conda_requires.txt

# latest setutools required for automatic cythonization
# setuptools>=1.1
# pyparsing>=1.5.7
# # not available in py3, use mysql-client instead
# # MySQL-python>1.2.3
PyYAML>=3.1.0
alignlib-lite>=0.2.3
biopython>=1.61
drmaa>=0.5
matplotlib-venn>=0.5
matplotlib>=1.3.0
networkx>=1.8.1
openpyxl>=1.5.7
pandas>=0.12.0
rdflib>=0.4.1
psycopg2>=2.5
rpy2>=2.6

# not part of CGATCore?
sqlalchemy
sqlite

# Bioinformatic tools required to get the tests pass
bwa
gat
multiqc
picard
ucsc-gtftogenepred
fastqc
bowtie
bowtie2
trimmomatic
sra-tools
fastq-screen
blast
meme
star
subread
gatk
snpeff

sailfish
salmon
kallisto
cufflinks
hisat2

# idr
# macs2: separate env: py27
# sicer: separate env: py26

# Note: uninstall conda perl
# pipeline_windows
r-ggplot2

# genesets
bioconductor-hpar

bioconductor-deseq
bioconductor-deseq2
bioconductor-edger
r-gmd

# pipeline_geneset special packages
httplib2
intermine
toposort
mygene

# peakcalling
ucsc-bedgraphtobigwig

# pipeline_exome
beautifulsoup4

# pipeline_peakcalling and pipeline_rnaseqqc
seaborn