Mercurial > repos > lparsons > cutadapt
comparison README @ 9:93d58ffe39f1 draft
Updated to version 1.6
| author | lparsons |
|---|---|
| date | Mon, 06 Oct 2014 14:01:06 -0400 |
| parents | 2d6671b10919 |
| children |
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| 8:2d6671b10919 | 9:93d58ffe39f1 |
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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 | 3 |
| 4 Installation - Tool Shed | 4 Installation - Tool Shed |
| 5 --------------------------- | 5 ------------------------ |
| 6 | 6 |
| 7 The recommended way to install cutadapt as a tool in Galaxy is to the use the | 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). | 8 Galaxy Tool Shed (http://wiki.galaxyproject.org/Tool%20Shed). |
| 9 | 9 |
| 10 This will allow cutadapt to be installed automatically and keep track of older | 10 This will allow cutadapt to be installed automatically and keep track of older |
| 12 | 12 |
| 13 | 13 |
| 14 Installation - Manual | 14 Installation - Manual |
| 15 --------------------- | 15 --------------------- |
| 16 | 16 |
| 17 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 |
| 18 2 - Copy cutadapt.xml to $GALAXY_HOME/tools/cutadapt | |
| 19 3 - Add the tool to the $GALAXY_HOME/tool_conf.xml tool-registry file | |
| 20 | 18 |
| 21 Optional steps to setup and run Galaxy functional tests | 19 2. Copy cutadapt.xml to $GALAXY_HOME/tools/cutadapt |
| 22 | 20 |
| 23 4 - Copy test-data/* to $GALAXY_HOME/test-data/ | 21 3. Add the tool to the $GALAXY_HOME/tool_conf.xml tool-registry file |
| 24 5 - Set GALAXY_TEST_TOOL_CONF environment variable to a tool_conf.xml file that | 22 |
| 23 **Optional steps to setup and run Galaxy functional tests** | |
| 24 | |
| 25 4. Copy test-data/* to $GALAXY_HOME/test-data/ | |
| 26 | |
| 27 5. Set GALAXY_TEST_TOOL_CONF environment variable to a tool_conf.xml file that | |
| 25 contains the tools you want to test. (e.g. 'tool_conf.xml') | 28 contains the tools you want to test. (e.g. 'tool_conf.xml') |
| 26 6 - $GALAXY_HOME/run_functional_tests.sh -id cutadapt | 29 |
| 30 6. $GALAXY_HOME/run_functional_tests.sh -id cutadapt | |
| 27 See the Galaxy Wiki for more information: http://wiki.g2.bx.psu.edu/ | 31 See the Galaxy Wiki for more information: http://wiki.g2.bx.psu.edu/ |
| 28 | 32 |
| 29 | 33 |
| 30 Configuration of Adapters | 34 Configuration of Adapters |
| 31 ------------------------- | 35 ------------------------- |
| 32 | 36 |
| 33 A list of predefined adapters may be specified in the fastx_clipper_sequences.txt | 37 A list of predefined adapters may be specified in the cutadapt_adapters.txt |
| 34 file which resides in the tool-data directory underneath the Galaxy root. A sample | 38 file which resides in the tool-data directory underneath the Galaxy root. A sample |
| 35 file is provided. | 39 file is provided. |
| 36 | 40 |
| 37 | 41 |
| 38 Limitations | 42 Limitations of the Galaxy wrapper |
| 39 ----------- | 43 --------------------------------- |
| 40 | 44 |
| 45 Reading adapters from a fasta file is not supported | |
| 41 Colorspace data support is not implemented | 46 Colorspace data support is not implemented |
| 42 Name adapters support is not implemented | 47 Only one "Strip suffix" is suppored |
| 48 | |
| 49 | |
| 50 Galaxy Wrapper Development | |
| 51 -------------------------- | |
| 52 | |
| 53 Author: Lance Parsons <lparsons@princeton.edu> | |
| 54 | |
| 55 Repository: [https://bitbucket.org/lance_parsons/cutadapt\_galaxy\_wrapper](https://bitbucket.org/lance_parsons/cutadapt_galaxy_wrapper) |