Workflow extraction breaks on a bwa step
Hi, I wonder if it's a known problem. I had a quick look through the mailing list, but didn't see any relevant messages: An extraction of a workflow from a history breaks on the bwa step: Error - <type 'exceptions.ValueError'>: invalid literal for int() with base 10: 'False' URL: http://galaxy.hpc.ufl.edu/workflow/build_from_current_history File '/galaxy/run/prod/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/run/prod/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/run/prod/lib/galaxy/web/framework/middleware/remoteuser.py', line 91 in __call__ return self.app( environ, start_response ) File '/galaxy/run/prod/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/run/prod/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/galaxy/run/prod/lib/galaxy/web/controllers/workflow.py', line 1253 in build_from_current_history param_values = job.get_param_values( trans.app ) File '/galaxy/run/prod/lib/galaxy/model/__init__.py', line 263 in get_param_values param_dict = tool.params_from_strings( param_dict, app, ignore_errors=ignore_errors ) File '/galaxy/run/prod/lib/galaxy/tools/__init__.py', line 2041 in params_from_strings return params_from_strings( self.inputs, params, app, ignore_errors ) File '/galaxy/run/prod/lib/galaxy/tools/parameters/__init__.py', line 94 in params_from_strings value = params[key].value_from_basic( value, app, ignore_errors ) File '/galaxy/run/prod/lib/galaxy/tools/parameters/grouping.py', line 462 in value_from_basic rval[ input.name ] = input.value_from_basic( value[ input.name ], app, ignore_errors ) File '/galaxy/run/prod/lib/galaxy/tools/parameters/basic.py', line 136 in value_from_basic return self.to_python( value, app ) File '/galaxy/run/prod/lib/galaxy/tools/parameters/basic.py', line 267 in to_python raise err ValueError: invalid literal for int() with base 10: 'False'
This is a pre-migration bwa. I've not updated this Galaxy instance, yet. Here is a paste of used all options: Will you select a reference genome from your history or use a built-in index? history Select a reference from history 3: StaphAureus_USA300_FPR3757 .fasta Is this library mate-paired? paired Forward FASTQ file 4: FASTQ Groomer on data 1 Reverse FASTQ file 5: FASTQ Groomer on data 2 BWA settings to use full Maximum edit distance (aln -n) 0 Fraction of missing alignments given 2% uniform base error rate (aln -n) 0.04 Maximum number of gap opens (aln -o) 1 Maximum number of gap extensions (aln -e) -1 Disallow long deletion within [value] bp towards the 3'-end (aln -d) 16 Disallow insertion/deletion within [value] bp towards the end (aln -i) 5 Number of first subsequences to take as seed (aln -l) -1 Maximum edit distance in the seed (aln -k) 2 Mismatch penalty (aln -M) 3 Gap open penalty (aln -O) 11 Gap extension penalty (aln -E) 4 Proceed with suboptimal alignments if there are no more than INT equally best hits. (aln -R) None Disable iterative search (aln -N) False Maximum number of alignments to output in the XA tag for reads paired properly (samse/sampe -n) 3 Maximum number of alignments to output in the XA tag for disconcordant read pairs (excluding singletons) (sampe -N) 10 Maximum insert size for a read pair to be considered as being mapped properly (sampe -a) 500 Maximum occurrences of a read for pairing (sampe -o) 100000 Specify the read group for this file? (samse/sampe -r) yes Read group identifier (ID). Each @RG line must have a unique ID. The value of ID is used in the RG tags of alignment records. Must be unique among all read groups in header section. M0004_RG Sequencing center that produced the read (CN) Description (DS) Date that run was produced (DT) Flow order (FO). The array of nucleotide bases that correspond to the nucleotides used for each flow of each read. The array of nucleotide bases that correspond to the key sequence of each read (KS) Library name (LB) M0004_LB Programs used for processing the read group (PG) BWA Predicted median insert size (PI) Platform/technology used to produce the reads (PL) ILLUMINA Platform unit (PU) M0004_PU Sample (SM) M0004_SM Suppress the header in the output SAM file False
Hi Alex, Thanks for reporting this error. This is likely caused by the change in type for one of the parameters used in the tool between when the original job was run and when the workflow extraction was attempted. I've committed a fix in changeset 8169:6ff28399645a and also added a warning message when extracting workflows that have differences in tool versions in changeset 8170:4ce18911037c. If this isn't the likely cause (the original tool run was recent and the extraction was performed with the same tool version) or if you still have the issue after apply the fix, please let us know. Thanks for using Galaxy, Dan On Nov 6, 2012, at 5:51 PM, Oleksandr Moskalenko wrote:
Hi,
I wonder if it's a known problem. I had a quick look through the mailing list, but didn't see any relevant messages:
An extraction of a workflow from a history breaks on the bwa step:
Error - <type 'exceptions.ValueError'>: invalid literal for int() with base 10: 'False' URL: http://galaxy.hpc.ufl.edu/workflow/build_from_current_history File '/galaxy/run/prod/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/run/prod/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/run/prod/lib/galaxy/web/framework/middleware/remoteuser.py', line 91 in __call__ return self.app( environ, start_response ) File '/galaxy/run/prod/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/run/prod/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/galaxy/run/prod/lib/galaxy/web/controllers/workflow.py', line 1253 in build_from_current_history param_values = job.get_param_values( trans.app ) File '/galaxy/run/prod/lib/galaxy/model/__init__.py', line 263 in get_param_values param_dict = tool.params_from_strings( param_dict, app, ignore_errors=ignore_errors ) File '/galaxy/run/prod/lib/galaxy/tools/__init__.py', line 2041 in params_from_strings return params_from_strings( self.inputs, params, app, ignore_errors ) File '/galaxy/run/prod/lib/galaxy/tools/parameters/__init__.py', line 94 in params_from_strings value = params[key].value_from_basic( value, app, ignore_errors ) File '/galaxy/run/prod/lib/galaxy/tools/parameters/grouping.py', line 462 in value_from_basic rval[ input.name ] = input.value_from_basic( value[ input.name ], app, ignore_errors ) File '/galaxy/run/prod/lib/galaxy/tools/parameters/basic.py', line 136 in value_from_basic return self.to_python( value, app ) File '/galaxy/run/prod/lib/galaxy/tools/parameters/basic.py', line 267 in to_python raise err ValueError: invalid literal for int() with base 10: 'False'
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participants (2)
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Daniel Blankenberg -
Oleksandr Moskalenko