Jan Beich 25beeff079 devel/boost-*: update to 1.66.0 ... Changes: http://www.boost.org/users/history/version_1_66_0.html PR: 223922 Exp-run by: antoine Differential Revision: https://reviews.freebsd.org/D13279		2018-01-18 04:11:02 +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	devel/boost-*: update to 1.66.0	2018-01-18 04:11:02 +00:00
cd-hit	Bump PORTREVISION for ports depending on the canonical version of GCC	2017-09-10 20:55:38 +00:00
cdbfasta	Update WWW: SF redirects to https://sourceforge.net/projects/<PROJECT_NAME>/	2017-01-20 20:33:30 +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	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	- 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	Never set WRKSRC when using USE_GITHUB.	2017-01-03 18:12:13 +00:00
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	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	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	biology/lamarc: Fix build on DF (taken from dports)	2016-12-18 04:34:33 +00:00
libgtextutils	Use USES=pathfix where applicable.	2016-10-21 15:21:13 +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
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	Mark various leaf ports broken on aarch64, and, where appropriate, other	2016-11-11 09:31:02 +00:00
ncbi-blast+	Bump PORTREVISION for ports depending on the canonical version of GCC	2017-09-10 20:55:38 +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	Never set WRKSRC when using USE_GITHUB.	2017-01-03 18:12:13 +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
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	Mark some ports failing on power64. In cases where the error message	2017-05-13 03:35:51 +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 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	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	- Update biology/seqan and bilogy/seqan-apps to version 2.2.0 [1]	2016-09-14 19:38:58 +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	devel/boost-*: update to 1.66.0	2018-01-18 04:11:02 +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	Update WWW: SF redirects to https://sourceforge.net/projects/<PROJECT_NAME>/	2017-01-20 20:33:30 +00:00
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	Update Qt5 ports to 5.9.3.	2018-01-06 21:30:31 +00:00
vcftools	biology/vcftools: Upgrade to latest release 0.1.15	2017-11-27 23:05:40 +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	[new port] biology/canu: Single molecule sequence assembler	2017-12-22 01:30:26 +00:00