Mercurial > repos > lparsons > cutadapt
comparison README @ 8:2d6671b10919 draft
Updated to support cutadapt version 1.1 (also include automatic dependency installation)
| author | lparsons |
|---|---|
| date | Mon, 26 Nov 2012 17:37:26 -0500 |
| parents | 1dada50cca8a |
| children | 93d58ffe39f1 |
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| 7:1dda185ea2d0 | 8:2d6671b10919 |
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| 1 Galaxy tool definition for cutadapt (http://code.google.com/p/cutadapt/) | 1 Galaxy tool definition for cutadapt (http://code.google.com/p/cutadapt/) |
| 2 | 2 |
| 3 Installation | 3 |
| 4 ------------ | 4 Installation - Tool Shed |
| 5 --------------------------- | |
| 6 | |
| 7 The recommended way to install cutadapt as a tool in Galaxy is to the use the | |
| 8 Galaxy Tool Shed (http://wiki.galaxyproject.org/Tool%20Shed). | |
| 9 | |
| 10 This will allow cutadapt to be installed automatically and keep track of older | |
| 11 versions of cutadapt and the tool wrapper. | |
| 12 | |
| 13 | |
| 14 Installation - Manual | |
| 15 --------------------- | |
| 5 | 16 |
| 6 1 - Install the cutadapt package and make sure it is in path for Galaxy | 17 1 - Install the cutadapt package and make sure it is in path for Galaxy |
| 7 2 - Copy cutadapt.xml to $GALAXY_HOME/tools/cutadapt | 18 2 - Copy cutadapt.xml to $GALAXY_HOME/tools/cutadapt |
| 8 3 - Add the tool to the $GALAXY_HOME/tool_conf.xml tool-registry file | 19 3 - Add the tool to the $GALAXY_HOME/tool_conf.xml tool-registry file |
| 9 | 20 |
| 14 contains the tools you want to test. (e.g. 'tool_conf.xml') | 25 contains the tools you want to test. (e.g. 'tool_conf.xml') |
| 15 6 - $GALAXY_HOME/run_functional_tests.sh -id cutadapt | 26 6 - $GALAXY_HOME/run_functional_tests.sh -id cutadapt |
| 16 See the Galaxy Wiki for more information: http://wiki.g2.bx.psu.edu/ | 27 See the Galaxy Wiki for more information: http://wiki.g2.bx.psu.edu/ |
| 17 | 28 |
| 18 | 29 |
| 30 Configuration of Adapters | |
| 31 ------------------------- | |
| 32 | |
| 33 A list of predefined adapters may be specified in the fastx_clipper_sequences.txt | |
| 34 file which resides in the tool-data directory underneath the Galaxy root. A sample | |
| 35 file is provided. | |
| 36 | |
| 37 | |
| 19 Limitations | 38 Limitations |
| 20 ----------- | 39 ----------- |
| 21 | 40 |
| 22 Colorspace data support is not implemented | 41 Colorspace data support is not implemented |
| 23 Prefix and Suffix to read names not implemented | 42 Name adapters support is not implemented |
| 24 Length-tag addition to read name not implemented |