Mercurial > repos > jeremie > package_pindel_0_2_5

comparison tool_dependencies.xml @ 15:176476c2ce6f draft

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author jeremie
date Thu, 19 Jun 2014 10:39:06 -0400
parents 9d540c67d888
children 687a1b9e97b5
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14:9d540c67d888 15:176476c2ce6f
6 <package name="pindel" version="0.2.5"> 6 <package name="pindel" version="0.2.5">
7 <install version="1.0"> 7 <install version="1.0">
8 <actions> 8 <actions>
9 <!-- <action type="shell_command">git clone https://github.com/genome/pindel.git pindel</action> --> 9 <!-- <action type="shell_command">git clone https://github.com/genome/pindel.git pindel</action> -->
10 <action type="download_by_url" target_filename="pindel-master.zip">https://github.com/genome/pindel/archive/master.zip</action> 10 <action type="download_by_url" target_filename="pindel-master.zip">https://github.com/genome/pindel/archive/master.zip</action>
11 <!-- <action type="shell_command">ls</action> 11 <action type="shell_command">ls</action>
12 <action type="move_directory_files"> 12 <!-- <action type="move_directory_files">
13 <source_directory>.</source_directory> 13 <source_directory>.</source_directory>
14 <destination_directory>$INSTALL_DIR</destination_directory> 14 <destination_directory>$INSTALL_DIR</destination_directory>
15 </action> 15 </action>
16 <action type="shell_command">unzip pindel-master.zip -d pindel</action> 16 <action type="shell_command">unzip pindel-master.zip -d pindel</action>
17 <action type="shell_command">cd master</action> --> 17 <action type="shell_command">cd master</action> -->
18 <action type="shell_command">make all SAMTOOLS=~/samtools</action> 18 <action type="shell_command">make all SAMTOOLS=~/samtools THREADS=2</action>
19 <!-- <action type="shell_command">./INSTALL ~/samtools</action> --> 19 <!-- <action type="shell_command">./INSTALL ~/samtools</action> -->
20 <action type="move_file"> 20 <action type="move_file">
21 <source>pindel</source> 21 <source>pindel</source>
22 <destination>$INSTALL_DIR/</destination> 22 <destination>$INSTALL_DIR/</destination>
23 </action> 23 </action>