Mercurial > repos > lparsons > cutadapt
diff README @ 9:93d58ffe39f1 draft
Updated to version 1.6
| author | lparsons |
|---|---|
| date | Mon, 06 Oct 2014 14:01:06 -0400 |
| parents | 2d6671b10919 |
| children |
line wrap: on
line diff
--- a/README Mon Nov 26 17:37:26 2012 -0500 +++ b/README Mon Oct 06 14:01:06 2014 -0400 @@ -1,8 +1,8 @@ Galaxy tool definition for cutadapt (http://code.google.com/p/cutadapt/) -Installation - Tool Shed ---------------------------- +Installation - Tool Shed +------------------------ The recommended way to install cutadapt as a tool in Galaxy is to the use the Galaxy Tool Shed (http://wiki.galaxyproject.org/Tool%20Shed). @@ -14,29 +14,42 @@ Installation - Manual --------------------- -1 - Install the cutadapt package and make sure it is in path for Galaxy -2 - Copy cutadapt.xml to $GALAXY_HOME/tools/cutadapt -3 - Add the tool to the $GALAXY_HOME/tool_conf.xml tool-registry file +1. Install the cutadapt package and make sure it is in path for Galaxy + +2. Copy cutadapt.xml to $GALAXY_HOME/tools/cutadapt + +3. Add the tool to the $GALAXY_HOME/tool_conf.xml tool-registry file -Optional steps to setup and run Galaxy functional tests + **Optional steps to setup and run Galaxy functional tests** + +4. Copy test-data/* to $GALAXY_HOME/test-data/ -4 - Copy test-data/* to $GALAXY_HOME/test-data/ -5 - Set GALAXY_TEST_TOOL_CONF environment variable to a tool_conf.xml file that +5. Set GALAXY_TEST_TOOL_CONF environment variable to a tool_conf.xml file that contains the tools you want to test. (e.g. 'tool_conf.xml') -6 - $GALAXY_HOME/run_functional_tests.sh -id cutadapt + +6. $GALAXY_HOME/run_functional_tests.sh -id cutadapt See the Galaxy Wiki for more information: http://wiki.g2.bx.psu.edu/ Configuration of Adapters ------------------------- -A list of predefined adapters may be specified in the fastx_clipper_sequences.txt +A list of predefined adapters may be specified in the cutadapt_adapters.txt file which resides in the tool-data directory underneath the Galaxy root. A sample file is provided. -Limitations ------------ +Limitations of the Galaxy wrapper +--------------------------------- + +Reading adapters from a fasta file is not supported +Colorspace data support is not implemented +Only one "Strip suffix" is suppored -Colorspace data support is not implemented -Name adapters support is not implemented + +Galaxy Wrapper Development +-------------------------- + +Author: Lance Parsons <lparsons@princeton.edu> + +Repository: [https://bitbucket.org/lance_parsons/cutadapt\_galaxy\_wrapper](https://bitbucket.org/lance_parsons/cutadapt_galaxy_wrapper)