Mercurial > repos > portiahollyoak > temp

diff temp.xml @ 2:7ac983da5ad8 draft

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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
author portiahollyoak
date Mon, 25 Apr 2016 13:24:46 -0400
parents 39cbc0965e07
children 7c1d80867e88
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--- a/temp.xml	Mon Apr 25 13:15:41 2016 -0400
+++ b/temp.xml	Mon Apr 25 13:24:46 2016 -0400
@@ -14,6 +14,7 @@
 
         ln -f -s "$alignment.metadata.bam_index" "$alignment.element_identifier".bam.bai &&
         ln -f -s "$alignment" "$alignment.element_identifier".bam &&
+        samtools ;
         bash $__tool_directory__/scripts/TEMP_Insertion.sh -i "$alignment.element_identifier".bam -s $__tool_directory__/scripts -r "$consensus_te_seqs" -t "$bed_te_locations" -m 3 -f "$median_insertsize" -c \${GALAXY_SLOTS:-2} &&
         bash $__tool_directory__/scripts/TEMP_Absence.sh -i "$alignment.element_identifier".bam -s $__tool_directory__/scripts -r "$bed_te_locations" -t "$reference2bit" -f 500 -c \${GALAXY_SLOTS:-2} &&
         mv "$alignment.element_identifier".insertion.bp.bed $insertion_bed &&