/bioconda-recipes

Finished Python 3.6 migration #4888

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merged 126 commits into from Jun 3, 2017
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2 .travis.yml
@@ -11,7 +11,7 @@ services:
install: scripts/travis-setup.sh
-script: travis_wait 119 scripts/travis-run.sh
+script: scripts/travis-run.sh
env:
global:
View
14 recipes/amos/build.sh
@@ -1,8 +1,20 @@
+# fix automake
+sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $PREFIX/bin/aclocal
+sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $PREFIX/bin/automake
+
+# fix autoconf
+sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $PREFIX/bin/autom4te
+sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $PREFIX/bin/autoheader
+sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $PREFIX/bin/autoreconf
+sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $PREFIX/bin/ifnames
+sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $PREFIX/bin/autoscan
+sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $PREFIX/bin/autoupdate
+
rm -r test tutorial
export LDFLAGS="-L$PREFIX/lib"
export CPPFLAGS="-I$PREFIX/include"
./bootstrap
./configure \
- --prefix=$PREFIX
+ --prefix=$PREFIX
make
make install
View
10 recipes/amos/meta.yaml
@@ -14,8 +14,7 @@ source:
build:
number: 3
# OSX failing due to missing dependencies in OSX branch
- skip: True # [osx]
-
+ skip: true # [osx]
test:
commands:
@@ -25,11 +24,12 @@ requirements:
build:
- gcc
- zlib
- - boost
+ - boost
- autoconf
+ - automake
- blat
- mummer
- - perl-threaded
+ - perl
- perl-statistics-descriptive
- perl-xml-parser
- perl-dbi
@@ -38,7 +38,7 @@ requirements:
run:
- mummer
- - perl-threaded
+ - perl
- perl-statistics-descriptive
- perl-xml-parser
- perl-dbi
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7 recipes/bcbio-nextgen/meta.yaml
@@ -84,9 +84,10 @@ test:
# Reason: image not found
#- bcbio.distributed.ipython
commands:
- - bcbio_nextgen.py -h
- - bcbio_setup_genome.py -h
- - bcbio_prepare_samples.py -h
+ # click requires a unicode locale
+ - LANG=C.UTF-8 bcbio_nextgen.py -h
+ - LANG=C.UTF-8 bcbio_setup_genome.py -h
+ - LANG=C.UTF-8 bcbio_prepare_samples.py -h
about:
home: https://github.com/chapmanb/bcbio-nextgen
View
3 recipes/bcl2fastq-nextseq/meta.yaml
@@ -30,7 +30,8 @@ requirements:
test:
commands:
- - bcl_to_fastq -h &> /dev/null
+ # click requires a unicode locale
+ - LANG=C.UTF-8 bcl_to_fastq -h &> /dev/null
about:
home: https://github.com/brwnj/bcl2fastq
View
28 recipes/biokit/meta.yaml
@@ -6,13 +6,10 @@ source:
fn: biokit-0.4.1.tar.gz
url: https://pypi.python.org/packages/e3/fe/9bc827910cbd19a1a03bb5b0a1c4aa583903696526d7f6e51fbc9f849e28/biokit-0.4.1.tar.gz
md5: 755efcfa4982fd23d31d1ebdd4972c22
-# patches:
- # List any patch files here
- # - fix.patch
build:
skip: True # [py34]
- number: 2
+ number: 4
# Set xmltodict >= 0.10.2 to use conda-forge version instead of bioconda
# Same with easydev
@@ -25,6 +22,9 @@ requirements:
- colormap
- scipy
- xmltodict
+ - numpydoc
+ - bioservices
+ - mesalib
run:
- python
@@ -34,25 +34,21 @@ requirements:
- colormap
- scipy
- xmltodict
- #- matplotlib
- #- libgcc # [not osx]
- #- glib
+ - numpydoc
+ - bioservices
+ - matplotlib
+ - libgcc
+ - mesalib
#- xz
#- libxcb
# Could not manage to import it without an libXext issue from conda-forge ? and
-# matplotlib v1.5.3 or v2.0.0. Hopefully, this will be resolved in the future
+# matplotlib v1.5.3 or v2.0.0. Hopefully, this will be resolved in the future
test:
- # Python imports
- # imports:
- #- biokit
+ imports:
+ - biokit
about:
home: ['http://pypi.python.org/pypi/biokit']
license: BSD
summary: 'Set of visualisation and analysis tools for biological data sets'
-
-
-extra:
- recipe-maintainers:
- - cokelaer
View
18 recipes/biom-format/2.1.5/meta.yaml
@@ -9,19 +9,12 @@ source:
build:
- # noarch_python: True
preserve_egg_dir: True
entry_points:
- # Put any entry points (scripts to be generated automatically) here. The
- # syntax is module:function. For example
- #
- # - biom-format = biom-format:main
- #
- # Would create an entry point called biom-format that calls biom-format.main()
-
- biom=biom.cli:cli
-
number: 3
+ # click needs to be patched in order to properly detect unicode in py3k
+ skip: true # [py3k]
requirements:
build:
@@ -43,6 +36,8 @@ requirements:
- numpy >=1.3.0
- future >=0.15.0
- scipy >=0.13.0
+ # missing scipy dependency
+ - libgcc
test:
# Python imports
@@ -51,9 +46,8 @@ test:
- biom.cli
commands:
- # You can put test commands to be run here. Use this to test that the
- # entry points work.
- - biom --help
+ # click requires a unicode locale
+ - LANG=C.UTF-8 biom --help
about:
home: http://www.biom-format.org
View
1 recipes/biomaj/meta.yaml
@@ -48,6 +48,5 @@ test:
about:
home: http://biomaj.genouest.org
license: GNU Affero General Public License v3 or later (AGPLv3+)
- summary: 'BioMAJ'
license_family: AGPL
summary: Automates the update cycle and the supervision of the locally mirrored databank repository
View
3 recipes/biopython/1.65/build.sh
@@ -1,3 +0,0 @@
-#!/bin/bash
-
-$PYTHON setup.py install
View
113 recipes/biopython/1.65/meta.yaml
@@ -1,113 +0,0 @@
-{% set name = "biopython" %}
-{% set version = "1.65" %}
-{% set sha256 = "6d591523ba4d07a505978f6e1d7fac57e335d6d62fb5b0bcb8c40bdde5c8998e" %}
-
-
-package:
- name: {{ name|lower }}
- version: {{ version }}
-
-source:
- fn: {{ name }}-{{ version }}.tar.gz
- url: https://pypi.python.org/packages/4e/77/8590d61dcda439d83f378106954e748db1a71e565335168a966642133ef8/biopython-1.65.tar.gz
- sha256: {{ sha256 }}
-
-about:
- home: http://www.biopython.org/
- license: Biopython License Agreement
- license_file: LICENSE
- summary: 'Freely available tools for computational molecular biology.'
-
-build:
- number: 0
- skip: True # [py34]
-
-requirements:
- build:
- - python
- - numpy x.x
- - reportlab
- - mmtf-python
-
- run:
- - python
- - numpy x.x
- - reportlab
- - mmtf-python
-
-test:
- imports:
- - Bio
- - Bio.Align
- - Bio.Align.Applications
- - Bio.AlignIO
- - Bio.Alphabet
- - Bio.Application
- - Bio.Blast
- - Bio.CAPS
- - Bio.Compass
- - Bio.Crystal
- - Bio.Data
- - Bio.Emboss
- - Bio.Entrez
- - Bio.ExPASy
- - Bio.FSSP
- - Bio.GA
- - Bio.GA.Crossover
- - Bio.GA.Mutation
- - Bio.GA.Repair
- - Bio.GA.Selection
- - Bio.GenBank
- - Bio.Geo
- - Bio.Graphics
- - Bio.Graphics.GenomeDiagram
- - Bio.HMM
- - Bio.KEGG
- - Bio.KEGG.Compound
- - Bio.KEGG.Enzyme
- - Bio.KEGG.KGML
- - Bio.KEGG.Map
- - Bio.Medline
- - Bio.NMR
- - Bio.NeuralNetwork
- - Bio.NeuralNetwork.BackPropagation
- - Bio.NeuralNetwork.Gene
- - Bio.Nexus
- - Bio.PDB
- - Bio.PDB.QCPSuperimposer
- # - Bio.PDB.mmtf Introduced in 1.68
- - Bio.Pathway
- - Bio.Pathway.Rep
- - Bio.Phylo
- - Bio.Phylo.Applications
- - Bio.Phylo.PAML
- - Bio.PopGen
- - Bio.PopGen.Async
- - Bio.PopGen.FDist
- - Bio.PopGen.GenePop
- - Bio.PopGen.SimCoal
- - Bio.Restriction
- - Bio.SCOP
- - Bio.SVDSuperimposer
- - Bio.SearchIO
- - Bio.SearchIO.BlastIO
- - Bio.SearchIO.ExonerateIO
- - Bio.SearchIO.HmmerIO
- - Bio.SearchIO._model
- - Bio.SeqIO
- - Bio.SeqUtils
- - Bio.Sequencing
- - Bio.Sequencing.Applications
- - Bio.Statistics
- - Bio.SubsMat
- - Bio.SwissProt
- - Bio.TogoWS
- - Bio.UniGene
- - Bio.UniProt
- - Bio.Wise
- - Bio._py3k
- - Bio.codonalign
- - Bio.motifs
- - Bio.motifs.applications
- - Bio.motifs.jaspar
- - BioSQL
View
5 recipes/busco/1.2/build.sh
@@ -1,5 +0,0 @@
-#!/bin/bash
-
-mkdir -p $PREFIX/bin/
-cp BUSCO_v1.2.py $PREFIX/bin
-ln -s $PREFIX/bin/BUSCO_v1.2.py $PREFIX/bin/busco
View
33 recipes/busco/1.2/meta.yaml
@@ -1,33 +0,0 @@
-package:
- name: busco
- version: "1.2"
-
-build:
- number: 1
-
-source:
- fn: busco-v1.2.tar.gz
- url: http://busco.ezlab.org/files/BUSCO_v1.2.tar.gz
- md5: 4b4551ccdbc8e64d18295fc8d8729d84
-
-requirements:
- build:
- - python
- run:
- - python
- - blast
- - hmmer
- # - emboss
-
-about:
- home: http://busco.ezlab.org/
- license: GPL
- summary: BUSCO provides measures for quantitative assessment of genome
- assembly, gene set, and transcriptome completeness based on
- evolutionarily informed expectations of gene content from
- near-universal single-copy orthologs selected from OrthoDB.
-
-test:
- commands:
- - BUSCO_v1.2.py -h > /dev/null
- - busco -h > /dev/null
View
2 recipes/bx-python/0.7.1/build.sh
@@ -1,2 +0,0 @@
-#!/bin/sh
-$PYTHON setup.py install
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