Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam
changeset 3:436d89c21432
Uploaded
author | yhoogstrate |
---|---|
date | Tue, 17 Dec 2013 04:57:46 -0500 |
parents | ede8c645ed22 |
children | 473e1c58d3ae |
files | tool_dependencies.xml |
diffstat | 1 files changed, 2 insertions(+), 2 deletions(-) [+] |
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--- a/tool_dependencies.xml Tue Dec 17 04:52:45 2013 -0500 +++ b/tool_dependencies.xml Tue Dec 17 04:57:46 2013 -0500 @@ -6,7 +6,7 @@ <action type="shell_command">svn checkout https://github.com/mydatascience/parallel-mpileup/trunk samtools-mpileup-parallel && cd samtools-mpileup-parallel && cd $(ls |grep samtools-) && make && cp samtools ../ && ls -als && cd .. && ls -als</action> <action type="move_file"> <source>samtools</source> - <destination>$INSTALL_DIR/bin</destination> + <destination>$INSTALL_DIR/bin/samtools-mpileup-parallel</destination> </action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> @@ -21,7 +21,7 @@ <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 && pwd && ls -als</action> + <action type="shell_command">wget http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.6.jar && mkdir VarScan && cp VarScan.v2.3.6.jar VarScan/ && pwd && ls -als</action> <action type="move_file"> <source>VarScan.v2.3.6.jar</source> <destination>$INSTALL_DIR/bin</destination>