Mercurial > repos > iuc > trinity_run_de_analysis

annotate README.rst @ 0:0b06ab8d5f88 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
author iuc
date Mon, 01 Aug 2016 11:52:05 -0400
parents
children 2a30d7dfe8de
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
0b06ab8d5f88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
iuc
parents:
diff changeset
1 Trinity memory usage
0b06ab8d5f88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
iuc
parents:
diff changeset
2 ====================
0b06ab8d5f88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
iuc
parents:
diff changeset
3
0b06ab8d5f88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
iuc
parents:
diff changeset
4 As described on the official Trinity website
0b06ab8d5f88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
iuc
parents:
diff changeset
5 `FAQ <http://trinityrnaseq.sourceforge.net/trinity_faq.html#ques_comp_resources_required>`_,
0b06ab8d5f88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
iuc
parents:
diff changeset
6 trinity requires a large amount of memory to perform the assembly: "roughly
0b06ab8d5f88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
iuc
parents:
diff changeset
7 ~1G of RAM per 1M reads to be assembled"
0b06ab8d5f88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
iuc
parents:
diff changeset
8
0b06ab8d5f88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
iuc
parents:
diff changeset
9 By default, this tool is configured to limit the memory consumption to 30G.
0b06ab8d5f88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
iuc
parents:
diff changeset
10 You might need to lower this limit if the machine(s) executing the jobs have less memory available.
0b06ab8d5f88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
iuc
parents:
diff changeset
11 If you have a lot of reads to assemble and a machine with enough memory, you can increase it.
0b06ab8d5f88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
iuc
parents:
diff changeset
12 In both cases, you can edit the TRINITY_MEM_OPTIONS in the file:
0b06ab8d5f88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
iuc
parents:
diff changeset
13
0b06ab8d5f88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
iuc
parents:
diff changeset
14 <tool_dependency_dir>/environment_settings/TRINITY_MEM_OPTIONS/iuc/trinity/<hash_string>/env.sh
0b06ab8d5f88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
iuc
parents:
diff changeset
15
0b06ab8d5f88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
iuc
parents:
diff changeset
16 to lower the maximum memory usage to 2G for example:
0b06ab8d5f88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
iuc
parents:
diff changeset
17
0b06ab8d5f88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
iuc
parents:
diff changeset
18 TRINITY_MEM_OPTIONS='--max_memory 2G --bflyHeapSpaceMax 2G'