Mercurial > repos > iuc > trinity_analyze_diff_expr
annotate README.rst @ 19:c0096052b35b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
author | iuc |
---|---|
date | Tue, 11 Apr 2023 19:55:15 +0000 |
parents | de949e8c076d |
children |
rev | line source |
---|---|
0
d4128a4e49ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff
changeset
|
1 Trinity memory usage |
d4128a4e49ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff
changeset
|
2 ==================== |
d4128a4e49ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff
changeset
|
3 |
d4128a4e49ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff
changeset
|
4 As described on the official Trinity website |
d4128a4e49ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff
changeset
|
5 `FAQ <http://trinityrnaseq.sourceforge.net/trinity_faq.html#ques_comp_resources_required>`_, |
d4128a4e49ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff
changeset
|
6 trinity requires a large amount of memory to perform the assembly: "roughly |
d4128a4e49ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff
changeset
|
7 ~1G of RAM per 1M reads to be assembled" |
d4128a4e49ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff
changeset
|
8 |
3
24d072085816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
iuc
parents:
0
diff
changeset
|
9 By default, this tool is configured to limit the memory consumption to 1G. |
0
d4128a4e49ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff
changeset
|
10 You might need to lower this limit if the machine(s) executing the jobs have less memory available. |
d4128a4e49ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff
changeset
|
11 If you have a lot of reads to assemble and a machine with enough memory, you can increase it. |
12
de949e8c076d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit f3d9db3063d2cba26e6fbe82a3eee4e1a6fe0bd5"
iuc
parents:
6
diff
changeset
|
12 |
de949e8c076d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit f3d9db3063d2cba26e6fbe82a3eee4e1a6fe0bd5"
iuc
parents:
6
diff
changeset
|
13 This tool uses the GALAXY_MEMORY_MB environmental variable to limit the its memory usage. If you use a supported cluster type, you just need to limit the memory in the destination section of the job_conf.xml file to the amount of available memory (in MB), for example with a Slurm cluster:: |
de949e8c076d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit f3d9db3063d2cba26e6fbe82a3eee4e1a6fe0bd5"
iuc
parents:
6
diff
changeset
|
14 |
de949e8c076d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit f3d9db3063d2cba26e6fbe82a3eee4e1a6fe0bd5"
iuc
parents:
6
diff
changeset
|
15 <destination id="cluster_high_mem" runner="slurm |
de949e8c076d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit f3d9db3063d2cba26e6fbe82a3eee4e1a6fe0bd5"
iuc
parents:
6
diff
changeset
|
16 <param id="nativeSpecification">--mem=1024</param> |
de949e8c076d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit f3d9db3063d2cba26e6fbe82a3eee4e1a6fe0bd5"
iuc
parents:
6
diff
changeset
|
17 </destination> |
de949e8c076d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit f3d9db3063d2cba26e6fbe82a3eee4e1a6fe0bd5"
iuc
parents:
6
diff
changeset
|
18 |
de949e8c076d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit f3d9db3063d2cba26e6fbe82a3eee4e1a6fe0bd5"
iuc
parents:
6
diff
changeset
|
19 If you cluster type does not support memory limit detection, you can also set manually the GALAXY_MEMORY_MB environmental variable in the destination section of the job_conf.xml file to the amount of available memory (in MB):: |
0
d4128a4e49ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff
changeset
|
20 |
5
96be11bb913d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents:
3
diff
changeset
|
21 <?xml version="1.0"?> |
96be11bb913d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents:
3
diff
changeset
|
22 <!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). --> |
96be11bb913d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents:
3
diff
changeset
|
23 <job_conf> |
96be11bb913d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents:
3
diff
changeset
|
24 <plugins> |
96be11bb913d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents:
3
diff
changeset
|
25 <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> |
96be11bb913d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents:
3
diff
changeset
|
26 </plugins> |
96be11bb913d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents:
3
diff
changeset
|
27 <handlers> |
96be11bb913d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents:
3
diff
changeset
|
28 <handler id="main"/> |
96be11bb913d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents:
3
diff
changeset
|
29 </handlers> |
96be11bb913d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents:
3
diff
changeset
|
30 <destinations> |
96be11bb913d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents:
3
diff
changeset
|
31 <destination id="local" runner="local"> |
12
de949e8c076d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit f3d9db3063d2cba26e6fbe82a3eee4e1a6fe0bd5"
iuc
parents:
6
diff
changeset
|
32 <env id="GALAXY_MEMORY_MB">1024</env> |
5
96be11bb913d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents:
3
diff
changeset
|
33 </destination> |
96be11bb913d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents:
3
diff
changeset
|
34 </destinations> |
96be11bb913d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents:
3
diff
changeset
|
35 </job_conf> |
0
d4128a4e49ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff
changeset
|
36 |
3
24d072085816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
iuc
parents:
0
diff
changeset
|
37 |