From 11f7c34b66e948e59fc1b905d27a0796428b7a63 Mon Sep 17 00:00:00 2001 From: sajvanderzeeuw <s.a.j.van_der_zeeuw@lumc.nl> Date: Thu, 5 Nov 2015 15:51:15 +0100 Subject: [PATCH] changes in docs 0.5.0 carp --- docs/pipelines/carp.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/docs/pipelines/carp.md b/docs/pipelines/carp.md index ff3aef353..e869bb1b5 100644 --- a/docs/pipelines/carp.md +++ b/docs/pipelines/carp.md @@ -53,7 +53,7 @@ While optional settings are: 1. `aligner`: which aligner to use (`bwa` or `bowtie`) 2. `macs2`: Here only the callpeak modus is implemented. But one can set all the options from [macs2 callpeak](https://github -.com/taoliu/MACS/#call-peaks) +.com/taoliu/MACS/#call-peaks) in this settings config. Note that the config value is: macs2_callpeak ## Running Carp As with other pipelines in the Biopet suite, Carp can be run by specifying the pipeline after the `pipeline` subcommand: @@ -68,9 +68,11 @@ If you already have the `biopet` environment module loaded, you can also simply biopet pipeline carp -config </path/to/config.json> -qsub -jobParaEnv BWA -run ~~~ -It is also a good idea to specify retries (we recomend `-retry 3` up to `-retry 5`) so that cluster glitches do not interfere with your pipeline runs. +It is also a good idea to specify retries (we recomend `-retry 4` up to `-retry 8`) so that cluster glitches do not interfere +with your pipeline runs. ## Getting Help If you have any questions on running Carp, suggestions on how to improve the overall flow, or requests for your favorite ChIP-seq related program to be added, feel free to post an issue to our issue tracker at [https://git.lumc.nl/biopet/biopet/issues](https://git.lumc.nl/biopet/biopet/issues). +Or contact us directly via: [SASC email](mailto: SASC@lumc.nl) -- GitLab