# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1450471053 21600
# Node ID 74de1ccc51db1b600941dc54f3fed214457660d1
# Parent  ed07bcc39f6eda216945269a883a2712fa516193
Add GRCh38  hg38,  minor fixes.

diff -r ed07bcc39f6e -r 74de1ccc51db create_reference_dataset.xml
--- a/create_reference_dataset.xml	Wed May 06 14:31:57 2015 -0500
+++ b/create_reference_dataset.xml	Fri Dec 18 14:37:33 2015 -0600
@@ -11,6 +11,7 @@
  <inputs>
   <conditional name="genome">
     <param name="choice" type="select" label="Select a Genome Build">
+      <option value="GRCh38">Homo_sapiens GRCh38  hg38</option>
       <option value="GRCh37">Homo_sapiens GRCh37  hg19</option>
       <option value="NCBI36">Homo_sapiens NCBI36 hg18</option>
       <option value="GRCm38">Mus_musculus GRCm38 mm10</option>
@@ -18,6 +19,20 @@
       <option value="Rnor_5.0">Rattus_norvegicus Rnor_5.0 rn5</option>
       <option value="user_specified">User specified</option>
     </param>
+    <when value="GRCh38">
+      <param name="ensembl_organism" type="hidden" value="homo_sapiens"/>
+      <param name="ensembl_prefix" type="hidden" value="Homo_sapiens"/>
+      <param name="ensembl_genome_version" type="hidden" value="GRCh38"/>
+      <param name="ensembl_version" type="hidden" value="80"/>
+      <param name="ncbi_organism" type="hidden" value="Homo_sapiens"/>
+      <param name="ncbi_prefix" type="hidden" value="Hs"/>
+      <param name="ucsc_genome_version" type="hidden" value="hg38"/>
+      <param name="chromosomes" type="hidden" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y,MT"/>
+      <param name="mt_chromosome" type="hidden" value="MT"/>
+      <param name="gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding"/>
+      <param name="ig_gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene"/>
+      <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
+    </when>
     <when value="GRCh37">
       <param name="ensembl_organism" type="hidden" value="homo_sapiens"/>
       <param name="ensembl_prefix" type="hidden" value="Homo_sapiens"/>
@@ -220,6 +235,9 @@
 gene_sources = $genome.gene_sources
 ig_gene_sources = $genome.ig_gene_sources
 rrna_gene_sources = $genome.rrna_gene_sources
+gene_biotypes = $genome.gene_sources
+ig_gene_biotypes = $genome.ig_gene_sources
+rrna_gene_biotypes = $genome.rrna_gene_sources
 
 #raw
 # Remove temp files
diff -r ed07bcc39f6e -r 74de1ccc51db datamanager_create_reference.xml
--- a/datamanager_create_reference.xml	Wed May 06 14:31:57 2015 -0500
+++ b/datamanager_create_reference.xml	Fri Dec 18 14:37:33 2015 -0600
@@ -17,6 +17,7 @@
  <inputs>
   <conditional name="genome">
     <param name="choice" type="select" label="Select a Genome Build">
+      <option value="GRCh38">Homo_sapiens GRCh38  hg38</option>
       <option value="GRCh37">Homo_sapiens GRCh37  hg19</option>
       <option value="NCBI36">Homo_sapiens NCBI36 hg18</option>
       <option value="GRCm38">Mus_musculus GRCm38 mm10</option>
@@ -24,6 +25,20 @@
       <option value="Rnor_5.0">Rattus_norvegicus Rnor_5.0 rn5</option>
       <option value="user_specified">User specified</option>
     </param>
+    <when value="GRCh38">
+      <param name="ensembl_organism" type="hidden" value="homo_sapiens"/>
+      <param name="ensembl_prefix" type="hidden" value="Homo_sapiens"/>
+      <param name="ensembl_genome_version" type="hidden" value="GRCh38"/>
+      <param name="ensembl_version" type="hidden" value="80"/>
+      <param name="ncbi_organism" type="hidden" value="Homo_sapiens"/>
+      <param name="ncbi_prefix" type="hidden" value="Hs"/>
+      <param name="ucsc_genome_version" type="hidden" value="hg38"/>
+      <param name="chromosomes" type="hidden" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y,MT"/>
+      <param name="mt_chromosome" type="hidden" value="MT"/>
+      <param name="gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding"/>
+      <param name="ig_gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene"/>
+      <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
+    </when>
     <when value="GRCh37">
       <param name="ensembl_organism" type="hidden" value="homo_sapiens"/>
       <param name="ensembl_prefix" type="hidden" value="Homo_sapiens"/>
@@ -221,6 +236,9 @@
 gene_sources = $genome.gene_sources
 ig_gene_sources = $genome.ig_gene_sources
 rrna_gene_sources = $genome.rrna_gene_sources
+gene_biotypes = $genome.gene_sources
+ig_gene_biotypes = $genome.ig_gene_sources
+rrna_gene_biotypes = $genome.rrna_gene_sources
 
 #raw
 # Remove temp files
@@ -228,7 +246,7 @@
 remove_job_temp_files                       = yes
 #end raw
   </configfile>
-  <configfile name="defuse_script">
+  <configfile name="defuse_script">#slurp
 #!/bin/bash
 ## define some things for cheetah proccessing
 #set $amp = chr(38)
diff -r ed07bcc39f6e -r 74de1ccc51db defuse.xml
--- a/defuse.xml	Wed May 06 14:31:57 2015 -0500
+++ b/defuse.xml	Fri Dec 18 14:37:33 2015 -0600
@@ -79,7 +79,7 @@
   <param name="keep_output" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Save DeFuse working directory files" 
          help="The defuse output working directory can be helpful for determining errors that may have occurred during the run, 
                but they require considerable diskspace, and should be deleted and purged when no longer needed."/>
-  <param name="do_get_reads" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Run get_reads on each cluster"/>
+  <param name="do_get_reads" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Run get_reads on each cluster"/>
  </inputs>
  <stdio>
    <exit_code range="1:"  level="fatal" description="Error Running Defuse" />
@@ -570,8 +570,10 @@
 cp $defuse_config $config_txt
 ## make a data_dir  and ln -s the input fastq
 mkdir -p data_dir
-ln -s $left_pairendreads data_dir/reads_1.fastq
-ln -s $right_pairendreads data_dir/reads_2.fastq
+## ln -s "$left_pairendreads" data_dir/reads_1.fastq
+## ln -s "$right_pairendreads" data_dir/reads_2.fastq
+cp "$left_pairendreads" data_dir/reads_1.fastq
+cp "$right_pairendreads" data_dir/reads_2.fastq
 ## ln to output_dir in from_work_dir
 #if $defuse_out.__str__ != 'None':
 mkdir -p $defuse_out.dataset.extra_files_path