Mercurial > repos > lparsons > cutadapt
comparison README @ 0:8b064ea16722
Initial version with multiple adapter support
| author | Lance Parsons <lparsons@princeton.edu> |
|---|---|
| date | Fri, 13 May 2011 15:54:01 -0400 |
| parents | |
| children | 1dada50cca8a |
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| 1 Galaxy tool definition for cutadapt (http://code.google.com/p/cutadapt/) | |
| 2 | |
| 3 Installation | |
| 4 ------------ | |
| 5 | |
| 6 1 - Install the cutadapt package and make sure it is in path for Galaxy | |
| 7 2 - Copy cutadapt.xml and cutadapt_galaxy_wrapper.py to $GALAXY_HOME/tools/cutadapt | |
| 8 3 - Add the tool to the $GALAXY_HOME/tool_conf.xml tool-registry file | |
| 9 | |
| 10 | |
| 11 Limitations | |
| 12 ----------- | |
| 13 | |
| 14 Colorspace data is not implemented | |
| 15 Discard trimmed reads is not implemented (broken in cutadapt 0.9.3) | |
| 16 Storing of "rest fo read" after the adapter (-r), too-short reads (--too-short-output), and untrimmed-reads (--untreimmed-output) are not implemented | |
| 17 Quality cutoff (-q) not implemented | |
| 18 Prefix and Suffix to read names not implemented | |
| 19 Length-tag addition to read name not implemented |