# for python3
# conda repos: defaults, r, bioconda, conda-forge

nomkl  # using MKL can change MACS2 output randomly on different platforms

idr ==2.0.4.2
tabix
samtools ==1.9
htslib ==1.9
sambamba ==0.6.6
samstats ==0.2.1
bedtools ==2.29.0
picard ==2.20.7
trimmomatic ==0.39

ucsc-fetchchromsizes ==357  # 377 in docker/singularity image
ucsc-wigtobigwig ==357
ucsc-bedgraphtobigwig ==357
ucsc-bigwiginfo ==357
ucsc-bedclip ==357
ucsc-bedtobigbed ==357
ucsc-twobittofa ==357
ucsc-bigWigAverageOverBed ==357

r ==3.5.1  # 3.4.4 in docker/singularity image
r-snow
r-snowfall
r-bitops
r-catools
bioconductor-rsamtools
r-spp ==1.15.5  # 1.14 in docker/singularity image, 1.16 has lwcc() error
libiconv

bwa ==0.7.17
bowtie2 ==2.3.4.3
pysam ==0.15.3
pybedtools ==0.8.0
phantompeakqualtools ==1.2.2
pybigwig ==0.3.13
openssl ==1.0.2t  # important to get the same random seed for "shuf"
deeptools ==3.3.1
cutadapt ==2.5
preseq ==2.0.3
pyfaidx ==0.5.5.2

macs2 ==2.2.4

jsondiff ==1.1.1
libgcc
requests
ncurses
gnuplot
ghostscript
wget
pyopenssl  # for caper/croo to presign bucket URIs
grep
tar

numpy
scipy
pandas
jinja2
gsl
matplotlib

java-jdk

caper
croo