diff README.rst @ 0:1e8a2c87461a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit ed037d83415937b11a45a4611584e71e99ad1da0
author iuc
date Thu, 23 Mar 2017 10:18:11 -0400
children 570f2b1f3cd9
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Thu Mar 23 10:18:11 2017 -0400
@@ -0,0 +1,18 @@
+Trinity memory usage
+As described on the official Trinity website
+`FAQ <http://trinityrnaseq.sourceforge.net/trinity_faq.html#ques_comp_resources_required>`_,
+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.
+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:
+to lower the maximum memory usage to 2G for example:
+TRINITY_MEM_OPTIONS='--max_memory 2G --bflyHeapSpaceMax 2G'