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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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4:0a872e59164c 5:1dada50cca8a
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3 Installation 3 Installation
4 ------------ 4 ------------
5 5
6 1 - Install the cutadapt package and make sure it is in path for Galaxy 6 1 - Install the cutadapt package and make sure it is in path for Galaxy
7 2 - Copy cutadapt.xml and cutadapt_galaxy_wrapper.py to $GALAXY_HOME/tools/cutadapt 7 2 - Copy cutadapt.xml to $GALAXY_HOME/tools/cutadapt
8 3 - Add the tool to the $GALAXY_HOME/tool_conf.xml tool-registry file 8 3 - Add the tool to the $GALAXY_HOME/tool_conf.xml tool-registry file
9
10 Optional steps to setup and run Galaxy functional tests
11
12 4 - Copy test-data/* to $GALAXY_HOME/test-data/
13 5 - Set GALAXY_TEST_TOOL_CONF environment variable to a tool_conf.xml file that
14 contains the tools you want to test. (e.g. 'tool_conf.xml')
15 6 - $GALAXY_HOME/run_functional_tests.sh -id cutadapt
16 See the Galaxy Wiki for more information: http://wiki.g2.bx.psu.edu/
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10 18
11 Limitations 19 Limitations
12 ----------- 20 -----------
13 21
14 Colorspace data is not implemented 22 Colorspace data support is not implemented
15 Discard trimmed reads is not implemented (broken in cutadapt 0.9.3)
16 Storing of "rest fo read" after the adapter (-r), too-short reads (--too-short-output), and untrimmed-reads (--untreimmed-output) are not implemented
17 Quality cutoff (-q) not implemented
18 Prefix and Suffix to read names not implemented 23 Prefix and Suffix to read names not implemented
19 Length-tag addition to read name not implemented 24 Length-tag addition to read name not implemented