def trim_galore_filter(options, input_fn, output_dir, adapter_seq=None):
''' writes command for running fastx_trimmer
options should be a string -Q 33'''
server = myos.which_server()
if server == 'broad':
en = '/home/unix/dfernand/bin/trim_galore/trim_galore'
if adapter_seq is not None:
cmd = '%s -o %s -a %s %s %s' % (en, output_dir, adapter_seq,
options, input_fn)
else:
cmd = '%s -o %s %s %s' % (en, output_dir, options, input_fn)
elif server == 'slurm':
en = '/n/dulacfs2/Users/dfernand/de/software/trim_galore_v0.3.3/trim_galore'
if adapter_seq is not None:
cmd = 'module load centos6/python-2.7.3; module load centos6/cutadapt-1.2.1_python-2.7.3;%s -o %s -a %s %s %s' % (
en, output_dir, adapter_seq, options, input_fn)
else:
cmd = 'module load centos6/cutadapt-1.2.1_python-2.7.3;%s -o %s %s %s' % (
en, output_dir, options, input_fn)
elif server == 'legacy':
en = '/n/dulacfs2/Users/dfernand/de/software/trim_galore_v0.3.3/trim_galore'
if adapter_seq is not None:
cmd = 'module load hpc/python-2.7.3; module load bio/cutadapt-1.2.1;%s -o %s -a %s %s %s' % (
en, output_dir, adapter_seq, options, input_fn)
else:
cmd = 'module load hpc/python-2.7.3; module load bio/cutadapt-1.2.1;%s -o %s %s %s' % (
en, output_dir, options, input_fn)
return cmd
def shapeit2(options):
''' options must contains all arguments for shapeit2 after the executable fullname'''
server = myos.which_server()
if server == 'slurm' or server == 'legacy':
en = '/n/junliufs1/software/shapeit2/shapeit.v2.r727.linux.x64'
cmd = '%s %s' %(en, options)
return cmd
def __init__(self):
self.server = myos.which_server()
if self.server == 'broad':
self.igv_fn = '/home/unix/dfernand/bin/IGVTools/igvtools.jar'
elif self.server == 'slurm' or self.server == 'legacy':
self.dep_cmd = myos.load_dependencies_cmd(['bio/igvtools-2.2.2'])
self.igv_fn = '/n/sw/igvtools-2.2.2/igvtools.jar'
def shapeit2(options):
''' options must contains all arguments for shapeit2 after the executable fullname'''
server = myos.which_server()
if server == 'slurm' or server == 'legacy':
en = '/n/junliufs1/software/shapeit2/shapeit.v2.r727.linux.x64'
cmd = '%s %s' % (en, options)
return cmd
def __init__(self):
self.server = myos.which_server()
if self.server == 'broad':
self.igv_fn = '/home/unix/dfernand/bin/IGVTools/igvtools.jar'
elif self.server == 'slurm' or self.server == 'legacy':
self.dep_cmd = myos.load_dependencies_cmd(['bio/igvtools-2.2.2'])
self.igv_fn = '/n/sw/igvtools-2.2.2/igvtools.jar'
def fastqc(input_fns, output_dir):
''' writes command for running fastx_trimmer
options should be a string -Q 33'''
server = myos.which_server()
if server == 'broad':
en = 'perl /broad/software/free/Linux/redhat_5_x86_64/pkgs/fastqc_0.10.1/FastQC/fastqc'
elif server == 'slurm' or server == 'legacy':
en = 'perl /n/dulacfs2/Users/dfernand/de/software/FastQC/fastqc'
cmd = '%s -o %s %s' % (en, output_dir, input_fns)
return cmd
def fastqc(input_fns, output_dir):
''' writes command for running fastx_trimmer
options should be a string -Q 33'''
server = myos.which_server()
if server == 'broad':
en = 'perl /broad/software/free/Linux/redhat_5_x86_64/pkgs/fastqc_0.10.1/FastQC/fastqc'
elif server == 'slurm' or server == 'legacy':
en = 'perl /n/dulacfs2/Users/dfernand/de/software/FastQC/fastqc'
cmd = '%s -o %s %s' %(en, output_dir, input_fns)
return cmd
def fastq_dump(in_fn, out_dir, options):
''' writes command for running fastq-dump
options should be a string --split-3 for paired-end data'''
server = myos.which_server()
if server == 'broad':
en = 'fastq-dump'
cmd = '%s %s --outdir %s %s' %(en, options, out_dir, in_fn)
elif server == 'slurm' or server == 'legacy':
en = 'fastq-dump'
cmd = 'module load bio/sratoolkit.2.3.3-4; %s %s --outdir %s %s' %(en, options, out_dir, in_fn)
return cmd
def trim_galore_filter(adapter_seq, options, input_fn, output_dir):
''' writes command for running fastx_trimmer
options should be a string -Q 33'''
server = myos.which_server()
if server == 'broad':
en = '/home/unix/dfernand/bin/trim_galore/trim_galore'
cmd = '%s -o %s -a %s %s %s' %(en, output_dir, adapter_seq, options, input_fn)
elif server == 'odyssey':
en = '/n/dulacfs2/Users/dfernand/de/software/trim_galore_v0.3.3/trim_galore'
cmd = 'module load centos6/cutadapt-1.2.1_python-2.7.3;%s -o %s -a %s %s %s' %(en, output_dir, adapter_seq, options, input_fn)
return cmd
def fastq_dump(in_fn, out_dir, options):
''' writes command for running fastq-dump
options should be a string --split-3 for paired-end data'''
server = myos.which_server()
if server == 'broad':
en = 'fastq-dump'
cmd = '%s %s --outdir %s %s' % (en, options, out_dir, in_fn)
elif server == 'slurm' or server == 'legacy':
en = 'fastq-dump'
cmd = 'module load bio/sratoolkit.2.3.3-4; %s %s --outdir %s %s' % (
en, options, out_dir, in_fn)
return cmd
def __init__(self):
self.server = myos.which_server()
if self.server == 'broad':
self.dep_cmd = myos.load_dependencies_cmd(['.bedops-2.0.0b'])
elif self.server == 'slurm' or self.server == 'legacy':
self.dep_cmd = myos.load_dependencies_cmd(['centos6/bedops-2.3.0'])
def __init__(self):
self.server = myos.which_server()
if self.server == 'broad':
self.dep_cmd = myos.load_dependencies_cmd(['.bedops-2.0.0b'])
elif self.server == 'slurm' or self.server == 'legacy':
self.dep_cmd = myos.load_dependencies_cmd(['centos6/bedops-2.3.0'])