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 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'])