Mercurial > repos > jjohnson > optitype
diff optitype.xml @ 5:044f0a2e2a36 draft default tip
Uploaded
| author | jjohnson |
|---|---|
| date | Tue, 08 Aug 2017 11:59:10 -0400 |
| parents | 111d2508ab15 |
| children |
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--- a/optitype.xml Mon Aug 07 15:46:02 2017 -0400 +++ b/optitype.xml Tue Aug 08 11:59:10 2017 -0400 @@ -3,10 +3,7 @@ <requirements> <requirement type="package" version="1.2.1">optitype</requirement> </requirements> - <stdio> - <exit_code range="1:" level="fatal" description="Error Running optitype" /> - </stdio> - <command> + <command detect_errors="aggressive"> <![CDATA[ #set $fastqs = [] #if str( $fastq_input.fastq_input_selector ) == "paired": @@ -21,9 +18,8 @@ ln -s "${fastq_input.fastq_input1}" reads.fastq #set $fastqs = ['reads.fastq'] #end if -&& cp \$OPTITYPE_DIR/config.ini . -&& sed "s/path_to_razers3/`which razers3`/" '$optitype_config' | sed "s/threads=16/threads=\$GALAXY_SLOTS/" > config.ini -&& ln -s \$OPTITYPE_DIR/data data +&& RAZERS3=`which razers3` +&& sed "s#path_to_razers3#\$RAZERS3#" '$optitype_config' | sed "s/threads=16/threads=\$GALAXY_SLOTS/" > config.ini #set $input_fq = ' '.join($fastqs) && OptiTypePipeline.py $read_type --input ${' '.join($fastqs)}