Mercurial > repos > jjohnson > defuse
comparison README @ 5:3bd1087db05e draft
Add dependecies for bowtie, blat, and faToTwoBit
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Fri, 04 Jan 2013 15:01:19 -0600 |
| parents | 679a5c7b1294 |
| children | 1ea6445491d4 |
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| 4:679a5c7b1294 | 5:3bd1087db05e |
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| 7 Manual: | 7 Manual: |
| 8 http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.4.2 | 8 http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.4.2 |
| 9 | 9 |
| 10 The included tool_dependencies.xml will download and install the defuse code. | 10 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. | 11 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. | |
| 12 | 13 |
| 13 | 14 |
| 14 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. | 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. |
| 15 | 16 |
| 16 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. | 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. |
| 30 We were able to follow the same basic procedures to set up a reference for Mouse mm9. | 31 We were able to follow the same basic procedures to set up a reference for Mouse mm9. |
| 31 | 32 |
| 32 These datasets should be referenced in the tool-data/defuse.loc file. | 33 These datasets should be referenced in the tool-data/defuse.loc file. |
| 33 | 34 |
| 34 | 35 |
| 36 External Tools | |
| 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. | |
| 38 Download bowtie: | |
| 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. | |
| 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. | |
| 41 Download blat and faToTwoBit | |
| 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. | |
| 43 Download R | |
| 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. | |
| 45 Install the kernlab package. Run R, then at the prompt type install.packages("kernlab") | |
| 46 Creating required derivative files | |
| 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. | |
| 48 create_reference_dataset.pl -c config.txt | |
| 35 | 49 |
| 50 | |
| 51 |