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changeset 40:02733e77f84f

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planemo upload commit 7f6183b769772449fbcee903686b8d5ec5b7439f-dirty
author jpayne
date Wed, 14 Feb 2018 13:10:23 -0500
parents 1fe3b14f7f1b
children 9022b00a9198
files 1_map_reads.xml 2_call_sites.xml 3_filter_regions.xml 4_merge_sites.xml 5_call_consensus.xml 7_smp_matrix.xml
diffstat 6 files changed, 11 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- a/1_map_reads.xml	Wed Feb 14 13:06:44 2018 -0500
+++ b/1_map_reads.xml	Wed Feb 14 13:10:23 2018 -0500
@@ -7,6 +7,7 @@
         <!-- <requirement type="package" version="3.5">python</requirement> -->
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
+        export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
         env &&
         #if $reads.reads_select == 'collection'
             export files="$reads.coll.forward $reads.coll.reverse"          &&
--- a/2_call_sites.xml	Wed Feb 14 13:06:44 2018 -0500
+++ b/2_call_sites.xml	Wed Feb 14 13:10:23 2018 -0500
@@ -10,6 +10,8 @@
         <!-- <requirement type="package" version="3.5">python</requirement> -->
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
+    export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
+    env &&
     python $__tool_directory__/snp-cache.py snp_sitecalls 
         "\$(md5sum $input $sample | cut -c -32 | md5sum | cut -c -32)"
         -c "
--- a/3_filter_regions.xml	Wed Feb 14 13:06:44 2018 -0500
+++ b/3_filter_regions.xml	Wed Feb 14 13:10:23 2018 -0500
@@ -8,6 +8,8 @@
         <!-- <requirement type="package" version="3.5">python</requirement> -->
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
+        export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
+        env &&
         mkdir -p ./samples/sample/                      &&
         cp $calls ./samples/sample/var.flt.vcf      &&
         echo "\$PWD/samples/sample" > ./alignment.txt   &&
--- a/4_merge_sites.xml	Wed Feb 14 13:06:44 2018 -0500
+++ b/4_merge_sites.xml	Wed Feb 14 13:10:23 2018 -0500
@@ -8,6 +8,8 @@
         <!-- <requirement type="package" version="3.5">python</requirement> -->
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
+        export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
+        env &&
         python $__tool_directory__/snp-wind.py ./
                 #for $call in $calls
                     -n $call.element_identifier -f $call
--- a/5_call_consensus.xml	Wed Feb 14 13:06:44 2018 -0500
+++ b/5_call_consensus.xml	Wed Feb 14 13:10:23 2018 -0500
@@ -7,6 +7,8 @@
         <!-- <requirement type="package" version="3.5">python</requirement> -->
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
+        export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
+        env &&
         #set $identifier = $call_pileup.name.split(' ')[0]
         python $__tool_directory__/snp-cache.py snp_consenus_calls
             "\$(md5sum $snps $calls $call_pileup | cut -c -32 | md5sum | cut -c -32)"
--- a/7_smp_matrix.xml	Wed Feb 14 13:06:44 2018 -0500
+++ b/7_smp_matrix.xml	Wed Feb 14 13:10:23 2018 -0500
@@ -8,6 +8,8 @@
         <!-- <requirement type="package" version="3.5">python</requirement> -->
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
+        export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
+        env &&
         python $__tool_directory__/snp-wind.py ./ -p "consensus.fasta"
             #for $fa in sorted($cons, key=lambda f: f.element_identifier)
                 -n $fa.element_identifier -f $fa