requirements.txt

# channels : defaults, r, bioconda

bowtie ==1.1.2
bowtie2 == 2.2.8
ncurses
samtools ==1.9
htslib ==1.9 # 1.5 in bioconda needed libbz2.so.1.0
bedtools ==2.28.0 #2.26 has a bug of get wrong fields number for tagAlign.gz 
picard ==2.18.2 #1.126 
ucsc-fetchchromsizes
ucsc-wigtobigwig
ucsc-bedgraphtobigwig
ucsc-bigwiginfo
ucsc-bedclip
ucsc-bigWigAverageOverBed
ucsc-bedtobigbed
ucsc-twobittofa
macs2=2.1.1.20160309 
boost ==1.60.0#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#==0.14.1 #0.8.2.1
pybedtools==0.7.10 #0.6.9 
pigz
zlib
sambamba ==0.6.6#0.6.5
r ==3.2.2
r-snow
r-snowfall
r-bitops
r-catools
bioconductor-rsamtools
r-spp ==1.13
cutadapt ==1.16
preseq ==2.0.3 #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 ==0.5.3#0.4.7.1
seqtk ==1.2