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comparison README @ 11:b22f8634ff84 draft

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planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
author jjohnson
date Sun, 17 Jan 2016 14:11:06 -0500
parents 1ea6445491d4
children c3167ccca38c
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10:f65857c1b92e 11:b22f8634ff84
1 The DeFuse galaxy tool is based on DeFuse_Version_0.6.0 1 The DeFuse galaxy tool is based on DeFuse_Version_0.6.2
2 http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page 2 http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page
3 https://bitbucket.org/dranew/defuse
3 4
4 DeFuse is a software package for gene fusion discovery using RNA-Seq data. The software uses clusters of discordant paired end alignments to inform a split read alignment analysis for finding fusion boundaries. The software also employs a number of heuristic filters in an attempt to reduce the number of false positives and produces a fully annotated output for each predicted fusion. 5 DeFuse is a software package for gene fusion discovery using RNA-Seq data. The software uses clusters of discordant paired end alignments to inform a split read alignment analysis for finding fusion boundaries. The software also employs a number of heuristic filters in an attempt to reduce the number of false positives and produces a fully annotated output for each predicted fusion.
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7 Manual: 8 Manual:
8 http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.6.0 9 http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.6.2
9 10
10 The included tool_dependencies.xml will download and install the defuse code. 11 The included tool_dependencies.xml will download and install the defuse code.
11 It will set the environment variable: "DEFUSE_PATH" to the location of the defuse install. 12 It will set the environment variable: "DEFUSE_PATH" to the location of the defuse install.
12 The tool_dependencies.xml also has the download for bowtie. 13 The tool_dependencies.xml also has the download for bowtie.
13 14
32 The create_reference_dataset.pl script will download the genome and other source files, and build any derivative files including bowtie indices, gmap indices, and 2bit files. Run the following command. Expect this step to take at least 12 hours. 33 The create_reference_dataset.pl script will download the genome and other source files, and build any derivative files including bowtie indices, gmap indices, and 2bit files. Run the following command. Expect this step to take at least 12 hours.
33 create_reference_dataset.pl -c config.txt 34 create_reference_dataset.pl -c config.txt
34 35
35 These datasets should be referenced in the tool-data/defuse.loc file. 36 These datasets should be referenced in the tool-data/defuse.loc file.
36 37
38 The create_reference_dataset will run the create_reference_dataset.pl script to generate deFuse genome reference data in a galaxy dataset.
39 This should me made available in the future as a Galaxy DataManager.
37 40
38 External Tools ( http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.6.0 ) 41
42 Galaxy will try to auto-install dependencies:
43
44 External Tools ( http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.6.2 )
39 deFuse relies on other publically available tools as part of its pipeline. Some of these tools are not included with the deFuse download. Obtain these tools as detailed below. 45 deFuse relies on other publically available tools as part of its pipeline. Some of these tools are not included with the deFuse download. Obtain these tools as detailed below.
40 Download samtools 46 Download samtools
41 The latest version of samtools can be downloaded from sourceforge: https://sourceforge.net/projects/samtools/files/samtools. 47 The latest version of samtools can be downloaded from sourceforge: https://sourceforge.net/projects/samtools/files/samtools.
42 Set the samtools_bin entry in config.txt to the fully qualified paths of the samtools binary. 48 Set the samtools_bin entry in config.txt to the fully qualified paths of the samtools binary.
43 Download bowtie 49 Download bowtie