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Repository 'cutadapt'
http://toolshed.g2.bx.psu.edu/view/lparsons/cutadapt
cutadapt
unrestricted
Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq)
Galaxy tool configuration and tests for the cutadapt sequence adapter removal tool.  The tool operates on fasta or fastq files.

Cutadapt: http://code.google.com/p/cutadapt/
8:2d6671b10919
lparsons
True
372

Repository README files - may contain important installation or license information

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


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).

This will allow cutadapt to be installed automatically and keep track of older
versions of cutadapt and the tool wrapper.


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

Optional steps to setup and run Galaxy functional tests

4 - Copy test-data/* to $GALAXY_HOME/test-data/
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 
    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
file which resides in the tool-data directory underneath the Galaxy root.  A sample
file is provided.


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

Colorspace data support is not implemented
Name adapters support is not implemented
Dependencies of this repository

Name Version Type
cutadapt 1.1 package

Contents of this repository

Name Description Version
Cutadapt Remove adapter sequences from Fastq/Fasta 1.1.a

Automated tool test results

Time tested: 2014-04-23 07:37:29
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 13181:7a7985a007fb
Galaxy database version: 118
Tool shed revision: 13123:e6876f691854
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: cutadapt
Tool version: cutadapt
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.1.a)
TypeNameVersion
cutadapt package 1.1
Installation directory
/ToolDepsMain/cutadapt/1.1/lparsons/cutadapt/2d6671b10919
Time tested: 2014-04-17 05:41:14
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 13085:c05752549163
Galaxy database version: 118
Tool shed revision: 12961:888478c66456
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: cutadapt
Tool version: cutadapt
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.1.a)
TypeNameVersion
cutadapt package 1.1
Installation directory
/ToolDepsMain/cutadapt/1.1/lparsons/cutadapt/2d6671b10919
Time tested: 2014-04-16 05:35:38
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 13065:1ad62c772728
Galaxy database version: 118
Tool shed revision: 12961:888478c66456
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: cutadapt
Tool version: cutadapt
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.1.a)
TypeNameVersion
cutadapt package 1.1
Installation directory
/ToolDepsMain/cutadapt/1.1/lparsons/cutadapt/2d6671b10919
Time tested: 2014-04-15 06:10:03
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 13058:1165a5a1221a
Galaxy database version: 118
Tool shed revision: 12961:888478c66456
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: cutadapt
Tool version: cutadapt
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.1.a)
TypeNameVersion
cutadapt package 1.1
Installation directory
/ToolDepsMain/cutadapt/1.1/lparsons/cutadapt/2d6671b10919

Categories
Fasta Manipulation
Sequence Analysis