diff README.rst @ 0:a21e229da9a1 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Mon Aug 01 14:43:15 2016 -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:
+
+<tool_dependency_dir>/environment_settings/TRINITY_MEM_OPTIONS/iuc/trinity/<hash_string>/env.sh
+
+to lower the maximum memory usage to 2G for example:
+
+TRINITY_MEM_OPTIONS='--max_memory 2G --bflyHeapSpaceMax 2G'