I am defining some tools for my own galaxy installation and I would like to
know if there is a more elegant solution for redirecting error output than
the one in the next config file:

<tool id="gatk_mio" name="calling with gatk">
  <description>calling with gatk</description>
      ln -s "${input}" input.bam ;
      samtools index input.bam;
      java -jar
/home/ralonso/software/GenomeAnalysisTK-3.3-0/GenomeAnalysisTK.jar -T
UnifiedGenotyper -R
/home/ralonso/BiB/Galaxy/data/Cclementina_v1.0_scaffolds.fa -I input.bam -o
$output *2&gt;/dev/null;*

    <param format="bam" name="input" type="data" label="bam"/>
      <data format="vcf" name="output" />



Best regards

many thanks

Roberto Alonso
Functional Genomics Unit
Bioinformatics and Genomics Department
Prince Felipe Research Center (CIPF)
C./Eduardo Primo Yúfera (Científic), nº 3
(junto Oceanografico)
46012 Valencia, Spain
Tel: +34 963289680 Ext. 1021
Fax: +34 963289574
E-Mail: ralo...@cipf.es
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

To search Galaxy mailing lists use the unified search at:

Reply via email to