Error = compress.err.$(Process).log
Output = compress.out.$(Process).log
-Log = /tmp/submission-compress.log
+Log = /tmp/submission-compress-%(user)s.log
initialdir = %(initialdir)s
queue
context = {'archivename': make_submission_name(ininame),
'filelist': " ".join(files),
- 'initialdir': os.getcwd()}
+ 'initialdir': os.getcwd(),
+ 'user': os.getlogin()}
condor_script = make_condor_name(ininame, 'archive')
condor_stream = open(condor_script,'w')
script = """Universe = vanilla
Executable = /usr/bin/lftp
-arguments = -c put ../%(archivename)s -o ftp://detrout@encodeftp.cse.ucsc.edu/
+arguments = -c put ../%(archivename)s -o ftp://detrout@encodeftp.cse.ucsc.edu/%(archivename)s
Error = upload.err.$(Process).log
Output = upload.out.$(Process).log
-Log = /tmp/submission-upload.log
+Log = /tmp/submission-upload-%(user)s.log
initialdir = %(initialdir)s
queue
"""
context = {'archivename': make_submission_name(ininame),
- 'initialdir': os.getcwd()}
+ 'initialdir': os.getcwd(),
+ 'user': os.getlogin()}
condor_script = make_condor_name(ininame, 'upload')
condor_stream = open(condor_script,'w')
('*.condor', None),
('*.daf', None),
('*.ddf', None),
- ('*denovo.genes.expr', 'GeneDeNovo'),
- ('*denovo.transcripts.expr','TranscriptDeNovo'),
- ('*novel.genes.expr', 'GeneDeNovo'),
- ('*novel.transcripts.expr', 'TranscriptDeNovo'),
- ('*genes.expr', 'GeneFPKM'),
- ('*transcripts.expr', 'TranscriptFPKM'),
- ('*transcript.expr', 'TranscriptFPKM'),
+ ('cufflinks-0.9.0-genes.expr', 'GeneDeNovo'),
+ ('cufflinks-0.9.0-transcripts.expr', 'TranscriptDeNovo'),
+ ('cufflinks-0.9.0-transcripts.gtf', 'GeneModel'),
+ ('GENCODE-v3c-genes.expr', 'GeneGencV3c'),
+ ('GENCODE-v3c-transcripts.expr', 'TranscriptGencV3c'),
+ ('GENCODE-v4-genes.expr', 'GeneGencV4'),
+ ('GENCODE-v4-transcripts.expr', 'TranscriptGencV4'),
+ ('GENCODE-v4-transcript.expr', 'TranscriptGencV4'),
('*_r1.fastq', 'FastqRd1'),
('*_r2.fastq', 'FastqRd2'),
('*.fastq', 'Fastq'),
"PlusSignal": {"MapAlgorithm": ma},
"MinusSignal": {"MapAlgorithm": ma},
"Signal": {"MapAlgorithm": ma},
+ "GeneModel": {"MapAlgorithm": ma},
"GeneDeNovo": {"MapAlgorithm": ma},
"TranscriptDeNovo": {"MapAlgorithm": ma},
- "GeneDeNovo": {"MapAlgorithm": ma},
- "TranscriptDeNovo": {"MapAlgorithm": ma},
- "GeneFPKM": {"MapAlgorithm": ma},
- "TranscriptFPKM": {"MapAlgorithm": ma},
- "TranscriptFPKM": {"MapAlgorithm": ma},
+ "GeneGencV3c": {"MapAlgorithm": ma},
+ "TranscriptGencV3c": {"MapAlgorithm": ma},
+ "GeneGencV4": {"MapAlgorithm": ma},
+ "TranscriptGencV4": {"MapAlgorithm": ma},
"FastqRd1": {"MapAlgorithm": "NA", "type": "fastq"},
"FastqRd2": {"MapAlgorithm": "NA", "type": "fastq"},
"Fastq": {"MapAlgorithm": "NA", "type": "fastq" },