# TODO: Do we really need to track replicate numbers?
import os, sys
from src.galaxyAnalysis import GalaxyAnalysis
from src.steps.mergeBamStep import MergeBamStep
###############
testOnly = False
###############
if sys.argv[1] == '--version':
settingsFile = os.path.split(os.path.abspath(
sys.argv[0]))[0] + '/' + "settingsE3.txt"
if os.path.isfile(
settingsFile): # Unfortunately can't get xml arg for settings
ana = GalaxyAnalysis(settingsFile, 'versions', 'hg19')
MergeBamStep(ana).writeVersions(allLevels=True) # Prints to stdout
else:
print "Can't locate " + settingsFile
exit(0)
galaxyInputBamA = sys.argv[1]
repA = sys.argv[2]
galaxyInputBamB = sys.argv[3]
repB = sys.argv[4]
galaxyOutMergedBam = sys.argv[5]
genome = sys.argv[6]
expType = sys.argv[7]
anaId = sys.argv[8]
# No longer command line parameters:
# <signalOutUniq[Minus]> [<signalOutUniqPlus>] <statsOutput> \
# <libId> <gender> <genome> <expType> <repNo> <analysisId>
import os, sys
import json
from src.galaxyAnalysis import GalaxyAnalysis
from src.steps.starAlignmentStep import StarAlignmentStep
###############
testOnly = False
###############
if sys.argv[1] == '--version':
settingsFile = os.path.split( os.path.abspath( sys.argv[0] ) )[0] + '/' + "settingsE3.txt"
if os.path.isfile( settingsFile ): # Unfortunately can't get xml arg for settings
ana = GalaxyAnalysis(settingsFile, 'versions', 'hg19')
ana.readType = 'paired'
StarAlignmentStep(ana).writeVersions(allLevels=True) # Prints to stdout
else:
print "Can't locate " + settingsFile
exit(0)
# Command line args:
pairedOrUnpaired = sys.argv[1]
galaxyInputFile = sys.argv[2]
galaxyEvalFile = sys.argv[3] # Look up tagLength and encoding
galaxyGenoBamOutput = sys.argv[4]
galaxyAnnoBamOutput = sys.argv[5]
galaxyBwAllOut = sys.argv[6]
galaxyBwUniqOut = sys.argv[7]
galaxyStatsOut = sys.argv[8]
import os, sys
import json
from src.galaxyAnalysis import GalaxyAnalysis
from src.steps.rsemStep import RsemStep
###############
testOnly = False
###############
if sys.argv[1] == '--version':
settingsFile = os.path.split(os.path.abspath(
sys.argv[0]))[0] + '/' + "settingsE3.txt"
if os.path.isfile(
settingsFile): # Unfortunately can't get xml arg for settings
ana = GalaxyAnalysis(settingsFile, 'versions', 'hg19')
ana.readType = 'paired'
RsemStep(ana).writeVersions(allLevels=True) # Prints to stdout
else:
print "Can't locate " + settingsFile
exit(0)
# Command line args:
galaxyBamInput = sys.argv[1]
galaxyEvalFile = sys.argv[2] # Look up tagLength and encoding
galaxyOutGenes = sys.argv[3]
galaxyOutTrans = sys.argv[4]
genome = sys.argv[5]
expType = sys.argv[6]
repNo = sys.argv[7]
anaId = sys.argv[8]
import os, sys
import json
from src.galaxyAnalysis import GalaxyAnalysis
from src.steps.hotspotStep import HotspotStep
###############
testOnly = False
###############
if sys.argv[1] == '--version':
settingsFile = os.path.split(os.path.abspath(
sys.argv[0]))[0] + '/' + "settingsE3.txt"
if os.path.isfile(
settingsFile): # Unfortunately can't get xml arg for settings
ana = GalaxyAnalysis(settingsFile, 'versions', 'hg19')
HotspotStep(ana).writeVersions(allLevels=True) # Prints to stdout
else:
print "Can't locate " + settingsFile
exit(0)
galaxyInputFile = sys.argv[1]
galaxyEvalFile = sys.argv[2] # Look up paired, tagLength
galaxyOutputHot = sys.argv[3]
galaxyOutputPeaks = sys.argv[4]
galaxyOutputDensity = sys.argv[5]
fullOrSample = sys.argv[6]
genome = sys.argv[7]
expType = sys.argv[8]
repNo = sys.argv[9]
anaId = sys.argv[10]
import os, sys
import json
from src.galaxyAnalysis import GalaxyAnalysis
from src.steps.fastqValidationStep import FastqValidationStep
###############
testOnly = False
###############
if sys.argv[1] == '--version':
settingsFile = os.path.split(os.path.abspath(
sys.argv[0]))[0] + '/' + "settingsE3.txt"
if os.path.isfile(
settingsFile): # Unfortunately can't get xml arg for settings
ana = GalaxyAnalysis(settingsFile, 'versions', 'hg19')
FastqValidationStep(ana).writeVersions(
allLevels=True) # Prints to stdout
else:
print "Can't locate " + settingsFile
exit(0)
# Command line args:
galaxyInputFile = sys.argv[1]
galaxyOutputHtml = sys.argv[2]
galaxyOutputDir = sys.argv[3]
galaxyOutSummary = sys.argv[4]
genome = sys.argv[5]
expType = sys.argv[6]
repNo = sys.argv[7]
anaId = sys.argv[8]
import os, sys
import json
from src.galaxyAnalysis import GalaxyAnalysis
from src.steps.bwaAlignmentStep import BwaAlignmentStep
###############
testOnly = False
###############
if sys.argv[1] == '--version':
settingsFile = os.path.split(os.path.abspath(
sys.argv[0]))[0] + '/' + "settingsE3.txt"
if os.path.isfile(
settingsFile): # Unfortunately can't get xml arg for settings
ana = GalaxyAnalysis(settingsFile, 'versions', 'hg19')
ana.readType = 'paired'
BwaAlignmentStep(ana).writeVersions(allLevels=True) # Prints to stdout
else:
print "Can't locate " + settingsFile
exit(0)
# Command line args:
pairedOrUnpaired = sys.argv[1]
galaxyInputFile = sys.argv[2]
galaxyEvalFile = sys.argv[3] # Look up tagLength and encoding
galaxyOutputFile = sys.argv[4]
gender = sys.argv[5]
genome = sys.argv[6]
expType = sys.argv[7]
repNo = sys.argv[8]
# Usage: python(2.7) bamToBigWigE3,py <inputBam> <bamEvalFile> <readFilter> <strand> \
# <galaxyOutSignal> <genome> <expType> <repNo> <analysisId>
import os, sys
import json
from src.galaxyAnalysis import GalaxyAnalysis
from src.steps.bamToBwStep import BamToBwStep
###############
testOnly = False
###############
if sys.argv[1] == '--version':
settingsFile = os.path.split( os.path.abspath( sys.argv[0] ) )[0] + '/' + "settingsE3.txt"
if os.path.isfile( settingsFile ): # Unfortunately can't get xml arg for settings
ana = GalaxyAnalysis(settingsFile, 'versions', 'hg19')
BamToBwStep(ana).writeVersions(allLevels=True) # Prints to stdout
else:
print "Can't locate " + settingsFile
exit(0)
galaxyInputFile = sys.argv[1]
galaxyEvalFile = sys.argv[2]
readFilter = sys.argv[3]
strand = sys.argv[4]
galaxyOutSignal = sys.argv[5]
genome = sys.argv[6]
expType = sys.argv[7]
repNo = sys.argv[8]
anaId = sys.argv[9]
# <genome> <expType> <repNo> <analysisId>
import os, sys
from src.galaxyAnalysis import GalaxyAnalysis
from src.steps.bamEvaluateStep import BamEvaluateStep
###############
testOnly = False
###############
if sys.argv[1] == '--version':
settingsFile = os.path.split(os.path.abspath(
sys.argv[0]))[0] + '/' + "settingsE3.txt"
if os.path.isfile(
settingsFile): # Unfortunately can't get xml arg for settings
ana = GalaxyAnalysis(settingsFile, 'versions', 'hg19')
BamEvaluateStep(ana).writeVersions(allLevels=True) # Prints to stdout
else:
print "Can't locate " + settingsFile
exit(0)
galaxyInputFile = sys.argv[1]
galaxyOutBamEval = sys.argv[2]
genome = sys.argv[3]
expType = sys.argv[4]
repNo = sys.argv[5]
anaId = sys.argv[6]
# No longer command line parameters:
scriptPath = os.path.split(os.path.abspath(sys.argv[0]))[0]
galaxyPath = '/'.join(scriptPath.split('/')[:-2])