def execute(choices, galaxyFn=None, username=''):
'''Is called when execute-button is pushed by web-user.
Should print output as HTML to standard out, which will be directed to a results page in Galaxy history. If getOutputFormat is anything else than HTML, the output should be written to the file with path galaxyFn.gtr
If needed, StaticFile can be used to get a path where additional files can be put (e.g. generated image files).
choices is a list of selections made by web-user in each options box.
'''
gi=GenomeInfo(choices[0])
gi.fullName = choices[1]
urls = choices[2].split()
gi.sourceUrls = urls
gi.genomeBuildSource = choices[3]
gi.genomeBuildName = choices[4]
gi.species = choices[5]
gi.speciesTaxonomyUrl = choices[6]
gi.assemblyDetails = choices[7]
gi.privateAccessList = [v.strip() for v in choices[8].replace(os.linesep, ' ').replace(',', ' ').split(' ') if v.find('@')>0]
gi.isPrivate = (choices[9] == 'Owners only')
gi.isExperimental = (choices[10] == 'Experimental only')
gi.ucscClade = choices[11]
gi.ucscGenome = choices[12]
gi.ucscAssembly = choices[13]
gi.store()
return "Updated genome %s." % gi.fullName
def execute(cls, choices, galaxyFn=None, username=''):
'''Is called when execute-button is pushed by web-user.
Should print output as HTML to standard out, which will be directed to a results page in Galaxy history. If getOutputFormat is anything else than HTML, the output should be written to the file with path galaxyFn.gtr
If needed, StaticFile can be used to get a path where additional files can be put (e.g. generated image files).
choices is a list of selections made by web-user in each options box.
'''
gi = GenomeInfo(choices[0])
gi.fullName = choices[1]
urls = choices[2].split()
gi.sourceUrls = urls
gi.genomeBuildSource = choices[3]
gi.genomeBuildName = choices[4]
gi.species = choices[5]
gi.speciesTaxonomyUrl = choices[6]
gi.assemblyDetails = choices[7]
gi.privateAccessList = [
v.strip() for v in choices[8].replace(os.linesep, ' ').replace(
',', ' ').split(' ') if v.find('@') > 0
]
gi.isPrivate = (choices[9] == 'Owners only')
gi.isExperimental = (choices[10] == 'Experimental only')
gi.ucscClade = choices[11]
gi.ucscGenome = choices[12]
gi.ucscAssembly = choices[13]
gi.store()
return "Updated genome %s." % gi.fullName
def execute(cls, choices, galaxyFn=None , username=''):
'''Is called when execute-button is pushed by web-user.
Should print output as HTML to standard out, which will be directed to a results page in Galaxy history.
If needed, StaticFile can be used to get a path where additional files can be put (e.g. generated image files).
choices is a list of selections made by web-user in each options box.
'''
#print 'Executing... with choices %s'%str(choices)
abbrv = choices[0]
name = choices[1]
#Should test that the genome is not in hyperbrowser.
gi = GenomeInfo(abbrv)
if gi.hasOrigFiles():
sys.stderr.write( "Genome "+abbrv+ " is already in the Genomic HyperBrowser. Remove the old first.")
else:
gi.fullName = name
if choices[2] == 'URL':
urls = choices[3].split()
gi.sourceUrls = urls
for url in urls:
try:
GenomeImporter.downloadGenomeSequence(abbrv, url)
except InvalidFormatError:
return
else:
basePath = os.sep.join([NONSTANDARD_DATA_PATH, abbrv] + GenomeInfo.getSequenceTrackName(abbrv))
fnSource = ExternalTrackManager.extractFnFromGalaxyTN(choices[4].split(':'))
fnDest = basePath+'/'+abbrv+'Sequence.fasta'
ensurePathExists(fnDest)
copyfile(fnSource, fnDest)
chrs=GenomeImporter.extractChromosomesFromGenome(abbrv)
gi.sourceChrNames = chrs
gi.installedBy = username
gi.genomeBuildSource = choices[5]
gi.genomeBuildName = choices[6]
gi.species = choices[7]
gi.speciesTaxonomyUrl = choices[8]
gi.assemblyDetails = choices[9]
gi.privateAccessList = [v.strip() for v in choices[10].replace(os.linesep, ' ').replace(',', ' ').split(' ') if v.find('@')>0]
gi.isPrivate = (choices[11] != 'All')
gi.isExperimental = (choices[12] != 'All')
gi.ucscClade = choices[13]
gi.ucscGenome = choices[14]
gi.ucscAssembly = choices[15]
galaxyFile=open(galaxyFn, "w")
galaxyFile.write( 'Genome abbreviation: ' + abbrv + os.linesep)
galaxyFile.write( 'Genome full name: ' + name + os.linesep)
galaxyFile.write( 'Track name: ' + ':'.join(GenomeInfo.getSequenceTrackName(abbrv)) + os.linesep)
galaxyFile.write( 'Temp chromosome names: ' + ' || '.join(chrs) + os.linesep)
#GenomeImporter.saveTempInfo(abbrv, name, chrs)
#print 'Chromosomes: '+chrs
gi.store()
def execute(cls, choices, galaxyFn=None, username=''):
'''Is called when execute-button is pushed by web-user.
Should print output as HTML to standard out, which will be directed to a results page in Galaxy history.
If needed, StaticFile can be used to get a path where additional files can be put (e.g. generated image files).
choices is a list of selections made by web-user in each options box.
'''
#print 'Executing... with choices %s'%str(choices)
abbrv = choices[0]
name = choices[1]
#Should test that the genome is not in hyperbrowser.
gi = GenomeInfo(abbrv)
if gi.hasOrigFiles():
sys.stderr.write(
"Genome " + abbrv +
" is already in the Genomic HyperBrowser. Remove the old first."
)
else:
gi.fullName = name
if choices[2] == 'URL':
urls = choices[3].split()
gi.sourceUrls = urls
for url in urls:
try:
GenomeImporter.downloadGenomeSequence(abbrv, url)
except InvalidFormatError:
return
else:
basePath = GenomeImporter.getBasePathSequence(abbrv)
fnSource = ExternalTrackManager.extractFnFromGalaxyTN(
choices[4].split(':'))
fnDest = basePath + os.path.sep + abbrv + '.fa'
ensurePathExists(fnDest)
copyfile(fnSource, fnDest)
if choices[16] == 'from URL':
urls = choices[3].split()
gi.sourceUrls = urls
for url in urls:
try:
GenomeImporter.downloadGffFile(abbrv, url)
except InvalidFormatError:
return
elif choices[16] == 'from history':
fnSource = ExternalTrackManager.extractFnFromGalaxyTN(
choices[18].split(':'))
fnDest = GenomeImporter.getCollectedPathGFF(abbrv)
ensurePathExists(fnDest)
copyfile(fnSource, fnDest)
chrs = GenomeImporter.extractChromosomesFromGenome(abbrv)
#gi.sourceChrNames = chrs
gi.installedBy = username
gi.genomeBuildSource = choices[5]
gi.genomeBuildName = choices[6]
gi.species = choices[7]
gi.speciesTaxonomyUrl = choices[8]
gi.assemblyDetails = choices[9]
gi.privateAccessList = [
v.strip()
for v in choices[10].replace(os.linesep, ' ').replace(
',', ' ').split(' ') if v.find('@') > 0
]
gi.isPrivate = (choices[11] != 'All')
gi.isExperimental = (choices[12] != 'All')
gi.ucscClade = choices[13]
gi.ucscGenome = choices[14]
gi.ucscAssembly = choices[15]
galaxyFile = open(galaxyFn, "w")
galaxyFile.write('Genome abbreviation: ' + abbrv + os.linesep)
galaxyFile.write('Genome full name: ' + name + os.linesep)
galaxyFile.write('Track name: ' +
':'.join(GenomeInfo.getSequenceTrackName(abbrv)) +
os.linesep)
galaxyFile.write('Temp chromosome names: ' + ' || '.join(chrs) +
os.linesep)
#GenomeImporter.saveTempInfo(abbrv, name, chrs)
#print 'Chromosomes: '+chrs
gi.store()
sys.exit(1)
for track in ProcTrackOptions.getSubtypes('TestGenome',
['GESourceTracks']):
ti = TrackInfo('TestGenome', ['GESourceTracks', track])
ti.trackName = [track]
ti.genome = 'ModelsForExternalTracks'
ti.store()
from quick.util.GenomeInfo import GenomeInfo
from datetime import datetime
gi = GenomeInfo('TestGenome')
gi.fullName = 'TestGenome'
gi.sourceUrls = ['http://hgdownload.cse.ucsc.edu/goldenPath/hg18/chromosomes/chr21.fa.gz', \
'http://hgdownload.cse.ucsc.edu/goldenPath/hg18/chromosomes/chrM.fa.gz']
#gi.sourceChrNames = ['chr21', 'chrM']
gi.installedBy = 'Setup.py'
gi.genomeBuildSource = 'NCBI'
gi.genomeBuildName = 'hg18'
gi.species = 'H**o Sapiens'
gi.speciesTaxonomyUrl = 'http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606'
gi.assemblyDetails = 'Chromosome 21 and M from the hg18 genome, used for testing purposes.'
gi.isPrivate = False
gi.privateAccessList = []
gi.isExperimental = False
gi.timeOfInstallation = datetime.now()
gi.store()
extractTestGenomeAndPreProcess(galaxy_dir)
ti.genome = 'ModelsForExternalTracks'
ti.store()
from quick.util.GenomeInfo import GenomeInfo
from datetime import datetime
gi = GenomeInfo('TestGenome')
gi.fullName = 'TestGenome'
gi.sourceUrls = ['http://hgdownload.cse.ucsc.edu/goldenPath/hg18/chromosomes/chr21.fa.gz', \
'http://hgdownload.cse.ucsc.edu/goldenPath/hg18/chromosomes/chrM.fa.gz']
gi.sourceChrNames = ['chr21', 'chrM']
gi.installedBy = 'Setup.py'
gi.genomeBuildSource = 'NCBI'
gi.genomeBuildName = 'hg18'
gi.species = 'H**o Sapiens'
gi.speciesTaxonomyUrl = 'http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606'
gi.assemblyDetails = 'Chromosome 21 and M from the hg18 genome, used for testing purposes.'
gi.isPrivate = False
gi.privateAccessList = []
gi.isExperimental = False
gi.timeOfInstallation = datetime.now()
gi.store()
def setupHB(galaxyPath='', ignoreVersionChecking=False, installationSetupFn=''):
hbPath = os.path.dirname(os.path.realpath(sys.argv[0]))
os.chdir(hbPath)
checkDependencies()
setupAllInstallationSpecificSetupFiles(hbPath, installationSetupFn)
galaxyPath = getWorkingGalaxyPath(galaxyPath)
if not ignoreVersionChecking:
