Mercurial > repos > jeremie > package_pindel_0_2_5
changeset 8:b5ae2adce876 draft default tip
Uploaded
author | jeremie |
---|---|
date | Fri, 04 Jul 2014 06:06:26 -0400 |
parents | b68c61d5e995 |
children | |
files | tool_dependencies.xml |
diffstat | 1 files changed, 10 insertions(+), 41 deletions(-) [+] |
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--- a/tool_dependencies.xml Wed Jul 02 06:23:08 2014 -0400 +++ b/tool_dependencies.xml Fri Jul 04 06:06:26 2014 -0400 @@ -9,50 +9,19 @@ <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> --> + <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="make_directory">samtools</action> - <action type="shell_command"> - cp $BAM_ROOT/bin/* samtools - </action> - <action type="shell_command"> - cp $BAM_ROOT/lib/* samtools - </action> - <action type="shell_command"> - cp $BAM_ROOT/include/bam/* samtools - </action> - <action type="shell_command">ls</action> - <action type="shell_command">pwd</action> - - <!-- <action type="shell_command"> - <source>$BAM_ROOT/lib</source> - <destination>./samtools</destination> - </action> - <action type="shell_command"> - <source_directory>$BAM_ROOT/include/bam</source_directory> - <destination_directory>./samtools</destination_directory> - </action> --> - - + <action type="shell_command">cp $BAM_ROOT/bin/* samtools</action> + <action type="shell_command">cp $BAM_ROOT/lib/* samtools</action> + <action type="shell_command">cp $BAM_ROOT/include/bam/* samtools</action> <action type="shell_command">./INSTALL samtools</action> - <action type="move_file"> - <source>pindel</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="move_file"> - <source>pindel2vcf</source> - <destination>$INSTALL_DIR/bin</destination> - </action> + <action type="move_file"><source>pindel</source><destination>$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> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install>