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freebsd-ports/biology
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Yuri Victorovich 0f34b9361d biology/py-biopython: Unbreak on python3; Add license 
Two items prevented python3 compatibility:
* Breakage of ASCII codec due to non-ascii characters in README: https://github.com/biopython/biopython/issues/1649
* The outdated dependency: print/py-reportlab1 instead of the modern version 3.X print/py-reportlab

Port changes:
* USES=python:2.7 -> USES=python
* Add pre-configure that clears the README file
* Add LICENSE/LICENSE_FILE

Testing:
* Ran the tutorial testcase http://biopython.org/DIST/docs/tutorial/Tutorial.html,
  particularly pdf writing through print/py-reportlab worked fine.

Asked the upstream to clarify the acceptable dependency version: https://github.com/biopython/biopython/issues/1650

Approved by:	portmgr blanket (unbreak for python3; add license)
2018-05-13 22:30:00 +00:00
..
ariadne Deprecate ports broken for more than 6 months 2018-05-05 10:49:36 +00:00
artemis
avida
babel
bamtools biology/bamtools: API and toolkit for handling BAM files 2018-03-28 13:26:31 +00:00
bcftools
bedtools biology/bedtools: Upgrade to 2.27.1 2018-04-19 16:44:59 +00:00
biococoa
blat
bowtie Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
bowtie2
bwa
canu biology/canu: Upgrade to 1.7 release 2018-04-26 04:16:15 +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
chemeq
clustalw
consed
crux Deprecate ports broken for more than 6 months 2018-05-05 10:49:36 +00:00
ddocent biology/ddocent: Bash pipeline for RAD sequencing 2018-04-20 01:34:05 +00:00
diamond biology/diamond: Update to version 0.9.21 2018-04-20 21:23:27 +00:00
emboss
fasta
fasta3
fastahack biology/fastahack: Utility for indexing and sequence extraction from FASTA files 2018-04-16 14:50:46 +00:00
fastdnaml
fastool
fastqc
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
fluctuate
freebayes biology/freebayes: Bayesian haplotype-based polymorphism discovery and genotyping 2018-04-20 00:07:27 +00:00
garlic Return maho@'s ports to the pool after his commit bit expired. 2018-03-11 11:20:43 +00:00
gff2ps
gmap
gperiodic
grappa
hmmer
htslib
hyphy New port, biology/hyphy: Hypothesis testing using Phylogenies 2018-05-11 00:05:16 +00:00
iolib
iqtree biology/iqtree: Update to version 1.6.5 2018-05-11 16:57:09 +00:00
jalview
jellyfish
kallisto
lagan
lamarc
libgtextutils biology/libgtextutils: Unbreak for FreeBSD 12 2018-03-29 15:41:07 +00:00
libsbml
linux-foldingathome
mafft
mapm3
migrate Mark broken on armvX and mips. 2018-03-18 13:48:07 +00:00
molden Mark BROKEN: checksum and size mismatch 2018-05-07 05:34:10 +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
mummer
muscle
ncbi-blast+ biology/ncbi-blast+: Upgrade to 2.7.1 2018-03-27 18:04:21 +00:00
ncbi-toolkit
njplot
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 Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
p5-TrimGalore
paml biology/paml: Set PORTVERSION directly 2018-04-26 15:36:30 +00:00
pbbam biology/pbbam: PacBio BAM C++ library, with SWIG bindings 2018-04-23 16:08:21 +00:00
pbcopper biology/pbcopper: Core C++ library for Pacific Biosciences tools 2018-04-23 16:23:53 +00:00
pbseqan biology/pbseqan: Pacific Biosciences patched and stripped down SeqAn 2018-04-21 17:21:30 +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
phyml Remove now-useless, commented-out lines. 2018-03-10 23:35:03 +00:00
plink Deprecate ports broken for more than 6 months 2018-05-05 10:49:36 +00:00
plinkseq
primer3
protomol
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 biology/py-biopython: Unbreak on python3; Add license 2018-05-13 22:30:00 +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 Switch all pypi.python.org WWWs to a new PyPi home pypi.org where 2018-04-25 16:42:37 +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 Switch all pypi.python.org WWWs to a new PyPi home pypi.org where 2018-04-25 16:42:37 +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
ruby-bio
rubygem-bio
samtools
seaview biology/seaview: Update version 4.6.3=>4.6.5 2018-04-24 12:31:32 +00:00
seqan
seqan1
seqan-apps devel/boost-*: update to 1.67.0 2018-04-18 13:57:42 +00:00
seqio
seqtk biology/seqtk: Tool for processing sequences in FASTA/FASTQ format 2018-04-03 20:57:05 +00:00
seqtools
sim4
slclust
smithwaterman biology/smithwaterman: Smith-waterman-gotoh alignment algorithm 2018-04-15 17:45:52 +00:00
ssaha Deprecate ports broken for more than 6 months 2018-05-05 10:49:36 +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
tabixpp biology/tabixpp: C++ wrapper to tabix indexer 2018-04-14 23:52:16 +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
tRNAscan-SE Deprecate ports broken for more than 6 months 2018-05-05 10:49:36 +00:00
ugene
unanimity biology/unanimity: Pacific Biosciences consensus library and applications 2018-04-24 14:16:46 +00:00
vcflib biology/vcflib: C++ library and CLI tools for parsing and manipulating VCF files 2018-04-17 03:11:39 +00:00
vcftools
velvet
wise
xmolwt
Makefile New port, biology/hyphy: Hypothesis testing using Phylogenies 2018-05-11 00:05:16 +00:00