requirements.txt

# channels : defaults, r, bioconda

bowtie ==1.1.2
bowtie2 ==2.2.6
ncurses
samtools ==1.2
htslib ==1.4 # 1.5 in bioconda needed libbz2.so.1.0
bedtools ==2.26.0 #2.22 # 2.21.0
picard ==1.126 # wanted 1.129 here but doesn't exist. instead 1.139 has backward compatibility issue, so take 1.126
ucsc-fetchchromsizes
ucsc-wigtobigwig
ucsc-bedgraphtobigwig
ucsc-bigwiginfo
ucsc-bedclip
ucsc-bigWigAverageOverBed
ucsc-bedtobigbed
ucsc-twobittofa
macs2 ==2.1.0
boost ==1.57.0
gnuplot #==5.0.3
numpy ==1.10.2 #1.9.0, 1.8.2 conflicts with ATAQC
scipy # ==0.17.0: to fix 'undefined symbol: PyUnicodeUCS2_DecodeUTF8'
matplotlib
libgfortran==3.0 # ataqc
pandas ==0.18.0 #==0.16.1 # ataqc
metaseq #==0.5.6 # ataqc
jinja2 # ataqc
graphviz==2.38.0
libtool
ghostscript # pdf2png
gsl # for preseq
pysam==0.8.2.1 # 0.8.3, 0.9 from bioconda has an issue with ATAQC (segmentation fault), need to use -c bcbio
pybedtools==0.6.9 # same issue as in pysam
pigz
zlib
sambamba ==0.6.5 # to fix seg fault error in 0.6.1
r ==3.2.2
r-snow
r-snowfall
r-bitops
r-catools
bioconductor-rsamtools
r-spp ==1.13
cutadapt ==1.9.1
preseq ==2.0.2 
trim-galore ==0.4.1 # for old trimmer
python-levenshtein # for old trimmer (trimAdapter.py)
#glibc #segmentation fault in conda with openssl
pyfaidx ==0.4.7.1
six ==1.4.1