# HG changeset patch
# User wolma
# Date 1465686644 14400
# Node ID c464064666258deb66c1168d29ea311637ebe9f1
# Parent  aba6d9b1c1f1f2d475f25ee4b56d6989059298e0
Uploaded

diff -r aba6d9b1c1f1 -r c46406466625 README.md
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Sat Jun 11 19:10:44 2016 -0400
@@ -0,0 +1,9 @@
+# README #
+
+This is the development repository for the **mimodd** package for Galaxy toolsheds.
+
+### What is this about? ###
+
+[MiModD](http://www.celegans.de/mimodd) is an integrated solution for mapping-by-sequencing analysis of whole-genome sequencing (WGS) data from laboratory model organisms. It enables geneticists to identify the genetic mutations present in an organism starting from just raw WGS read data and a reference genome without the help of a trained bioinformatician. Its linkage analysis engine NacreousMap represents a further development of and can be used as a drop-in replacement for CloudMap.
+
+The Galaxy Tool Shed installer for MiModD lets Galaxy server admins perform a one-click installation of a fully functional version of the software with no requirements other than gcc/c++ and the make utility preinstalled. For further information about installing MiModD from a Galaxy Tool Shed please refer to the [MiModD User Guide](http://mimodd.readthedocs.io/en/latest/INSTALL.html#tool-shed-installation).
\ No newline at end of file
diff -r aba6d9b1c1f1 -r c46406466625 annotate_variants.xml
--- a/annotate_variants.xml	Fri Apr 29 06:01:46 2016 -0400
+++ b/annotate_variants.xml	Sat Jun 11 19:10:44 2016 -0400
@@ -4,9 +4,9 @@
     <import>toolshed_macros.xml</import>
   </macros>
   <expand macro="requirements"/>
-  <version_command>mimodd version -q</version_command>
+  <version_command>python3 -m MiModD version -q</version_command>
   <command>
-  	mimodd annotate
+  	python3 -m MiModD annotate
 	
 	"$inputfile"
 	
diff -r aba6d9b1c1f1 -r c46406466625 bamsort.xml
--- a/bamsort.xml	Fri Apr 29 06:01:46 2016 -0400
+++ b/bamsort.xml	Sat Jun 11 19:10:44 2016 -0400
@@ -4,9 +4,9 @@
     <import>toolshed_macros.xml</import>
   </macros>
   <expand macro="requirements"/>
-  <version_command>mimodd version -q</version_command>
+  <version_command>python3 -m MiModD version -q</version_command>
   <command>
-	mimodd sort "$input.ifile" -o "$output" --iformat $input.iformat --oformat $oformat $by_name
+	python3 -m MiModD sort "$input.ifile" -o "$output" --iformat $input.iformat --oformat $oformat $by_name
   </command>
   
   <inputs>
diff -r aba6d9b1c1f1 -r c46406466625 cloudmap.xml
--- a/cloudmap.xml	Fri Apr 29 06:01:46 2016 -0400
+++ b/cloudmap.xml	Sat Jun 11 19:10:44 2016 -0400
@@ -1,9 +1,9 @@
 <tool id="nacreousmap" name="NacreousMap" version="0.1.7.2">
   <description>Map causative mutations by multi-variant linkage analysis.</description>
   <expand macro="requirements_rplot"/>
-  <version_command>mimodd version -q</version_command>
+  <version_command>python3 -m MiModD version -q</version_command>
   <command>
-    mimodd map ${opt.mode} "${opt.source.ifile}"
+    python3 -m MiModD map ${opt.mode} "${opt.source.ifile}"
     #if $str($opt.source.sample):
       -m "${opt.source.sample}"
     #end if
diff -r aba6d9b1c1f1 -r c46406466625 convert.xml
--- a/convert.xml	Fri Apr 29 06:01:46 2016 -0400
+++ b/convert.xml	Sat Jun 11 19:10:44 2016 -0400
@@ -4,7 +4,7 @@
     <import>toolshed_macros.xml</import>
   </macros>
   <expand macro="requirements"/>
-  <version_command>mimodd version -q</version_command>
+  <version_command>python3 -m MiModD version -q</version_command>
   <command>
   #if $str($mode.split_on_rgs) or $str($mode.oformat)=="fastq" or $str($mode.oformat)=="gz":
     echo "Your input data is now getting processed by MiModD. The output will be split into several files based on the read groups found in the input.\nThis history item will remain in the busy state until the job is finished.\nAfter the job is showing as finished, Galaxy will start adding the results files to your history one by one.\n\nThis may take a while to complete! \n\nYou should refresh your history to see if new files have arrived.\n\nThis message is for your information only and can be deleted from the history once the job has finished." > $output_split_on_read_groups;
@@ -12,7 +12,7 @@
     mkdir converted_data;
   #end if
   
-	mimodd convert 
+	python3 -m MiModD convert 
  
   	#for $i in $mode.input_list
 	    "${i.file1}"
diff -r aba6d9b1c1f1 -r c46406466625 covstats.xml
--- a/covstats.xml	Fri Apr 29 06:01:46 2016 -0400
+++ b/covstats.xml	Sat Jun 11 19:10:44 2016 -0400
@@ -4,9 +4,9 @@
     <import>toolshed_macros.xml</import>
   </macros>
   <expand macro="requirements"/>
-  <version_command>mimodd version -q</version_command>
+  <version_command>python3 -m MiModD version -q</version_command>
   <command> 
-	mimodd covstats "$ifile" --ofile "$output_vcf"
+	python3 -m MiModD covstats "$ifile" --ofile "$output_vcf"
   </command>
 
   <inputs>
diff -r aba6d9b1c1f1 -r c46406466625 deletion_predictor.xml
--- a/deletion_predictor.xml	Fri Apr 29 06:01:46 2016 -0400
+++ b/deletion_predictor.xml	Sat Jun 11 19:10:44 2016 -0400
@@ -4,9 +4,9 @@
     <import>toolshed_macros.xml</import>
   </macros>
   <expand macro="requirements"/>
-  <version_command>mimodd version -q</version_command>
+  <version_command>python3 -m MiModD version -q</version_command>
   <command>
-    mimodd delcall
+    python3 -m MiModD delcall
     #for $l in $list_input
         "${l.bamfile}"
     #end for
diff -r aba6d9b1c1f1 -r c46406466625 fileinfo.xml
--- a/fileinfo.xml	Fri Apr 29 06:01:46 2016 -0400
+++ b/fileinfo.xml	Sat Jun 11 19:10:44 2016 -0400
@@ -4,9 +4,9 @@
     <import>toolshed_macros.xml</import>
   </macros>
   <expand macro="requirements"/>
-  <version_command>mimodd version -q</version_command>
+  <version_command>python3 -m MiModD version -q</version_command>
   <command>
-    mimodd info "$ifile" -o "$outputfile" --verbose --oformat $oformat
+    python3 -m MiModD info "$ifile" -o "$outputfile" --verbose --oformat $oformat
   </command>
 
   <inputs>
diff -r aba6d9b1c1f1 -r c46406466625 reheader.xml
--- a/reheader.xml	Fri Apr 29 06:01:46 2016 -0400
+++ b/reheader.xml	Sat Jun 11 19:10:44 2016 -0400
@@ -1,10 +1,10 @@
 <tool id="reheader" name="Reheader BAM file" version="0.1.7.2">
   <description>From a BAM file generate a new file with the original header (if any) replaced or modified by that found in a second SAM file</description>
   <expand macro="requirements"/>
-  <version_command>mimodd version -q</version_command>
+  <version_command>python3 -m MiModD version -q</version_command>
   <command>    
     #if ($str($rg.treat_rg) != "ignore" and $str($rg.rginfo.source) == "from_form") or $str($co.treat_co) != "ignore":
-      mimodd header 
+      python3 -m MiModD header 
       #if $str($rg.treat_rg) != "ignore" and $str($rg.rginfo.source) == "from_form":
         #for $rginfo in $rg.rginfo.rg
       	  #if $str($rginfo.source_id):
@@ -60,7 +60,7 @@
 	  #end if
       | 
     #end if
-    mimodd reheader "$inputfile" --sq ignore
+    python3 -m MiModD reheader "$inputfile" --sq ignore
     --rg ${rg.treat_rg}
     #if $str($rg.treat_rg) != "ignore":
       #if $str($rg.rginfo.source) == "from_file":
diff -r aba6d9b1c1f1 -r c46406466625 sam_header.xml
--- a/sam_header.xml	Fri Apr 29 06:01:46 2016 -0400
+++ b/sam_header.xml	Sat Jun 11 19:10:44 2016 -0400
@@ -4,9 +4,9 @@
     <import>toolshed_macros.xml</import>
   </macros>
   <expand macro="requirements"/>
-  <version_command>mimodd version -q</version_command>
+  <version_command>python3 -m MiModD version -q</version_command>
   <command>
-  	mimodd header
+  	python3 -m MiModD header
 
 	--rg-id "$rg_id"
 	--rg-sm "$rg_sm"
diff -r aba6d9b1c1f1 -r c46406466625 snap_caller.xml
--- a/snap_caller.xml	Fri Apr 29 06:01:46 2016 -0400
+++ b/snap_caller.xml	Sat Jun 11 19:10:44 2016 -0400
@@ -4,9 +4,9 @@
     <import>toolshed_macros.xml</import>
   </macros>
   <expand macro="requirements"/>
-  <version_command>mimodd version -q</version_command>
+  <version_command>python3 -m MiModD version -q</version_command>
   <command> 
-	mimodd snap-batch -s
+	python3 -m MiModD snap-batch -s
 	## SNAP calls (considering different cases)
 
 	#for $i in $datasets
diff -r aba6d9b1c1f1 -r c46406466625 snp_caller_caller.xml
--- a/snp_caller_caller.xml	Fri Apr 29 06:01:46 2016 -0400
+++ b/snp_caller_caller.xml	Sat Jun 11 19:10:44 2016 -0400
@@ -4,9 +4,9 @@
     <import>toolshed_macros.xml</import>
   </macros>
   <expand macro="requirements"/>
-  <version_command>mimodd version -q</version_command>
+  <version_command>python3 -m MiModD version -q</version_command>
   <command>
-	mimodd varcall
+	python3 -m MiModD varcall
 
 	"$ref_genome"
 	#for $l in $list_input
diff -r aba6d9b1c1f1 -r c46406466625 snpeff_genomes.xml
--- a/snpeff_genomes.xml	Fri Apr 29 06:01:46 2016 -0400
+++ b/snpeff_genomes.xml	Sat Jun 11 19:10:44 2016 -0400
@@ -4,9 +4,9 @@
     <import>toolshed_macros.xml</import>
   </macros>
   <expand macro="requirements"/>
-  <version_command>mimodd version -q</version_command>
+  <version_command>python3 -m MiModD version -q</version_command>
   <command>
-  	mimodd snpeff-genomes -o "$outputfile"
+  	python3 -m MiModD snpeff-genomes -o "$outputfile"
   </command>
   <outputs>
     <data name="outputfile" format="tabular" />
diff -r aba6d9b1c1f1 -r c46406466625 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Apr 29 06:01:46 2016 -0400
+++ b/tool_dependencies.xml	Sat Jun 11 19:10:44 2016 -0400
@@ -4,13 +4,13 @@
     <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
   <package name="R" version="3.2.1">
-    <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="d9f7d84125b7" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
   <package name="readline" version="6.3">
     <repository changeset_revision="ca1a9400d4e1" name="package_readline_6_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
   <package name="python3" version="3.4">
-    <repository changeset_revision="5e5653b689ca" name="package_python_3_4_x_lean" owner="wolma" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="83407422ec16" name="package_python_3_4_x_lean" owner="wolma" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
     
   <package name="mimodd" version="0.1.7.2">
@@ -18,7 +18,7 @@
       <actions>
       <!-- prepare a python3 venv to install into -->
         <action type="set_environment_for_install">
-          <repository changeset_revision="5e5653b689ca" name="package_python_3_4_x_lean" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu">
+          <repository changeset_revision="83407422ec16" name="package_python_3_4_x_lean" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu">
             <package name="python3" version="3.4" />
           </repository>
         </action>
@@ -50,7 +50,7 @@
           <repository changeset_revision="ca1a9400d4e1" name="package_readline_6_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
             <package name="readline" version="6.3" />
           </repository>
-          <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+          <repository changeset_revision="d9f7d84125b7" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
             <package name="R" version="3.2.1" />
           </repository>
         </action>
@@ -77,8 +77,11 @@
         
       <!-- configure environment -->
         <action type="set_environment">
-          <!-- make the mimodd entry script discoverable -->
-          <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/MiModD_venv/bin</environment_variable>
+          <!-- to make MiModD accessible it is sufficient to simply add the 
+               venvs site-packages directory to PYTHONPATH; 
+               SITE_PACKAGES_RELPATH will be made available by the python3 
+               package, which all MiModD toolwrappers require -->
+          <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/MiModD_venv/$SITE_PACKAGES_RELPATH</environment_variable>
         </action>
       </actions>
     </install>
diff -r aba6d9b1c1f1 -r c46406466625 toolshed_macros.xml
--- a/toolshed_macros.xml	Fri Apr 29 06:01:46 2016 -0400
+++ b/toolshed_macros.xml	Sat Jun 11 19:10:44 2016 -0400
@@ -1,16 +1,16 @@
 <macros>
   <xml name="requirements">
     <requirements>
+      <requirement type="package" version="3.4">python3</requirement>
       <requirement type="package" version="0.1.7.2">mimodd</requirement>
-      <requirement type="package" version="3.4">python3</requirement>
     </requirements>
   </xml>
   <xml name="requirements_rplot">
     <requirements>
+      <requirement type="package" version="3.4">python3</requirement>
       <requirement type="package" version="0.1.7.2">mimodd</requirement>
-      <requirement type="package" version="3.4">python3</requirement>
       <requirement type="package" version="3.2.1">R</requirement>
       <requirement type="package" version="6.3">readline</requirement>
     </requirements>
   </xml>
-</macros>
\ No newline at end of file
+</macros>
diff -r aba6d9b1c1f1 -r c46406466625 varextract.xml
--- a/varextract.xml	Fri Apr 29 06:01:46 2016 -0400
+++ b/varextract.xml	Sat Jun 11 19:10:44 2016 -0400
@@ -4,9 +4,9 @@
     <import>toolshed_macros.xml</import>
   </macros>
   <expand macro="requirements"/>
-  <version_command>mimodd version -q</version_command>
-  <command> 
-	mimodd varextract "$ifile"
+  <version_command>python3 -m MiModD version -q</version_command>
+  <command>
+	python3 -m MiModD varextract "$ifile"
 	#if $len($sitesinfo)
 	    -p
 	    #for $source in $sitesinfo
diff -r aba6d9b1c1f1 -r c46406466625 vcf_filter.xml
--- a/vcf_filter.xml	Fri Apr 29 06:01:46 2016 -0400
+++ b/vcf_filter.xml	Sat Jun 11 19:10:44 2016 -0400
@@ -4,9 +4,9 @@
     <import>toolshed_macros.xml</import>
   </macros>
   <expand macro="requirements"/>
-  <version_command>mimodd version -q</version_command>
+  <version_command>python3 -m MiModD version -q</version_command>
   <command> 
-	mimodd vcf-filter
+	python3 -m MiModD vcf-filter
 	"$inputfile"
 	-o "$outputfile"
 	#if len($datasets):