Mercurial > repos > fcaramia > somatic_sniper
diff tool_dependencies.xml @ 20:6106d7e4c740 draft
Uploaded
| author | fcaramia |
|---|---|
| date | Wed, 19 Jun 2013 22:17:33 -0400 |
| parents | 72c57a6cd428 |
| children | 462a6a45fd77 |
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--- a/tool_dependencies.xml Wed Jun 19 20:56:35 2013 -0400 +++ b/tool_dependencies.xml Wed Jun 19 22:17:33 2013 -0400 @@ -12,20 +12,16 @@ <source>samtools</source> <destination>$INSTALL_DIR/bin</destination> </action> - <action type="set_environment"> - <environment_variable name="SAMTOOLS_ROOT" action="set_to">$INSTALL_DIR/bin</environment_variable> - </action> - <action type="shell_command">echo $SAMTOOLS_ROOT</action> + - - <!--action type="download_file">https://github.com/genome/somatic-sniper/archive/master.zip</action> + <action type="download_file">https://github.com/genome/somatic-sniper/archive/master.zip</action> <action type="download_file">https://github.com/genome/build-common/tarball/master</action> <action type="shell_command">unzip master.zip</action> <action type="shell_command">tar -xzvf master</action> <action type="shell_command">rm -rf somatic-sniper-master/build-common/</action> <action type="shell_command">mv genome-build-common-077bd57/ somatic-sniper-master/build-common/</action> - <action type="shell_command">cmake somatic-sniper-master/</action> - <action type="shell_command">make somatic-sniper-master/</action> + <action type="shell_command">cmake -D Samtools_INCLUDE_DIR:PATH=$INSTALL_DIR/bin somatic-sniper-master/ </action> + <!--action type="shell_command">make somatic-sniper-master/</action> <action type="shell_command">mv somatic-sniper-master/bin/bam-somaticsniper $INSTALL_DIR/bin</action> <action type="set_environment">