# HG changeset patch
# User jpayne
# Date 1557243852 14400
# Node ID f58616a4b2f3aebd60429dd1e55ecd410e543367
# Parent  e7cac7790476cc7051709df89d230ff29b702e86
planemo upload commit 2107f35724b3f897c9414be40a9d14663cba9f4d-dirty

diff -r e7cac7790476 -r f58616a4b2f3 1_map_reads.xml
--- a/1_map_reads.xml	Wed Apr 25 16:35:27 2018 -0400
+++ b/1_map_reads.xml	Tue May 07 11:44:12 2019 -0400
@@ -4,7 +4,7 @@
         <requirement type="package" version="1.0.6">bzip2</requirement>
         <requirement type="package" version="2.3.4">bowtie2</requirement>
         <requirement type="package" version="1.5.11">boto3</requirement>
-        <!-- <requirement type="package" version="3.5">python</requirement> -->
+        <requirement type="package" version="3.6">python</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
diff -r e7cac7790476 -r f58616a4b2f3 2_call_sites.xml
--- a/2_call_sites.xml	Wed Apr 25 16:35:27 2018 -0400
+++ b/2_call_sites.xml	Tue May 07 11:44:12 2019 -0400
@@ -7,11 +7,11 @@
         <requirement type="package">picard</requirement>
         <requirement type="package">varscan</requirement>
         <requirement type="package" version="1.5.11">boto3</requirement>
-        <!-- <requirement type="package" version="3.5">python</requirement> -->
+        <requirement type="package" version="3.6">python</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
     export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
-    env &&
+    # env &&
     python $__tool_directory__/snp-cache.py snp_sitecalls 
         "\$(md5sum $input $sample | cut -c -32 | md5sum | cut -c -32)"
         -c "
diff -r e7cac7790476 -r f58616a4b2f3 3_filter_regions.xml
--- a/3_filter_regions.xml	Wed Apr 25 16:35:27 2018 -0400
+++ b/3_filter_regions.xml	Tue May 07 11:44:12 2019 -0400
@@ -5,11 +5,11 @@
         <requirement type="package" version="1.0.6">bzip2</requirement>
         <requirement type="package" version="1.0.1">snp-pipeline</requirement>
         <requirement type="package" version="1.5.11">boto3</requirement>
-        <!-- <requirement type="package" version="3.5">python</requirement> -->
+        <requirement type="package" version="3.6">python</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
-        env &&
+        # env &&
         mkdir -p ./samples/sample/                      &&
         cp $calls ./samples/sample/var.flt.vcf      &&
         echo "\$PWD/samples/sample" > ./alignment.txt   &&
diff -r e7cac7790476 -r f58616a4b2f3 4_merge_sites.xml
--- a/4_merge_sites.xml	Wed Apr 25 16:35:27 2018 -0400
+++ b/4_merge_sites.xml	Tue May 07 11:44:12 2019 -0400
@@ -5,11 +5,11 @@
         <requirement type="package" version="1.2">samtools</requirement>
         <requirement type="package" version="1.0.6">bzip2</requirement>
         <requirement type="package" version="1.0.1">snp-pipeline</requirement>
-        <!-- <requirement type="package" version="3.5">python</requirement> -->
+        <requirement type="package" version="3.6">python</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
-        env &&
+        # env &&
         python $__tool_directory__/snp-wind.py ./
                 #for $call in $calls
                     -n $call.element_identifier -f $call
diff -r e7cac7790476 -r f58616a4b2f3 5_call_consensus.xml
--- a/5_call_consensus.xml	Wed Apr 25 16:35:27 2018 -0400
+++ b/5_call_consensus.xml	Tue May 07 11:44:12 2019 -0400
@@ -4,11 +4,11 @@
         <requirement type="package" version="1.0.6">bzip2</requirement>
         <requirement type="package" version="1.0.1">snp-pipeline</requirement>
         <requirement type="package" version="1.5.11">boto3</requirement>
-        <!-- <requirement type="package" version="3.5">python</requirement> -->
+        <requirement type="package" version="3.6">python</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
-        env &&
+        # 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)"
diff -r e7cac7790476 -r f58616a4b2f3 6_merge_vcfs.xml
--- a/6_merge_vcfs.xml	Wed Apr 25 16:35:27 2018 -0400
+++ b/6_merge_vcfs.xml	Tue May 07 11:44:12 2019 -0400
@@ -5,12 +5,12 @@
         <requirement type="package" version="1.0.6">bzip2</requirement>
         <requirement type="package" version="1.0.1">snp-pipeline</requirement>
         <requirement type="package" version="0.2.5">tabix</requirement>
-        <!-- <requirement type="package" version="3.5">python</requirement> -->
+        <requirement type="package" version="3.6">python</requirement>
         <requirement type="package" version="1.6">htslib</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
-        env &&
+        # env &&
         ls -lah \$CONDA_DEFAULT_ENV/bin &&
         ls -lah \$CONDA_DEFAULT_ENV/lib &&
         python $__tool_directory__/snp-wind.py ./ -p "consensus.vcf"
diff -r e7cac7790476 -r f58616a4b2f3 7_smp_matrix.xml
--- a/7_smp_matrix.xml	Wed Apr 25 16:35:27 2018 -0400
+++ b/7_smp_matrix.xml	Tue May 07 11:44:12 2019 -0400
@@ -5,11 +5,11 @@
         <requirement type="package" version="1.0.6">bzip2</requirement>
         <requirement type="package" version="1.0.1">snp-pipeline</requirement>
         <requirement type="package" version="0.2.5">tabix</requirement>
-        <!-- <requirement type="package" version="3.5">python</requirement> -->
+        <requirement type="package" version="3.6">python</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
-        env &&
+        # 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