Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam
changeset 4:473e1c58d3ae
Uploaded
author | yhoogstrate |
---|---|
date | Tue, 17 Dec 2013 05:03:29 -0500 |
parents | 436d89c21432 |
children | 637f78452b3a |
files | tool_dependencies.xml |
diffstat | 1 files changed, 2 insertions(+), 2 deletions(-) [+] |
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--- a/tool_dependencies.xml Tue Dec 17 04:57:46 2013 -0500 +++ b/tool_dependencies.xml Tue Dec 17 05:03:29 2013 -0500 @@ -3,7 +3,7 @@ <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 ../ && ls -als && cd .. && ls -als</action> + <action type="shell_command">svn checkout https://github.com/mydatascience/parallel-mpileup/trunk samtools-mpileup-parallel && cd samtools-mpileup-parallel && cd $(ls |grep samtools-) && make && cp samtools ../</action> <action type="move_file"> <source>samtools</source> <destination>$INSTALL_DIR/bin/samtools-mpileup-parallel</destination> @@ -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 && mkdir VarScan && cp VarScan.v2.3.6.jar VarScan/ && pwd && ls -als</action> + <action type="download_by_url">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>