def main():
#print "running"
filename = sys.argv[1]
params = hg.fileToParams(filename)
batch = params['batch'].split('\n')
genome = params['dbkey']
sys.stdout = open(filename, "w", 0)
username = params['userEmail'] if params.has_key('userEmail') else ''
GalaxyInterface.runBatchLines(batch, filename, genome, username)
def main():
#print "running"
tool = sys.argv[1]
filename = sys.argv[2]
filename = os.path.realpath(filename)
params = hg.fileToParams(filename)
titan_workdir = '/xanadu/project/rrresearch/galaxy_developer/database/tmp/'
titan_filename = titan_workdir + os.path.basename(filename)
shutil.copy(filename, titan_filename)
print titan_filename
#os.system('ssh titan.uio.no sbatch hb-titan/batchrun.sh ' + filename)
filename_log = titan_filename + '.log'
filename_err = titan_filename + '.err'
filename_done = titan_filename + '.done'
log = open(filename_log, "w+")
sbatch_script = '/xanadu/home/morj/hb-titan/'+tool+'.sh'
sbatch = ['ssh', 'titan.uio.no', 'sbatch --output='+filename_log+' --error='+filename_err + ' ' + sbatch_script + ' ' + titan_filename]
#sbatch = ['/site/bin/sbatch', '--output='+filename_log, '--error='+filename_err, sbatch_script, filename]
print sbatch
submitproc = subprocess.Popen(sbatch, stderr=log)
submitproc.wait()
log.seek(0)
line = log.readline()
log.close()
words = line.split(' ')
if len(words) > 4:
job_id = words[4].strip()
else:
job_id = None
print line, job_id
time.sleep(10)
while (not os.path.exists(filename_done)):
time.sleep(10)
#os.unlink(filename + '.done')
shutil.copy(titan_filename, filename)
log = open(filename_log, "r")
for line in log:
print line
log.close()
err = open(filename_err, "r")
for line in err:
print >> sys.stderr, line
err.close()
def main():
filename = sys.argv[1]
output = filename
params = hg.fileToParams(filename)
file_path = params.get('file_path')
genome = params.get('dbkey')
track1Name = params.get('track1')
method = params.get('method')
if method == 'binfile':
binfile = params.get('binfile').split(',')
binspec = hg.getDataFilePath(file_path, binfile[1])
regspec = binfile[2]
elif method != 'auto':
regspec = method
binspec = params.get(method)
else:
regspec = params.get('region', '*')
binspec = params.get('binsize', '*')
intensityname = params.get('intensityname') if params.has_key('intensityname') else None
track1File = params.get('track1file')
if track1Name == 'galaxy' and track1File != None:
tfa = track1File.split(',')
tracks1 = ['galaxy', tfa[2], hg.getDataFilePath(file_path, tfa[1]), unquote(tfa[3])]
else:
tracks1 = track1Name.split(':')
if intensityname not in [None, '']:
intensityname = intensityname.split(':')
else:
intensityname = 'galaxy:hbfunction:'+filename+':Create intensity track'
numctrltracks = int(params.get('numctrltracks'))
ctrltracks = []
for num in range(numctrltracks):
trackName = params.get('track' + str(num+2))
trackFile = params.get('track' + str(num+2) + 'file')
if trackName == 'galaxy' and trackFile != None:
tfa = trackFile.split(',')
track = ['galaxy', tfa[2], hg.getDataFilePath(file_path, tfa[1]), unquote(tfa[3])]
else:
track = trackName.split(':')
ctrltracks.append(track)
sys.stdout = open(output, "w", 0)
#print 'GalaxyInterface.createIntensityTrack', (tracks1, ctrltracks, intensityname, region, binSize, genome)
GalaxyInterface.createIntensityTrack(tracks1, ctrltracks, intensityname, regspec, binspec, genome, output)
def main():
os.umask(0002)
filename = sys.argv[1]
params = fileToParams(filename)
username = params['userEmail'] if params.has_key('userEmail') else ''
genome = params['dbkey']
integratedTrackName = params['integratedname'].split(':')
private = not params['access_public'] if params.has_key('access_public') else True
historyTrackName = trackNameForHistoryItem('historyitem', params)
sys.stdout = open(filename, "w", 0)
#print 'GalaxyInterface.integrateTrackFromHistory',(genome, historyTrackName, integratedTrackName, private, username)
GalaxyInterface.integrateTrackFromHistory(genome, historyTrackName, integratedTrackName, username)
def main():
os.umask(0002)
filename = sys.argv[1]
params = fileToParams(filename)
username = params['userEmail'] if params.has_key('userEmail') else ''
genome = params['dbkey']
integratedTrackName = params['integratedname'].split(':')
private = not params['access_public'] if params.has_key('access_public') else True
historyTrackName = trackNameForHistoryItem('historyitem', params)
sys.stdout = open(filename, "w", 0)
#print 'GalaxyInterface.integrateTrackFromHistory',(genome, historyTrackName, integratedTrackName, private, username)
GalaxyInterface.integrateTrackFromHistory(genome, historyTrackName, integratedTrackName, privateAccess=private, username=username)
def main():
#print "running"
filename = sys.argv[1]
params = hg.fileToParams(filename)
trackIn = params['intrack'].split(':')
trackOut = params['outtrack'].split(':')
methodLines = params['method'].split('\n')
segLength = params['min_length']
genome = params['dbkey']
username = params['userEmail'] if params.has_key('userEmail') else ''
print 'GalaxyInterface.createSegmentation', (genome, trackIn, trackOut, methodLines, segLength)
sys.stdout = open(filename, "w", 0)
GalaxyInterface.createSegmentation(genome, trackIn, trackOut, methodLines, segLength, username)
def main():
filename = sys.argv[1]
params = hg.fileToParams(filename)
genome = params['dbkey']
inTrackName = params['track1']
trackName = params['customname']
binSize = params['customwinsize']
method = params['customfunction']
output = filename
inTracks = None
if inTrackName:
inTracks = inTrackName.split(':')
track = trackName.split(':')
#funcStr = restore_text(method).replace('XX', '\n')
funcStr = method
print 'GalaxyInterface.createCustomTrack ',(genome, inTracks, track, binSize, funcStr)
sys.stdout = open(output, "w", 0)
GalaxyInterface.createCustomTrack(genome, inTracks, track, binSize, funcStr)
def main():
#print "running"
filename = sys.argv[1]
params = hg.fileToParams(filename)
batch = params['batch'].split('\n')
genome = params['dbkey']
sys.stdout = open(filename, "w", 0)
try:
print '''
<html>
<head>
<link href="/static/style/base.css" rel="stylesheet" type="text/css" />
<script type="text/javascript" src="/static/scripts/jquery.js"></script>
<script type="text/javascript">
var done = false;
function toggleDebug() {
$(".debug").toggle();
return false;
}
</script>
</head>
<body>
<p style="text-align:right"><a href="#" onclick="return toggleDebug()">Toggle debug</a></p>
'''
#print '''<script type="text/javascript" src="/static/scripts/jquery.js"></script>
# <script type="text/javascript">
# var done = false;
# var job = { filename: "%s", pid: %d };
#
# var dead = document.cookie.indexOf("dead=" + job.pid) >= 0 ? true : false;
#
# function check_job() {
# if (!done) {
# if (!dead) {
# $.getJSON("/hyper/check_job", job, function (status) {
# if (status.running) {
# location.reload(true);
# } else {
# document.cookie = "dead=" + job.pid;
# location.reload(true);
# }
# }
# );
# } else {
# alert("This job did not finish successfully: " + job.filename);
# }
# }
# }
#
# setTimeout("if (!done) check_job();", 2000);
# </script>
#''' % (filename, os.getpid())
#print 'GalaxyInterface.runBatchLines', (batch, filename, genome)
GalaxyInterface.runBatchLines(batch, filename, genome)
finally:
print '''
