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comparison README @ 8:2d6671b10919 draft

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Updated to support cutadapt version 1.1 (also include automatic dependency installation)
author lparsons
date Mon, 26 Nov 2012 17:37:26 -0500
parents 1dada50cca8a
children 93d58ffe39f1
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7:1dda185ea2d0 8:2d6671b10919
1 Galaxy tool definition for cutadapt (http://code.google.com/p/cutadapt/) 1 Galaxy tool definition for cutadapt (http://code.google.com/p/cutadapt/)
2 2
3 Installation 3
4 ------------ 4 Installation - Tool Shed
5 ---------------------------
6
7 The recommended way to install cutadapt as a tool in Galaxy is to the use the
8 Galaxy Tool Shed (http://wiki.galaxyproject.org/Tool%20Shed).
9
10 This will allow cutadapt to be installed automatically and keep track of older
11 versions of cutadapt and the tool wrapper.
12
13
14 Installation - Manual
15 ---------------------
5 16
6 1 - Install the cutadapt package and make sure it is in path for Galaxy 17 1 - Install the cutadapt package and make sure it is in path for Galaxy
7 2 - Copy cutadapt.xml to $GALAXY_HOME/tools/cutadapt 18 2 - Copy cutadapt.xml to $GALAXY_HOME/tools/cutadapt
8 3 - Add the tool to the $GALAXY_HOME/tool_conf.xml tool-registry file 19 3 - Add the tool to the $GALAXY_HOME/tool_conf.xml tool-registry file
9 20
14 contains the tools you want to test. (e.g. 'tool_conf.xml') 25 contains the tools you want to test. (e.g. 'tool_conf.xml')
15 6 - $GALAXY_HOME/run_functional_tests.sh -id cutadapt 26 6 - $GALAXY_HOME/run_functional_tests.sh -id cutadapt
16 See the Galaxy Wiki for more information: http://wiki.g2.bx.psu.edu/ 27 See the Galaxy Wiki for more information: http://wiki.g2.bx.psu.edu/
17 28
18 29
30 Configuration of Adapters
31 -------------------------
32
33 A list of predefined adapters may be specified in the fastx_clipper_sequences.txt
34 file which resides in the tool-data directory underneath the Galaxy root. A sample
35 file is provided.
36
37
19 Limitations 38 Limitations
20 ----------- 39 -----------
21 40
22 Colorspace data support is not implemented 41 Colorspace data support is not implemented
23 Prefix and Suffix to read names not implemented 42 Name adapters support is not implemented
24 Length-tag addition to read name not implemented