# default Conda environment for atac/chip

python >=3
bwa ==0.7.17
bowtie2 ==2.3.4.3
tbb ==2020.2 # use old version to fix libtbb.so.2 error for bowtie2
samtools ==1.9
htslib ==1.9
bedtools ==2.29.0
sambamba ==0.6.6

pysam ==0.15.3
pybedtools ==0.8.0
pybigwig ==0.3.13

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

deeptools ==3.3.1
cutadapt ==2.5
preseq ==2.0.3
pyfaidx ==0.5.5.2
bedops ==2.4.39

ptools_bin

jsondiff ==1.1.1
ghostscript
tabix
matplotlib
numpy
scikit-learn
scipy
pandas
jinja2
gsl

samstats ==0.2.1
idr ==2.0.4.2

java-jdk

picard ==2.20.7
trimmomatic ==0.39

openssl ==1.0.2u # to fix missing libssl.so.1.0.0 for UCSC tools (bedClip, ...)
