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 '''