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environment.yaml
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environment.yaml
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name: epiGBS
channels:
- conda-forge
- bioconda
- defaults
- r
dependencies:
- numpy
- bcftools=1.3.1=1
- bioconductor-biobase=2.36.2=r3.4.1_0
- bioconductor-biocgenerics=0.24.0=r3.4.1_0
- bioconductor-biocparallel=1.12.0=r3.4.1_0
- bioconductor-biostrings=2.44.2=r3.4.1_0
- bioconductor-bsgenome=1.44.2=r3.4.1_0
- bioconductor-delayedarray=0.2.7=0
- bioconductor-genomeinfodb=1.12.3=r3.4.1_0
- bioconductor-genomeinfodbdata==0.99.0=r3.4.1_0
- bioconductor-genomicalignments=1.12.2=r3.4.1_0
- bioconductor-genomicranges=1.28.6=r3.4.1_0
- bioconductor-iranges=2.12.0=r3.4.1_0
- bioconductor-rsamtools=1.28.0=r3.4.1_0
- bioconductor-rtracklayer=1.36.6=0
- bioconductor-s4vectors=0.16.0=r3.4.1_0
- bioconductor-summarizedexperiment=1.6.5=r3.4.1_0
- bioconductor-xvector=0.16.0=r3.4.1_0
- bioconductor-zlibbioc=1.24.0=r3.4.1_0
- blat=35=1
- bwa=0.7.16=pl5.22.0_0
- pear=0.9.6=2
- sambamba=0.6.6=0
- samtools=1.3.1=5
- seqtk=1.2=0
- star=2.5.3a=0
- tabix=0.2.5=0
- vsearch=2.5.0=0
- bzip2=1.0.6=1
- ca-certificates=2017.7.27.1=0
- cairo=1.14.6=4
- certifi=2017.7.27.1=py27_0
- curl=7.54.1=0
- fontconfig=2.12.1=4
- freetype=2.7=1
- gettext=0.19.7=1
- glib=2.51.4=0
- graphite2=1.3.9=0
- gsl=2.1=2
- harfbuzz=1.4.3=0
- icu=58.1=1
- jpeg=9b=2
- krb5=1.14.2=0
- libffi=3.2.1=3
- libiconv=1.14=4
- libpng=1.6.28=1
- libssh2=1.8.0=1
- libtiff=4.0.7=0
- libxml2=2.9.5=0
- ncurses=5.9=10
- openssl=1.0.2l=0
- pango=1.40.4=0
- pcre=8.39=0
- perl=5.22.0.1=0
- pip=9.0.1=py27_0
- pixman=0.34.0=0
- python=2.7.14=0
- r-base=3.4.1=0
- r-bh=1.62.0_1=r3.4.1_0
- r-bitops=1.0_6=r3.4.1_0
- r-futile.logger=1.4.3=r3.4.1_0
- r-futile.options=1.0.0=r3.4.1_0
- r-lambda.r=1.1.9=r3.4.1_0
- r-lattice=0.20_34=r3.4.1_0
- r-matrix=1.2_7.1=r3.4.1_0
- r-matrixstats=0.52.2=r3.4.1_0
- r-rcurl=1.95_4.8=r3.4.1_0
- r-snow=0.4_2=r3.4.1_0
- r-xml=3.98_1.6=r3.4.1_0
- readline=6.2=0
- setuptools=36.6.0=py27_1
- sqlite=3.13.0=1
- tk=8.5.19=2
- wheel=0.30.0=py27h2bc6bb2_1
- xz=5.2.3=0
- zlib=1.2.8=3
- libgcc=5.2.0=0
- wget=1.18=0
- pip:
- backports.functools-lru-cache==1.4
- backports.unittest-mock==1.3
- biom-format==2.1.6
- biopython==1.68
- chardet==3.0.4
- click==6.7
- cycler==0.10.0
- decorator==4.1.2
- funcsigs==1.0.2
- functools32==3.2.3.post2
- future==0.16.0
- genesis-pyapi==1.2.0
- idna==2.6
- matplotlib==2.0.0
- matplotlib-venn==0.11.5
- mock==2.0.0
- nested-dict==1.61
- networkx==2.0
- numpy==1.12.0
- orange-bioinformatics==2.6.22
- pandas==0.20.3
- pbr==3.1.1
- pyfaidx==0.4.8.1
- pygraphviz==1.3.1
- pyparsing==2.2.0
- pyqi==0.3.2
- pysam==0.10.0
- python-dateutil==2.6.1
- python-levenshtein==0.12.0
- pytz==2017.2
- pyvcf==0.6.8
- requests==2.18.4
- requests-cache==0.4.13
- scipy==0.18.1
- seqenv==1.3.0
- serverfiles==0.2.1
- sh==1.12.14
- singledispatch==3.4.0.3
- six==1.11.0
- slumber==0.7.1
- sphinx-rtd-theme==0.1.10a0
- subprocess32==3.2.7
- toolshed==0.4.6
- tqdm==4.19.4
- typing==3.6.2
- urllib3==1.22