annotate README @ 7:1dda185ea2d0

Added sample fastx_clipper_sequences.txt file
author Lance Parsons <lparsons@princeton.edu>
date Thu, 22 Dec 2011 11:46:33 -0500
parents 1dada50cca8a
children 2d6671b10919
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1 Galaxy tool definition for cutadapt (http://code.google.com/p/cutadapt/)
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
2
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
3 Installation
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
4 ------------
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
5
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
6 1 - Install the cutadapt package and make sure it is in path for Galaxy
5
1dada50cca8a Support for cutadapt 0.9.5, added quality trimming and additional output options
Lance Parsons <lparsons@princeton.edu>
parents: 0
diff changeset
7 2 - Copy cutadapt.xml to $GALAXY_HOME/tools/cutadapt
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
8 3 - Add the tool to the $GALAXY_HOME/tool_conf.xml tool-registry file
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
9
5
1dada50cca8a Support for cutadapt 0.9.5, added quality trimming and additional output options
Lance Parsons <lparsons@princeton.edu>
parents: 0
diff changeset
10 Optional steps to setup and run Galaxy functional tests
1dada50cca8a Support for cutadapt 0.9.5, added quality trimming and additional output options
Lance Parsons <lparsons@princeton.edu>
parents: 0
diff changeset
11
1dada50cca8a Support for cutadapt 0.9.5, added quality trimming and additional output options
Lance Parsons <lparsons@princeton.edu>
parents: 0
diff changeset
12 4 - Copy test-data/* to $GALAXY_HOME/test-data/
1dada50cca8a Support for cutadapt 0.9.5, added quality trimming and additional output options
Lance Parsons <lparsons@princeton.edu>
parents: 0
diff changeset
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
diff changeset
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
diff changeset
15 6 - $GALAXY_HOME/run_functional_tests.sh -id cutadapt
1dada50cca8a Support for cutadapt 0.9.5, added quality trimming and additional output options
Lance Parsons <lparsons@princeton.edu>
parents: 0
diff changeset
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
Lance Parsons <lparsons@princeton.edu>
parents: 0
diff changeset
17
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
18
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
19 Limitations
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
20 -----------
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
21
5
1dada50cca8a Support for cutadapt 0.9.5, added quality trimming and additional output options
Lance Parsons <lparsons@princeton.edu>
parents: 0
diff changeset
22 Colorspace data support is not implemented
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
23 Prefix and Suffix to read names not implemented
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
24 Length-tag addition to read name not implemented