Mercurial > repos > greg > assembly_post_processor

changeset 102:62df33ce7eaa draft

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Uploaded
author greg
date Thu, 07 Dec 2017 15:23:07 -0500
parents 7ca8ab9a46e9
children 6b071ce71267
files assembly_post_processor.xml
diffstat 1 files changed, 4 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/assembly_post_processor.xml	Thu Dec 07 10:28:43 2017 -0500
+++ b/assembly_post_processor.xml	Thu Dec 07 15:23:07 2017 -0500
@@ -35,6 +35,10 @@
 #end if
 --num_threads \${GALAXY_SLOTS:-4}
 &>proc.log
+&& if [[ $? -ne 0 ]]; then
+    exec &>/dev/tty;
+    cat proc.log >&2;
+fi
 && mv $output_dir/transcripts.cds '$output_cds'
 && mv $output_dir/transcripts.pep '$output_pep'
 && mv $output_dir/transcripts.cleaned.cds '$output_cleaned_cds'
@@ -48,9 +52,6 @@
         && mv $output_dir/transcripts.cleaned.nr.pep '$output_cleaned_nr_pep'
     #end if
 #end if
-&& if [[ $? -ne 0 ]]; then
-  cat proc.log >&2;
-fi
     ]]></command>
     <inputs>
         <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/>