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Jason W. Bacon f2f1fab1b6 biology/pear-merger: Memory-efficient and accurate paired-end read merger 
Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D14959
2018-04-04 17:21:39 +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
…
bamtools
biology/bamtools: API and toolkit for handling BAM files
2018-03-28 13:26:31 +00:00
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 PORTREVISIONs of all users of math/mpc that we just updated to
2018-03-10 17:46:04 +00:00
bowtie2
biology/bowtie2: Upgrade to 2.3.3.1
2017-11-30 02:59:16 +00:00
bwa
Multiple ports:
2018-01-31 01:07:07 +00:00
canu
Bump PORTREVISIONs of all users of math/mpc that we just updated to
2018-03-10 17:46:04 +00:00
cd-hit
Bump PORTREVISIONs of all users of math/mpc that we just updated to
2018-03-10 17:46:04 +00:00
cdbfasta
Multiple ports:
2018-01-31 01:07:07 +00:00
chemeq
biology/chemeq: fix build on GCC (taken from dports)
2016-12-18 04:22:26 +00:00
clustalw
…
consed
- Replace Mk/bsd.linux-apps.mk and Mk/bsd.linux-rpm.mk with
2016-09-05 19:23:42 +00:00
crux
Bump PORTREVISIONs of all users of math/mpc that we just updated to
2018-03-10 17:46:04 +00:00
diamond
biology/diamond: Update to version 0.9.19
2018-03-17 15:29:13 +00:00
emboss
- update libgd to 2.2.2
2016-07-20 09:33:31 +00:00
fasta
${RM} already has -f.
2016-10-21 12:51:40 +00:00
fasta3
…
fastdnaml
…
fastool
Multiple ports:
2018-01-31 01:07:07 +00:00
fastqc
[new port] biology/fastqc: Quality control tool for high throughput sequence data
2017-11-30 22:54:29 +00:00
fasttree
Mark the latest version broken on armvX. Note: 2.1.8.3 built ok.
2018-03-18 13:38:23 +00:00
fastx-toolkit
Multiple ports:
2018-01-31 01:07:07 +00:00
fluctuate
…
garlic
Return maho@'s ports to the pool after his commit bit expired.
2018-03-11 11:20:43 +00:00
gff2ps
…
gmap
Multiple ports:
2018-01-31 01:07:07 +00:00
gperiodic
Remove libintl.so.9 compatibility link that was added in r374303 to
2016-12-08 19:52:19 +00:00
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
Mark some ports failing on power64. In cases where the error message
2017-05-13 03:35:51 +00:00
iqtree
biology/iqtree: Update to version 1.6.3
2018-03-23 01:22:47 +00:00
jalview
…
jellyfish
Multiple ports:
2018-01-31 01:07:07 +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
biology/lamarc: Fix build on DF (taken from dports)
2016-12-18 04:34:33 +00:00
libgtextutils
biology/libgtextutils: Unbreak for FreeBSD 12
2018-03-29 15:41:07 +00:00
libsbml
- Update to 5.16.0
2018-01-01 08:24:53 +00:00
linux-foldingathome
- Replace Mk/bsd.linux-apps.mk and Mk/bsd.linux-rpm.mk with
2016-09-05 19:23:42 +00:00
mafft
…
mapm3
…
migrate
Mark broken on armvX and mips.
2018-03-18 13:48:07 +00:00
molden
Bump PORTREVISIONs of all users of math/mpc that we just updated to
2018-03-10 17:46:04 +00:00
mopac
Bump PORTREVISIONs of all users of math/mpc that we just updated to
2018-03-10 17:46:04 +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
Mark various leaf ports broken on aarch64, and, where appropriate, other
2016-11-11 09:31:02 +00:00
ncbi-blast+
biology/ncbi-blast+: Upgrade to 2.7.1
2018-03-27 18:04:21 +00:00
ncbi-toolkit
Remove libjpeg.so.11 compatibility link that was added in r374303 to
2016-12-08 16:39:11 +00:00
njplot
biology/njplot: Add site in MASTER_SITES because package builders are
2016-11-28 15:19:42 +00:00
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
Bump PORTREVISIONs of all users of math/mpc that we just updated to
2018-03-10 17:46:04 +00:00
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
Cleanup no longer needed CHMOD usage after r424898.
2016-11-02 22:45:14 +00:00
pear-merger
biology/pear-merger: Memory-efficient and accurate paired-end read merger
2018-04-04 17:21:39 +00:00
phrap
…
phred
…
phylip
- Update to 3.697
2018-01-01 08:40:22 +00:00
phyml
Remove now-useless, commented-out lines.
2018-03-10 23:35:03 +00:00
plink
Bump PORTREVISIONs of all users of math/mpc that we just updated to
2018-03-10 17:46:04 +00:00
plinkseq
Multiple ports:
2018-01-31 01:07:07 +00:00
primer3
…
protomol
Revision bump of all ports with USE_GL after consolidation of mesa-libs
2017-05-23 05:03:14 +00:00
psi88
Bump PORTREVISIONs of all users of math/mpc that we just updated to
2018-03-10 17:46:04 +00:00
py-biom-format
Bump PORTREVISIONs of all users of math/mpc that we just updated to
2018-03-10 17:46:04 +00:00
py-biopython
Bump PORTREVISIONs of all users of math/mpc that we just updated to
2018-03-10 17:46:04 +00:00
py-bx-python
Bump PORTREVISIONs of all users of math/mpc that we just updated to
2018-03-10 17:46:04 +00:00
py-cutadapt
Canonicalize PyPi WWWs:
2018-02-08 20:18:08 +00:00
py-macs2
Bump PORTREVISIONs of all users of math/mpc that we just updated to
2018-03-10 17:46:04 +00:00
py-pysam
biology/py-pysam: Update to 0.14.1
2018-03-21 08:12:32 +00:00
pycogent
Bump PORTREVISIONs of all users of math/mpc that we just updated to
2018-03-10 17:46:04 +00:00
pyfasta
Bump PORTREVISIONs of all users of math/mpc that we just updated to
2018-03-10 17:46:04 +00:00
python-nexus
- Update to 1.61
2018-04-01 11:52:08 +00:00
rainbow
biology/rainbow: Efficient clustering and assembling of short reads
2018-04-02 16:50:46 +00:00
recombine
When there is a do-install target, do not use a post-install target, do
2016-07-19 11:04:13 +00:00
ruby-bio
- Update to 1.5.1
2017-05-07 15:44:34 +00:00
rubygem-bio
Update to 1.5.1
2017-02-06 23:03:17 +00:00
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 4.6.2=>4.6.3
2018-01-05 17:40:41 +00:00
seqan
biology/seqan-apps, biology/seqan: Update to 2.4.0
2018-03-10 06:21:37 +00:00
seqan1
When there is a do-install target, do not use a post-install target, do
2016-07-19 11:04:13 +00:00
seqan-apps
biology/seqan-apps, biology/seqan: Update to 2.4.0
2018-03-10 06:21:37 +00:00
seqio
- Switch to options helpers
2017-11-26 09:00:21 +00:00
seqtk
biology/seqtk: Tool for processing sequences in FASTA/FASTQ format
2018-04-03 20:57:05 +00:00
seqtools
biology/seqtools: re-try on powerpc* after r449590
2017-12-12 03:38:56 +00:00
sim4
…
slclust
Multiple ports:
2018-01-31 01:07:07 +00:00
ssaha
Bump PORTREVISIONs of all users of math/mpc that we just updated to
2018-03-10 17:46:04 +00:00
stacks
biology/stacks: Software pipeline for building loci from short-read sequences
2018-03-31 13:16:05 +00:00
t_coffee
Bump PORTREVISIONs of all users of math/mpc that we just updated to
2018-03-10 17:46:04 +00:00
tinker
Bump PORTREVISIONs of all users of math/mpc that we just updated to
2018-03-10 17:46:04 +00:00
treepuzzle
…
trimadap
biology/trimadap: Trim adapter sequences from Illumina data
2018-04-03 18:23:54 +00:00
trimmomatic
Multiple ports:
2018-01-31 01:07:07 +00:00
tRNAscan-SE
Mark as broken ports with no public distfiles
2017-10-13 11:14:53 +00:00
ugene
Update Qt5 ports to 5.9.3.
2018-01-06 21:30:31 +00:00
vcftools
Multiple ports:
2018-01-31 01:07:07 +00:00
velvet
- Convert to option helper install target (add OPTIONS_DEFINE=DOCS
2018-01-11 18:09:00 +00:00
wise
Remove libintl.so.9 compatibility link that was added in r374303 to
2016-12-08 19:52:19 +00:00
xmolwt
Remove libintl.so.9 compatibility link that was added in r374303 to
2016-12-08 19:52:19 +00:00
Makefile
biology/pear-merger: Memory-efficient and accurate paired-end read merger
2018-04-04 17:21:39 +00:00