Mercurial > repos > jeremie > package_pindel_0_2_5
changeset 0:568c8f5371fc draft
Uploaded
| author | jeremie |
|---|---|
| date | Wed, 02 Jul 2014 04:39:19 -0400 |
| parents | |
| children | 7a1b7941a04f |
| 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 Wed Jul 02 04:39:19 2014 -0400 @@ -0,0 +1,39 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="samtools" version="0.1.18"> + <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" prior_installation_required="True" /> + </package> + <package name="pindel" version="0.2.5"> + <install version="1.0"> + <actions> + <action type="shell_command">git clone https://github.com/genome/pindel.git</action> + <action type="shell_command">git checkout tags/v0.2.5</action> + <action type="set_environment_for_install"> + <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu"> + <package name="samtools" version="0.1.18" /> + </repository> + </action> + <!-- <action type="shell_command"> + echo "$samtools + $PATH + $INSTALL_DIR + $BAM_ROOT" + </action> --> + <action type="shell_command">./INSTALL $BAM_ROOT</action> + <action type="move_file"> + <source>pindel</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>pindel2vcf</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="set_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> + </readme> + </package> +</tool_dependency>