Mercurial > repos > jjohnson > defuse
changeset 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 | 6e30713cefb0 |
| files | README defuse.xml tool_dependencies.xml |
| diffstat | 3 files changed, 92 insertions(+), 3 deletions(-) [+] |
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--- a/README Fri Jan 04 13:29:03 2013 -0600 +++ b/README Fri Jan 04 15:01:19 2013 -0600 @@ -9,6 +9,7 @@ The included tool_dependencies.xml will download and install the defuse code. It will set the environment variable: "DEFUSE_PATH" to the location of the defuse install. +The tool_dependencies.xml also has the download for bowtie. 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. @@ -32,4 +33,19 @@ These datasets should be referenced in the tool-data/defuse.loc file. +External Tools +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. +Download bowtie: +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. +Set the bowtie_bin and bowtie_build_bin entries in config.txt to the fully qualified paths of the bowtie and bowtie-build binaries. +Download blat and faToTwoBit +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. +Download R +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. +Install the kernlab package. Run R, then at the prompt type install.packages("kernlab") +Creating required derivative files +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. +create_reference_dataset.pl -c config.txt + +
--- a/defuse.xml Fri Jan 04 13:29:03 2013 -0600 +++ b/defuse.xml Fri Jan 04 15:01:19 2013 -0600 @@ -2,9 +2,9 @@ <description>identify fusion transcripts</description> <requirements> <requirement type="package" version="0.5.0">defuse</requirement> - <requirement type="package">bowtie</requirement> - <requirement type="package">blat</requirement> - <requirement type="package">fatotwobit</requirement> + <requirement type="package" version="0.12.7">bowtie</requirement> + <requirement type="package" version="34x10">blat</requirement> + <requirement type="package" version="34x10">fatotwobit</requirement> </requirements> <command interpreter="command"> /bin/bash $shscript </command> <inputs>
--- a/tool_dependencies.xml Fri Jan 04 13:29:03 2013 -0600 +++ b/tool_dependencies.xml Fri Jan 04 15:01:19 2013 -0600 @@ -18,4 +18,77 @@ </readme> </package> + <package name="bowtie" version="0.12.7"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie/0.12.7/bowtie-0.12.7-src.zip</action> + <action type="shell_command">make</action> + <action type="move_file"> + <source>bowtie</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bowtie-build</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bowtie-inspect</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> + Compiling Bowtie requires libpthread to be present on your system. + </readme> + </package> + + <package name="blat" version="34x10"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat</action> + <action type="shell_command">chmod 755 blat</action> + <action type="move_file"> + <source>blat</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> +This only handles blat for a non-commercial linux system. + +Please note that the Blat source and executables are freely available for +academic, nonprofit and personal use. Commercial licensing information is +available on the Kent Informatics website (http://www.kentinformatics.com/). + </readme> + </package> + + <package name="fatotwobit" version="34x10"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit</action> + <action type="shell_command">chmod 755 faToTwoBit</action> + <action type="move_file"> + <source>faToTwoBit</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> +This only handles faToTwoBit for a non-commercial linux system. + +Please note that the source and executables are freely available for +academic, nonprofit and personal use. Commercial licensing information is +available on the Kent Informatics website (http://www.kentinformatics.com/). + </readme> + </package> + </tool_dependency>