Mercurial > repos > jpayne > snp_pipeline

changeset 45:f58616a4b2f3

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planemo upload commit 2107f35724b3f897c9414be40a9d14663cba9f4d-dirty
author jpayne
date Tue, 07 May 2019 11:44:12 -0400
parents e7cac7790476
children d273453b30bb
files 1_map_reads.xml 2_call_sites.xml 3_filter_regions.xml 4_merge_sites.xml 5_call_consensus.xml 6_merge_vcfs.xml 7_smp_matrix.xml
diffstat 7 files changed, 13 insertions(+), 13 deletions(-) [+]
line wrap: on
line diff
--- 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" &&
--- 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 "
--- 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   &&
--- 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
--- 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)"
--- 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"
--- 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