Mercurial > repos > jeremie > package_pindel_0_2_5

comparison tool_dependencies.xml @ 18:72ef990f1ace draft

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author jeremie
date Thu, 19 Jun 2014 10:52:46 -0400
parents 6ae878251e83
children c483e3d493f0
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17:6ae878251e83 18:72ef990f1ace
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
12 <!-- <action type="shell_command">cd ..</action> 13 <!-- <action type="shell_command">cd ..</action>
13 <action type="shell_command">ls</action> --> 14 <action type="shell_command">ls</action> -->
14 <!-- <action type="move_directory_files"> 15 <!-- <action type="move_directory_files">
15 <source_directory>.</source_directory> 16 <source_directory>.</source_directory>
16 <destination_directory>$INSTALL_DIR</destination_directory> 17 <destination_directory>$INSTALL_DIR</destination_directory>
17 </action> 18 </action>
18 <action type="shell_command">unzip pindel-master.zip -d pindel</action> 19 <action type="shell_command">unzip pindel-master.zip -d pindel</action>
19 <action type="shell_command">cd master</action> --> 20 <action type="shell_command">cd master</action> -->
21 <action type="shell_command">make Makefile.local</action>
20 <action type="shell_command">make all SAMTOOLS=~/samtools THREADS=2</action> 22 <action type="shell_command">make all SAMTOOLS=~/samtools THREADS=2</action>
21 <!-- <action type="shell_command">./INSTALL ~/samtools</action> --> 23 <!-- <action type="shell_command">./INSTALL ~/samtools</action> -->
22 <action type="move_file"> 24 <action type="move_file">
23 <source>pindel</source> 25 <source>pindel</source>
24 <destination>$INSTALL_DIR/</destination> 26 <destination>$INSTALL_DIR/</destination>