def writeVersions(self,raFile=None,allLevels=False): '''Writes versions to to the log or a file.''' if allLevels: LogicalStep.writeVersions(self, raFile) if raFile != None: raFile.add('eap_run_hotspot', self.getToolVersion('eap_run_hotspot')) raFile.add('hotspot', self.getToolVersion( \ self.ana.toolsDir+'hotspot-distr/hotspot-deploy/bin/hotspot')) raFile.add('python2.7', self.getToolVersion('python2.7')) raFile.add('hotspot.py', self.getToolVersion('hotspot.py')) raFile.add('bedToBigBed', self.getToolVersion('bedToBigBed')) raFile.add('bedmap', self.getToolVersion('bedmap')) raFile.add('sort-bed', self.getToolVersion('sort-bed')) raFile.add('starchcat', self.getToolVersion('starchcat')) raFile.add('unstarch', self.getToolVersion('unstarch')) raFile.add('intersectBed',self.getToolVersion( \ self.ana.toolsDir+'bedtools/bin/intersectBed')) raFile.add('bedGraphPack',self.getToolVersion('bedGraphPack')) raFile.add('bedGraphToBigWig', self.getToolVersion('bedGraphToBigWig')) else: self.getToolVersion('eap_run_hotspot') self.getToolVersion(self.ana.toolsDir+'hotspot-distr/hotspot-deploy/bin/hotspot') self.getToolVersion('python2.7') self.getToolVersion('hotspot.py') self.getToolVersion('bedToBigBed') self.getToolVersion('bedmap') self.getToolVersion('sort-bed') self.getToolVersion('starchcat') self.getToolVersion('unstarch') self.getToolVersion(self.ana.toolsDir+'bedtools/bin/intersectBed') self.getToolVersion('bedGraphPack') self.getToolVersion('bedGraphToBigWig')
def writeVersions(self, raFile=None, allLevels=False): '''Writes versions to to the log or a file.''' if allLevels: LogicalStep.writeVersions(self, raFile) if raFile != None: raFile.add('samtools', samtools.version(self)) else: samtools.version(self)
def writeVersions(self, raFile=None, allLevels=False): """Writes versions to to the log or a file.""" if allLevels: LogicalStep.writeVersions(self, raFile) if raFile != None: raFile.add("samtools", samtools.version(self)) else: samtools.version(self)
def writeVersions(self,raFile=None,allLevels=False): '''Writes versions to to the log or a file.''' if allLevels: LogicalStep.writeVersions(self, raFile) if raFile != None: raFile.add('ucscUtils', ucscUtils.version(self,tool='fastqStatsAndSubsample')) raFile.add('fastqc', self.getToolVersion('fastqc')) else: ucscUtils.version(self,tool='fastqStatsAndSubsample') self.getToolVersion('fastqc')
def writeVersions(self, raFile=None, allLevels=False): '''Writes versions to to the log or a file.''' if allLevels: LogicalStep.writeVersions(self, raFile) if raFile != None: raFile.add('ucscUtils', ucscUtils.version(self, tool='fastqStatsAndSubsample')) raFile.add('fastqc', self.getToolVersion('fastqc')) else: ucscUtils.version(self, tool='fastqStatsAndSubsample') self.getToolVersion('fastqc')
def writeVersions(self,raFile=None,allLevels=False,scriptName=None): '''Writes versions to to the log or a file.''' if allLevels: LogicalStep.writeVersions(self, raFile) if raFile != None: if scriptName != None: raFile.add(scriptName, self.getToolVersion(scriptName)) raFile.add('bwa', self.getToolVersion('bwa')) raFile.add('samtools', self.getToolVersion('samtools')) else: if scriptName != None: self.getToolVersion(scriptName) self.getToolVersion('bwa') self.getToolVersion('samtools')
def writeVersions(self,raFile=None,allLevels=False,scriptName=None): '''Writes versions to to the log or a file.''' if allLevels: LogicalStep.writeVersions(self, raFile) if raFile != None: if scriptName != None: raFile.add(scriptName, self.getToolVersion(scriptName)) raFile.add('tophat', self.getToolVersion('tophat')) raFile.add('bowtie2', self.getToolVersion('bowtie2')) raFile.add('samtools', self.getToolVersion('samtools')) raFile.add('tophat_bam_xsA_tag_fix.pl', self.getToolVersion('tophat_bam_xsA_tag_fix.pl')) else: if scriptName != None: self.getToolVersion(scriptName) self.getToolVersion('tophat') self.getToolVersion('bowtie2') self.getToolVersion('samtools') self.getToolVersion('tophat_bam_xsA_tag_fix.pl')
def writeVersions(self,raFile=None,allLevels=False,scriptName=None): '''Writes versions to to the log or a file.''' if allLevels: LogicalStep.writeVersions(self, raFile) if raFile != None: if scriptName != None: raFile.add(scriptName, self.getToolVersion(scriptName)) raFile.add('edwBamStats', self.getToolVersion('edwBamStats')) raFile.add('samtools', self.getToolVersion('samtools')) raFile.add('Rscript', self.getToolVersion('Rscript')) raFile.add('run_spp.R', self.getToolVersion(self.ana.toolsDir+'run_spp.R')) else: if scriptName != None: self.getToolVersion(scriptName) self.getToolVersion('edwBamStats') self.getToolVersion('samtools') self.getToolVersion('Rscript') self.getToolVersion(self.ana.toolsDir+'run_spp.R')
def writeVersions(self,raFile=None,allLevels=False,scriptName=None): '''Writes versions to to the log or a file.''' if allLevels: LogicalStep.writeVersions(self, raFile) if raFile != None: if scriptName != None: raFile.add(scriptName, self.getToolVersion(scriptName)) raFile.add('macs', self.getToolVersion('macs2')) raFile.add('eap_macs2_xls_to_narrowPeak', self.getToolVersion('eap_macs2_xls_to_narrowPeak')) raFile.add('eap_narrowPeak_to_bigBed', self.getToolVersion('eap_narrowPeak_to_bigBed')) raFile.add('bedGraphToBigWig', self.getToolVersion('bedGraphToBigWig')) else: if scriptName != None: self.getToolVersion(scriptName) self.getToolVersion('macs2') self.getToolVersion('eap_macs2_xls_to_narrowPeak') self.getToolVersion('eap_narrowPeak_to_bigBed') self.getToolVersion('bedGraphToBigWig')
def writeVersions(self, raFile=None, allLevels=False, scriptName=None): '''Writes versions to to the log or a file.''' if allLevels: LogicalStep.writeVersions(self, raFile) if raFile != None: if scriptName != None: raFile.add(scriptName, self.getToolVersion(scriptName)) raFile.add('samtools', self.getToolVersion('samtools')) raFile.add('makewigglefromBAM-NH.py', \ self.getToolVersion('makewigglefromBAM-NH.py')) raFile.add('python2.7', self.getToolVersion('python2.7')) raFile.add('wigToBigWig', self.getToolVersion('wigToBigWig')) #raFile.add('perl', self.getToolVersion('perl')) else: if scriptName != None: self.getToolVersion(scriptName) self.getToolVersion('samtools') self.getToolVersion('makewigglefromBAM-NH.py') self.getToolVersion('python2.7') self.getToolVersion('wigToBigWig')
def writeVersions(self,raFile=None,allLevels=False,scriptName=None): '''Writes versions to to the log or a file.''' if allLevels: LogicalStep.writeVersions(self, raFile) if raFile != None: if scriptName != None: raFile.add(scriptName,self.getToolVersion(scriptName)) raFile.add('samtools', self.getToolVersion('samtools')) raFile.add('makewigglefromBAM-NH.py', \ self.getToolVersion('makewigglefromBAM-NH.py')) raFile.add('python2.7', self.getToolVersion('python2.7')) raFile.add('wigToBigWig', self.getToolVersion('wigToBigWig')) #raFile.add('perl', self.getToolVersion('perl')) else: if scriptName != None: self.getToolVersion(scriptName) self.getToolVersion('samtools') self.getToolVersion('makewigglefromBAM-NH.py') self.getToolVersion('python2.7') self.getToolVersion('wigToBigWig')
def writeVersions(self, raFile=None, allLevels=False, scriptName=None): '''Writes versions to to the log or a file.''' if allLevels: LogicalStep.writeVersions(self, raFile) if raFile != None: if scriptName != None: raFile.add(scriptName, self.getToolVersion(scriptName)) raFile.add('macs', self.getToolVersion('macs2')) raFile.add('eap_macs2_xls_to_narrowPeak', self.getToolVersion('eap_macs2_xls_to_narrowPeak')) raFile.add('eap_narrowPeak_to_bigBed', self.getToolVersion('eap_narrowPeak_to_bigBed')) raFile.add('bedGraphToBigWig', self.getToolVersion('bedGraphToBigWig')) else: if scriptName != None: self.getToolVersion(scriptName) self.getToolVersion('macs2') self.getToolVersion('eap_macs2_xls_to_narrowPeak') self.getToolVersion('eap_narrowPeak_to_bigBed') self.getToolVersion('bedGraphToBigWig')
def writeVersions(self, raFile=None, allLevels=False): '''Writes versions to to the log or a file.''' if allLevels: LogicalStep.writeVersions(self, raFile) if raFile != None: raFile.add('eap_run_hotspot', self.getToolVersion('eap_run_hotspot')) raFile.add('hotspot', self.getToolVersion( \ self.ana.toolsDir+'hotspot-distr/hotspot-deploy/bin/hotspot')) raFile.add('python2.7', self.getToolVersion('python2.7')) raFile.add('hotspot.py', self.getToolVersion('hotspot.py')) raFile.add('bedToBigBed', self.getToolVersion('bedToBigBed')) raFile.add('bedmap', self.getToolVersion('bedmap')) raFile.add('sort-bed', self.getToolVersion('sort-bed')) raFile.add('starchcat', self.getToolVersion('starchcat')) raFile.add('unstarch', self.getToolVersion('unstarch')) raFile.add('intersectBed',self.getToolVersion( \ self.ana.toolsDir+'bedtools/bin/intersectBed')) raFile.add('bedGraphPack', self.getToolVersion('bedGraphPack')) raFile.add('bedGraphToBigWig', self.getToolVersion('bedGraphToBigWig')) else: self.getToolVersion('eap_run_hotspot') self.getToolVersion(self.ana.toolsDir + 'hotspot-distr/hotspot-deploy/bin/hotspot') self.getToolVersion('python2.7') self.getToolVersion('hotspot.py') self.getToolVersion('bedToBigBed') self.getToolVersion('bedmap') self.getToolVersion('sort-bed') self.getToolVersion('starchcat') self.getToolVersion('unstarch') self.getToolVersion(self.ana.toolsDir + 'bedtools/bin/intersectBed') self.getToolVersion('bedGraphPack') self.getToolVersion('bedGraphToBigWig')