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freebsd-ports/biology
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Tobias C. Berner 51d04637cb New USES=eigen 
Usage:
    USES=eigen:<version>[,<type>]

    version: 2 or 3 (required)
    type:    build (default), run

  For example:
    USES=eigen:2,build,run
  will add a BUILD- and RUN_DEPENDS on math/eigen2, and
    USES=eigen:3
  will add a BUILD_DEPENDS on math/eigen3.

* Convert the existing ports to use it
  - biology/iqtree: remove run time dependency (seemed not to be needed)
  - graphics/movit: remove run time dependency (seemed not to be needed)
  - science/avogadro: add run time dependeny (installed cmake file requires it to be present)

Reviewed by:	rakuco, mat
Differential Revision:	https://reviews.freebsd.org/D13702
2018-01-02 16:49:24 +00:00
..
ariadne Mark as broken ports with no public distfiles 2017-10-13 11:14:53 +00:00
artemis Remove dead master sites 2017-10-13 11:14:32 +00:00
avida Try to bring some consistency to ports that have x86-specific pieces. 2017-12-21 10:23:19 +00:00
babel
bcftools Add a USES=python:env, that will not add a dependency on Python. 2017-12-04 15:27:29 +00:00
bedtools - Fix build on 11+ 2017-12-22 12:27:14 +00:00
biococoa Fix configure options for gnustep-make 2017-12-03 12:23:53 +00:00
blat - Update WWW 2017-06-10 09:01:19 +00:00
bowtie Bump PORTREVISION for ports depending on the canonical version of GCC 2017-09-10 20:55:38 +00:00
bowtie2 biology/bowtie2: Upgrade to 2.3.3.1 2017-11-30 02:59:16 +00:00
bwa [unbreak] biology/bwa: Remove old patch files 2017-12-01 02:42:54 +00:00
canu biology/canu: Replace += with = for depends 2017-12-22 14:14:11 +00:00
cd-hit Bump PORTREVISION for ports depending on the canonical version of GCC 2017-09-10 20:55:38 +00:00
cdbfasta
chemeq
clustalw
consed
crux For ports that are marked BROKEN on armv6, and also fail to build on 2017-11-30 06:13:34 +00:00
diamond biology/diamond: Update to version 0.9.14 2017-12-13 16:31:53 +00:00
emboss
fasta
fasta3
fastdnaml
fastool
fastqc [new port] biology/fastqc: Quality control tool for high throughput sequence data 2017-11-30 22:54:29 +00:00
fasttree biology/fasttree: update to version 2.1.10 2017-12-05 03:03:38 +00:00
fastx-toolkit
fluctuate
garlic
gff2ps
gmap Try to bring some consistency to ports that have x86-specific pieces. 2017-12-21 10:23:19 +00:00
gperiodic
grappa
hmmer Back out previous commits by jbeich demand. 2017-12-18 04:28:28 +00:00
htslib biology/htslib biology/bcftools biology/samtools: Update to 1.6 2017-10-25 10:19:50 +00:00
iolib
iqtree New USES=eigen 2018-01-02 16:49:24 +00:00
jalview
jellyfish Bump PORTREVISION for ports depending on the canonical version of GCC 2017-09-10 20:55:38 +00:00
kallisto [new port] biology/kallisto: Quantify abundances of transcripts from RNA-Seq data 2017-12-02 20:44:28 +00:00
lagan
lamarc
libgtextutils
libsbml - Update to 5.16.0 2018-01-01 08:24:53 +00:00
linux-foldingathome
mafft
mapm3
migrate
molden biology/molden: chase another intransparent upstream distfile upgrade. 2017-11-01 03:48:30 +00:00
mopac Bump PORTREVISION for ports depending on the canonical version of GCC 2017-09-10 20:55:38 +00:00
mrbayes Update devel/readline to 7.0 patch 3 2017-06-27 13:46:53 +00:00
mummer - Fix installing scripts and support binaries 2017-10-30 02:27:23 +00:00
muscle
ncbi-blast+ Bump PORTREVISION for ports depending on the canonical version of GCC 2017-09-10 20:55:38 +00:00
ncbi-toolkit
njplot
p5-AcePerl Fix license information for portgs that use "the same license as Perl". 2017-09-15 08:58:46 +00:00
p5-Bio-ASN1-EntrezGene Fix license information for portgs that use "the same license as Perl". 2017-09-15 08:58:46 +00:00
p5-Bio-Coordinate Fix license information for portgs that use "the same license as Perl". 2017-09-15 08:58:46 +00:00
p5-Bio-Das Fix license information for portgs that use "the same license as Perl". 2017-09-15 08:58:46 +00:00
p5-Bio-Das-Lite Fix license information for portgs that use "the same license as Perl". 2017-09-15 08:58:46 +00:00
p5-Bio-FeatureIO Add p5-Bio-FeatureIO 1.6.905 2017-09-15 19:17:17 +00:00
p5-Bio-GFF3 Fix license information for portgs that use "the same license as Perl". 2017-09-15 08:58:46 +00:00
p5-Bio-Glite
p5-Bio-Graphics Fix license information for portgs that use "the same license as Perl". 2017-09-15 08:58:46 +00:00
p5-Bio-MAGETAB
p5-Bio-NEXUS
p5-Bio-Phylo Update to 2.0.1 2017-12-26 23:20:28 +00:00
p5-Bio-SCF
p5-BioPerl Fix license information for portgs that use "the same license as Perl". 2017-09-15 08:58:46 +00:00
p5-BioPerl-Run Update to 1.007002 2017-09-15 19:17:44 +00:00
p5-transdecoder
p5-TrimGalore [new port] biology/p5-TrimGalore: Wrapper around Cutadapt and FastQC for adapter and quality trimming 2017-12-09 13:23:32 +00:00
paml
phrap
phred
phylip - Update to 3.697 2018-01-01 08:40:22 +00:00
phyml Disable the extra flag "-march=native" on arm to fix builds. 2017-12-27 07:36:05 +00:00
plink Mark as broken ports with no public distfiles 2017-10-13 11:14:53 +00:00
plinkseq
primer3
protomol
psi88 Bump PORTREVISION for ports depending on the canonical version of GCC 2017-09-10 20:55:38 +00:00
py-biom-format biology/py-biom-format: Add required dependency on math/py-pandas and do 2017-12-10 03:33:04 +00:00
py-biopython Convert Python ports to FLAVORS. 2017-11-30 15:50:30 +00:00
py-bx-python Convert Python ports to FLAVORS. 2017-11-30 15:50:30 +00:00
py-cutadapt Fix packaging with python3 2017-12-01 06:18:17 +00:00
py-macs2 biology/py-macs2: Restrict to python 2.7. 2017-12-05 02:59:01 +00:00
py-pysam Convert Python ports to FLAVORS. 2017-11-30 15:50:30 +00:00
pycogent - Those ports fail to build with python3 2017-12-11 16:54:20 +00:00
pyfasta Convert Python ports to FLAVORS. 2017-11-30 15:50:30 +00:00
python-nexus Convert Python ports to FLAVORS. 2017-11-30 15:50:30 +00:00
recombine
ruby-bio
rubygem-bio
samtools Add a USES=python:env, that will not add a dependency on Python. 2017-12-04 15:27:29 +00:00
seaview biology/seaview: Update version 4.6.1=>4.6.2 2017-07-21 17:33:10 +00:00
seqan
seqan1
seqan-apps Mark several ports newly broken on arm. 2017-12-11 07:18:48 +00:00
seqio - Switch to options helpers 2017-11-26 09:00:21 +00:00
seqtools biology/seqtools: re-try on powerpc* after r449590 2017-12-12 03:38:56 +00:00
sim4
slclust
ssaha Mark as broken ports with no public distfiles 2017-10-13 11:14:53 +00:00
t_coffee Bump PORTREVISION for ports depending on the canonical version of GCC 2017-09-10 20:55:38 +00:00
tinker Fix the context of some patches so that they apply with stricter patch(1) 2017-11-09 20:45:04 +00:00
treepuzzle
trimmomatic
tRNAscan-SE Mark as broken ports with no public distfiles 2017-10-13 11:14:53 +00:00
ugene Remove USES=execinfo. 2017-09-22 10:48:28 +00:00
vcftools biology/vcftools: Upgrade to latest release 0.1.15 2017-11-27 23:05:40 +00:00
velvet
wise
xmolwt
Makefile [new port] biology/canu: Single molecule sequence assembler 2017-12-22 01:30:26 +00:00