# HG changeset patch
# User iracooke
# Date 1399405535 14400
# Node ID 5a74b76d48fcb8388eb2e1e5b6139837b50c0d0b
# Parent  e6b36f17cea160691fcc2062fce1d2025f5db5eb
Uploaded

diff -r e6b36f17cea1 -r 5a74b76d48fc peptide_shaker.xml
--- a/peptide_shaker.xml	Mon May 05 03:44:02 2014 -0400
+++ b/peptide_shaker.xml	Tue May 06 15:45:35 2014 -0400
@@ -158,7 +158,7 @@
         ######################
         ## PeptideShakerCLI ##
         ######################
-        java  -Xmx${java_heapsize}m -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.PeptideShakerCLI
+        java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.PeptideShakerCLI
             -temp_folder `pwd`
             -experiment '${exp_str}'
             -sample '${samp_str}'
@@ -300,9 +300,6 @@
         <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting"
             help="(-mgf_spectrum_count)"/>
 
-        <param name="java_heapsize" type="integer" value="2000" label="Java Memory Limit in mb for PeptideShaker"
-            help="Increase this value if you encounter out of memory errors"/>
-
         <conditional name="species_type">
             <param name="species_type_selector" type="select" optional="true" label="The species type to use for the gene annotation"
                 help="(-species_type)">
@@ -692,7 +689,6 @@
             <param name="input_database" value="tinydb.fasta"/>
             <param name="peak_lists" value="tinyspectra.mgf"/>
             <param name="precursor_ion_tol" value="100"/>
-            <param name="java_heapsize" value="1500"/>
             <param name="fixed_modifications" value="carbamidomethyl c"/>
             <param name="variable_modifications" value="oxidation of m"/>
             <param name="min_charge" value="1"/>