freebsd-ports/biology
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* The outdated dependency: print/py-reportlab1 instead of the modern version 3.X print/py-reportlab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
artemis
avida
babel
bamtools
bcftools
bedtools
biococoa
blat
bowtie
bowtie2
bwa
canu
cd-hit
cdbfasta
chemeq
clustalw
consed
crux
ddocent
diamond
emboss
fasta
fasta3
fastahack
fastdnaml
fastool
fastqc
fasttree
fastx-toolkit
fluctuate
freebayes
garlic
gff2ps
gmap
gperiodic
grappa
hmmer
htslib
hyphy
iolib
iqtree
jalview
jellyfish
kallisto
lagan
lamarc
libgtextutils
libsbml
linux-foldingathome
mafft
mapm3
migrate
molden
mopac
mrbayes
mummer
muscle
ncbi-blast+
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
p5-TrimGalore
paml
pbbam
pbcopper
pbseqan
pear-merger
phrap
phred
phylip
phyml
plink
plinkseq
primer3
protomol
psi88
py-biom-format
py-biopython biology/py-biopython: Unbreak on python3; Add license 2018-05-13 22:30:00 +00:00
py-bx-python
py-cutadapt
py-macs2
py-pysam
pycogent
pyfasta
python-nexus
rainbow
recombine
ruby-bio
rubygem-bio
samtools
seaview
seqan
seqan1
seqan-apps
seqio
seqtk
seqtools
sim4
slclust
smithwaterman
ssaha
stacks
t_coffee
tabixpp
tinker
treepuzzle
trimadap
trimmomatic
tRNAscan-SE
ugene
unanimity
vcflib
vcftools
velvet
wise
xmolwt
Makefile