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Update to DeFuse verion 0.6.1 and change tool dependencies for autoinstall
author Jim Johnson <jj@umn.edu>
date Wed, 05 Jun 2013 15:37:57 -0500
parents 5545ec69acbd
children 547d8db4673e
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7:f4eadbd2e7c1 8:06675bd664ee
1 The DeFuse galaxy tool is based on DeFuse_Version_0.6.0 1 The DeFuse galaxy tool is based on DeFuse_Version_0.6.1
2 http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page 2 http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page
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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. 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.
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33 create_reference_dataset.pl -c config.txt 33 create_reference_dataset.pl -c config.txt
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35 These datasets should be referenced in the tool-data/defuse.loc file. 35 These datasets should be referenced in the tool-data/defuse.loc file.
36 36
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38 External Tools ( http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.6.0 ) 38 Galaxy will try to auto-install dependencies:
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40 External Tools ( http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.6.1 )
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. 41 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 42 Download samtools
41 The latest version of samtools can be downloaded from sourceforge: https://sourceforge.net/projects/samtools/files/samtools. 43 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. 44 Set the samtools_bin entry in config.txt to the fully qualified paths of the samtools binary.
43 Download bowtie 45 Download bowtie