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Add dependecies for bowtie, blat, and faToTwoBit
author Jim Johnson <jj@umn.edu>
date Fri, 04 Jan 2013 15:01:19 -0600
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679a5c7b1294 deFuse version 0.5.0 - Use tool_dependencies.xml
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1 The DeFuse galaxy tool is based on DeFuse_Version_0.5.0
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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.
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7 Manual:
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8 http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.4.2
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10 The included tool_dependencies.xml will download and install the defuse code.
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11 It will set the environment variable: "DEFUSE_PATH" to the location of the defuse install.
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12 The tool_dependencies.xml also has the download for bowtie.
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15 The defuse.pl command relies on a configuration file to specifiy options, the location of reference data, and other applications that it depends upon: bowtie, bowtie-build, samtools, blat, fatotwobit, R, and Rscript.
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17 The DeFuse galaxy tool can either construct the config.txt file that is mentioned in the defuse manual, or select an existing config.txt file in the users history.
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18 When constructing the config.txt file, the DeFuse tool uses the values selected in: tool-data/defuse.loc
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19 The dictionary field in the tool-data/defuse.loc can be used to set fields in the config.txt file, including the site specific location of reference data and the paths to the other application binaries.
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20 The "Defuse parameter settings" are used to alter options in the config.txt file.
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22 The DeFuse galaxy tool also generates a bash script to run defuse.
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23 That script will attempt to edit the config.txt file to specifiy any unset paths to applications that defuse relies upon:
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24 bowtie, bowtie-build, samtools, blat, fatotwobit, R, and Rscript
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25 The script uses the using the shell "which" command to discover the application path, so the required applications should in PATH environment variable.
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28 Generate Reference Datasets as described in the Manual:
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30 The manual has detailed instructions on how to set up reference datasets for Human hg19 and hg18.
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31 We were able to follow the same basic procedures to set up a reference for Mouse mm9.
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33 These datasets should be referenced in the tool-data/defuse.loc file.
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36 External Tools
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37 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.
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38 Download bowtie:
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39 The latest version of bowtie can be downloaded from sourceforge: http://sourceforge.net/projects/bowtie-bio/files/bowtie/. deFuse has been tested on version 0.12.5.
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40 Set the bowtie_bin and bowtie_build_bin entries in config.txt to the fully qualified paths of the bowtie and bowtie-build binaries.
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41 Download blat and faToTwoBit
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42 The latest blat tool suite can be downloaded from the ucsc website: http://hgdownload.cse.ucsc.edu/admin/exe/. Download blat and faToTwoBit and set the blat_bin and fatotwobit_bin entries in config.txt to the fully qualified paths of the blat and faToTwoBit binaries.
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43 Download R
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44 The latest version of R can be downloaded from the R project website: http://www.r-project.org/. Install R and then locate the R and Rscript executables, and set the r_bin and rscript_bin entries in config.txt to the path of those executables.
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45 Install the kernlab package. Run R, then at the prompt type install.packages("kernlab")
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46 Creating required derivative files
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47 Once the required files and tools have been downloaded, the create_reference_dataset.pl script will build any derivative files including bowtie indices and 2bit files. Run the following command. Expect this step to take at least 12 hours.
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48 create_reference_dataset.pl -c config.txt
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