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Support for cutadapt 0.9.5, added quality trimming and additional output options
author Lance Parsons <lparsons@princeton.edu>
date Fri, 22 Jul 2011 11:03:00 -0400
parents 8b064ea16722
children 2d6671b10919
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8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
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1 Galaxy tool definition for cutadapt (http://code.google.com/p/cutadapt/)
8b064ea16722 Initial version with multiple adapter support
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2
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
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3 Installation
8b064ea16722 Initial version with multiple adapter support
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4 ------------
8b064ea16722 Initial version with multiple adapter support
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5
8b064ea16722 Initial version with multiple adapter support
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6 1 - Install the cutadapt package and make sure it is in path for Galaxy
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1dada50cca8a Support for cutadapt 0.9.5, added quality trimming and additional output options
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7 2 - Copy cutadapt.xml to $GALAXY_HOME/tools/cutadapt
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8b064ea16722 Initial version with multiple adapter support
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8 3 - Add the tool to the $GALAXY_HOME/tool_conf.xml tool-registry file
8b064ea16722 Initial version with multiple adapter support
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parents:
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1dada50cca8a Support for cutadapt 0.9.5, added quality trimming and additional output options
Lance Parsons <lparsons@princeton.edu>
parents: 0
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10 Optional steps to setup and run Galaxy functional tests
1dada50cca8a Support for cutadapt 0.9.5, added quality trimming and additional output options
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1dada50cca8a Support for cutadapt 0.9.5, added quality trimming and additional output options
Lance Parsons <lparsons@princeton.edu>
parents: 0
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12 4 - Copy test-data/* to $GALAXY_HOME/test-data/
1dada50cca8a Support for cutadapt 0.9.5, added quality trimming and additional output options
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parents: 0
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13 5 - Set GALAXY_TEST_TOOL_CONF environment variable to a tool_conf.xml file that
1dada50cca8a Support for cutadapt 0.9.5, added quality trimming and additional output options
Lance Parsons <lparsons@princeton.edu>
parents: 0
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14 contains the tools you want to test. (e.g. 'tool_conf.xml')
1dada50cca8a Support for cutadapt 0.9.5, added quality trimming and additional output options
Lance Parsons <lparsons@princeton.edu>
parents: 0
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15 6 - $GALAXY_HOME/run_functional_tests.sh -id cutadapt
1dada50cca8a Support for cutadapt 0.9.5, added quality trimming and additional output options
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parents: 0
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16 See the Galaxy Wiki for more information: http://wiki.g2.bx.psu.edu/
1dada50cca8a Support for cutadapt 0.9.5, added quality trimming and additional output options
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parents:
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8b064ea16722 Initial version with multiple adapter support
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parents:
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19 Limitations
8b064ea16722 Initial version with multiple adapter support
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20 -----------
8b064ea16722 Initial version with multiple adapter support
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1dada50cca8a Support for cutadapt 0.9.5, added quality trimming and additional output options
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22 Colorspace data support is not implemented
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8b064ea16722 Initial version with multiple adapter support
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23 Prefix and Suffix to read names not implemented
8b064ea16722 Initial version with multiple adapter support
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24 Length-tag addition to read name not implemented