmap
gperiodic
grappa
groopm biology/groopm fails to build with python3 2019-01-07 09:44:42 +00:00
hisat2 New port: biology/hisat2: Program for mapping next-generation sequencing reads 2019-01-11 16:02:05 +00:00
hmmer
htslib
hyphy Change cmake default behaviour to outsource. 2018-12-25 20:25:39 +00:00
igv
infernal
iolib
iqtree biology/iqtree: switch to outsource cmake build 2018-12-27 18:34:44 +00:00
jalview
jellyfish
kallisto Update science/hdf5 to 1.10.4 2019-01-05 22:46:53 +00:00
lagan
lamarc
libgtextutils
libsbml Change cmake default behaviour to outsource. 2018-12-25 20:25:39 +00:00
linux-foldingathome
mafft
mapm3
migrate
molden
mopac
mrbayes
mummer
muscle
ncbi-blast+ Update dns/libidn2 to 2.1.0 2019-01-06 20:39:43 +00:00
ncbi-cxx-toolkit
ncbi-toolkit Update dns/libidn2 to 2.1.0 2019-01-06 20:39:43 +00:00
ngs-sdk
p5-AcePerl
p5-Bio-ASN1-EntrezGene
p5-Bio-Coordinate
p5-Bio-Das
p5-Bio-Das-Lite
p5-Bio-FeatureIO
p5-Bio-GFF3
p5-Bio-Glite
p5-Bio-Graphics
p5-Bio-MAGETAB
p5-Bio-NEXUS
p5-Bio-Phylo
p5-Bio-SCF
p5-BioPerl
p5-BioPerl-Run
p5-transdecoder
p5-TrimGalore
paml
pbbam
pbcopper
pbseqan
pear-merger
phrap
phred
phylip
phyml
plinkseq
primer3
protomol
psi88
py-biom-format
py-biopython
py-bx-python
py-cutadapt
py-fastTSNE
py-Genesis-PyAPI
py-gffutils
py-gtfparse
py-loompy biology/py-loompy: Update 2.0.16 -> 2.0.17 2019-02-02 21:38:48 +00:00
py-macs2
py-orange3-bioinformatics Fix Qt5 symbol version scripts to put the catch-all clause first. When 2019-01-16 11:13:44 +00:00
py-orange3-single-cell Fix Qt5 symbol version scripts to put the catch-all clause first. When 2019-01-16 11:13:44 +00:00
py-pyfaidx
py-pysam biology/py-pysam: Update 0.15.1 -> 0.15.2 2019-01-26 04:15:54 +00:00
pycogent
pyfasta
python-nexus
rainbow
recombine
ruby-bio
rubygem-bio
samtools
seaview
seqan
seqan1
seqan-apps Change cmake default behaviour to outsource. 2018-12-25 20:25:39 +00:00
seqio
seqtk
seqtools biology/seqtools: fix build on current, if lld is lld7 2019-01-07 19:54:40 +00:00
sim4
slclust
smithwaterman
stacks biology/stacks: Upgrade to 2.3 2019-01-12 15:53:00 +00:00
stringtie
t_coffee
tabixpp
treepuzzle
trimadap
trimmomatic
tRNAscan-SE
ugene Fix Qt5 symbol version scripts to put the catch-all clause first. When 2019-01-16 11:13:44 +00:00
unanimity Change cmake default behaviour to outsource. 2018-12-25 20:25:39 +00:00
vcflib
vcftools
velvet
wise
Makefile New port: biology/dsr-pdb: Simple C++ PDB reader (reads the protein description format) 2019-01-29 07:56:30 +00:00