Mercurial > repos > lparsons > cutadapt

view README @ 4:0a872e59164c

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Added discard_stderr_wrapper.sh script to catch report and redirect to stdout
author Lance Parsons <lparsons@princeton.edu>
date Wed, 25 May 2011 19:33:40 -0400
parents 8b064ea16722
children 1dada50cca8a
line wrap: on
line source

Galaxy tool definition for cutadapt (http://code.google.com/p/cutadapt/)

Installation
------------

1 - Install the cutadapt package and make sure it is in path for Galaxy
2 - Copy cutadapt.xml and cutadapt_galaxy_wrapper.py to $GALAXY_HOME/tools/cutadapt
3 - Add the tool to the $GALAXY_HOME/tool_conf.xml tool-registry file


Limitations
-----------

Colorspace data is not implemented
Discard trimmed reads is not implemented (broken in cutadapt 0.9.3)
Storing of "rest fo read" after the adapter (-r), too-short reads (--too-short-output), and untrimmed-reads (--untreimmed-output) are not implemented
Quality cutoff (-q) not implemented
Prefix and Suffix to read names not implemented
Length-tag addition to read name not implemented