Mercurial > repos > jeremie > package_pindel_0_2_5

comparison tool_dependencies.xml @ 11:aea585951b97 draft

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author jeremie
date Thu, 19 Jun 2014 10:17:34 -0400
parents ea5aad668099
children 4a11086ede4b
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10:ea5aad668099 11:aea585951b97
4 <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> 4 <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
5 </package> 5 </package>
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>
12 <action type="shell_command">cd ..</action>
13 <action type="shell_command">ls</action>
11 <!-- <action type="move_directory_files"> 14 <!-- <action type="move_directory_files">
12 <source_directory>.</source_directory> 15 <source_directory>.</source_directory>
13 <destination_directory>$INSTALL_DIR</destination_directory> 16 <destination_directory>$INSTALL_DIR</destination_directory>
14 </action> --> 17 </action> -->
15 <!-- <action type="shell_command">unzip pindel-master.zip -d pindel</action>--> --> 18 <!-- <action type="shell_command">unzip pindel-master.zip -d pindel</action>--> -->
16 <!-- <action type="shell_command">cd pindel</action> --> 19 <action type="shell_command">cd master</action>
17 <action type="shell_command">make SAMTOOLS=~/samtools</action> 20 <action type="shell_command">make SAMTOOLS=~/samtools</action>
21 <action type="shell_command">./INSTALL ~/samtools</action>
18 <action type="move_file"> 22 <action type="move_file">
19 <source>pindel</source> 23 <source>pindel</source>
20 <destination>$INSTALL_DIR/</destination> 24 <destination>$INSTALL_DIR/</destination>
21 </action> 25 </action>
22 <action type="set_environment"> 26 <action type="set_environment">