Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam
changeset 1:d0cd5668ec6b
Uploaded
| author | yhoogstrate |
|---|---|
| date | Tue, 17 Dec 2013 04:41:18 -0500 |
| parents | 212cc602c073 |
| children | ede8c645ed22 |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 39 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Dec 17 04:41:18 2013 -0500 @@ -0,0 +1,39 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="samtools-mpileup-parallel" version="1.0.19"> + <install version="1.0"> + <actions> + <action type="shell_command">svn checkout https://github.com/mydatascience/parallel-mpileup/trunk samtools-mpileup-parallel && cd samtools-mpileup-parallel && cd $(ls |grep samtools-) && make && cp samtools ../samtools-mpileup-parallel && ls -als && cd .. && ls -als</action> + <action type="move_file"> + <source>bin/samtools</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + <environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable> + </action> + </actions> + </install> + <readme> + Downloads and installs a modified version of samtools, able to paralellize the mpileup function. + </readme> + </package> + <package name="VarScan" version="2.3.6"> + <install version="1.0"> + <actions> + <action type="shell_command">wget http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.6.jar</action> + <action type="move_file"> + <source>VarScan.v2.3.6.jar</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + <environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable> + </action> + </actions> + </install> + <readme> + Downloads VarScan2. + </readme> + </package> +</tool_dependency>