diff README.rst @ 1:570f2b1f3cd9 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
author iuc
date Fri, 31 Mar 2017 11:37:12 -0400
parents 1e8a2c87461a
children bc4e467da875
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--- a/README.rst	Thu Mar 23 10:18:11 2017 -0400
+++ b/README.rst	Fri Mar 31 11:37:12 2017 -0400
@@ -6,13 +6,25 @@
 trinity requires a large amount of memory to perform the assembly: "roughly
 ~1G of RAM per 1M reads to be assembled"
-By default, this tool is configured to limit the memory consumption to 30G.
+By default, this tool is configured to limit the memory consumption to 1G.
 You might need to lower this limit if the machine(s) executing the jobs have less memory available.
 If you have a lot of reads to assemble and a machine with enough memory, you can increase it.
-In both cases, you can edit the TRINITY_MEM_OPTIONS in the file:
+In both cases, you can set the TRINITY_MAX_MEMORY environmental variable in the destination section of the job_conf.xml file:
-to lower the maximum memory usage to 2G for example:
+<?xml version="1.0"?>
+<!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). -->
+    <plugins>
+        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
+    </plugins>
+    <handlers>
+        <handler id="main"/>
+    </handlers>
+    <destinations>
+        <destination id="local" runner="local">
+            <env id="TRINITY_MAX_MEMORY">1G</env>
+        </destination>
+    </destinations>
-TRINITY_MEM_OPTIONS='--max_memory 2G --bflyHeapSpaceMax 2G'