changeset 11:2bc2f0d5e4e1 draft

change compute node selection params

--- a/trinityrnaseq.xml	Thu Apr 03 11:39:01 2014 -0500
+++ b/trinityrnaseq.xml	Thu Apr 03 13:54:44 2014 -0500
@@ -8,7 +8,7 @@
         <requirement type="package" version="1.0.0">bowtie</requirement>
     </requirements>
     <command>
-        Trinity.pl --JM $JM --CPU $CPU
+        Trinity.pl --JM $computenode --CPU \$GALAXY_SLOTS
         
         ## Inputs.
         #if str($inputs.paired_or_single) == "paired":
@@ -36,7 +36,7 @@
 
         ## Additional parameters.
         #if str($additional_params.use_additional) == "yes":
-			--min_kmer_cov $additional_params.min_kmer_cov --max_reads_per_graph $additional_params.max_reads_per_graph --bflyHeapSpaceMax $additional_params.bflyHeapSpaceMax
+			--min_kmer_cov $additional_params.min_kmer_cov --max_reads_per_graph $additional_params.max_reads_per_graph --bflyHeapSpaceMax $computenode
 			#if $additional_params.bfly_opts != 'None':
 				--bfly_opts " $additional_params.bfly_opts "
 			#end if
@@ -50,17 +50,12 @@
         &amp;&amp; \$TRINITY_HOME/util/TrinityStats.pl trinity_out_dir/Trinity.fasta
     </command>
     <inputs>
-        <param name="JM" type="select" label="JM" help="Amount of memory to allocate to Jellyfish for Kmer catalog construction">
-            <option value="1G">1G</option>
-            <option value="10G">10G</option>
-            <option value="50G">50G</option>
-            <option value="100G">100G</option>
-            <option value="200G">200G</option>
-            <option value="500G">500G</option>
-        </param>
-
-        <param name="CPU" type="integer" value="2" min="1" label="CPU" help="Number of CPUs to use by Trinity" />
-
+      <param name="computenode" type="select" label="Compute node" help="Select the size of node needed">
+        <option value="22G">22GB - 8 cores (itasca batch)</option>
+        <option value="62G">62GB - 16 cores</option>
+        <option value="126G">126GB - 16 cores</option>
+        <option value="256G">254GB - 16 cores</option>
+      </param>
 
         <conditional name="inputs">
             <param name="paired_or_single" type="select" label="Paired or Single-end data?">
@@ -101,13 +96,6 @@
                 <param name="min_kmer_cov" type="integer" value="1" min="1" label="inchworm_min_kmer_cov" help="Minimum kmer coverage required by Inchworm for initial contig construction" />
                 <param name="max_reads_per_graph" type="integer" value="20000000" min="10000" label="chrysalis_max_reads_per_graph" help="Maximum number of reads to be anchored within each transcript graph by Chrysalis" />
                 <param name="bfly_opts" type="text" value="None" label="bfly_opts" help="Options to pass on to Butterfly" />
-                <param name="bflyHeapSpaceMax" type="select" label="bflyHeapSpaceMax" help="Java heap space maximum value for Butterfly">
-                    <option value="1G">1G</option>
-                    <option value="2G">2G</option>
-                    <option value="4G" selected="true">4G</option>
-                    <option value="10G">10G</option>
-                    <option value="20G">20G</option>
-                </param>
                <param name="min_contig_length" type="integer" value="200" min="1" label="Minimum Contig Length" help=""/>
             </when>
         </conditional>
@@ -126,8 +114,6 @@
     <tests>
 
         <test>
-            <param name="JM" value="1G"/>
-            <param name="CPU" value="1"/>
             <param name="paired_or_single" value="single"/>
             <param name="input" ftype="fastq" value="reads.left.fq"/>
             <param name="library_type" value="None"/>
@@ -148,8 +134,6 @@
         </test>
 
         <test>
-            <param name="JM" value="1G"/>
-            <param name="CPU" value="1"/>
             <param name="paired_or_single" value="paired"/>
             <param name="left_input" ftype="fastq" value="reads.left.fq"/>
             <param name="right_input" ftype="fastq" value="reads.right.fq"/>