Mercurial > repos > peterjc > tmhmm_and_signalp
comparison tools/protein_analysis/tmhmm2.xml @ 19:4cd848c5590b draft
Uploaded v0.2.5 preview 3, use $NSLOTS in the PSORT wrappers.
| author | peterjc |
|---|---|
| date | Thu, 23 May 2013 12:49:18 -0400 |
| parents | af3174637834 |
| children | a538e182fab3 |
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| 18:2b35b5c4b7f4 | 19:4cd848c5590b |
|---|---|
| 3 <!-- If job splitting is enabled, break up the query file into parts --> | 3 <!-- If job splitting is enabled, break up the query file into parts --> |
| 4 <!-- Using 2000 chunks meaning 4 threads doing 500 each is ideal --> | 4 <!-- Using 2000 chunks meaning 4 threads doing 500 each is ideal --> |
| 5 <parallelism method="basic" split_inputs="fasta_file" split_mode="to_size" split_size="2000" merge_outputs="tabular_file"></parallelism> | 5 <parallelism method="basic" split_inputs="fasta_file" split_mode="to_size" split_size="2000" merge_outputs="tabular_file"></parallelism> |
| 6 <command interpreter="python"> | 6 <command interpreter="python"> |
| 7 tmhmm2.py "\$NSLOTS" $fasta_file $tabular_file | 7 tmhmm2.py "\$NSLOTS" $fasta_file $tabular_file |
| 8 ##I want the number of threads to be a Galaxy config option... | |
| 8 ##Set the number of threads in the runner entry in universe_wsgi.ini | 9 ##Set the number of threads in the runner entry in universe_wsgi.ini |
| 9 ##which (on SGE at least) will set the $NSLOTS environment variable. | 10 ##which (on SGE at least) will set the $NSLOTS environment variable. |
| 10 ##If the environment variable isn't set, get "", and defaults to one. | 11 ##If the environment variable isn't set, get "", and the python wrapper |
| 12 ##defaults to four threads. | |
| 11 </command> | 13 </command> |
| 12 <stdio> | 14 <stdio> |
| 13 <!-- Anything other than zero is an error --> | 15 <!-- Anything other than zero is an error --> |
| 14 <exit_code range="1:" /> | 16 <exit_code range="1:" /> |
| 15 <exit_code range=":-1" /> | 17 <exit_code range=":-1" /> |