Mercurial > repos > jeremie > package_pindel_0_2_5

comparison tool_dependencies.xml @ 25:88444ff7009f draft

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author jeremie
date Fri, 20 Jun 2014 08:59:35 -0400
parents e01d575b2e15
children 47817c968422
comparison
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24:e01d575b2e15 25:88444ff7009f
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="shell_command">ls</action> -->
12
13 <!-- <action type="shell_command">cd ..</action>
14 <action type="shell_command">ls</action> -->
15 <!-- <action type="move_directory_files"> 13 <!-- <action type="move_directory_files">
16 <source_directory>.</source_directory> 14 <source_directory>.</source_directory>
17 <destination_directory>$INSTALL_DIR</destination_directory> 15 <destination_directory>$INSTALL_DIR</destination_directory>
18 </action> 16 </action>
19 <action type="shell_command">unzip pindel-master.zip -d pindel</action> 17 <action type="shell_command">unzip pindel-master.zip -d pindel</action>
26 COLOUSINGBD15_TIME=60 24 COLOUSINGBD15_TIME=60
27 COLOWOBD15_TIME=80 25 COLOWOBD15_TIME=80
28 SIM1CHRVS20305_TIME=60" > Makefile.local 26 SIM1CHRVS20305_TIME=60" > Makefile.local
29 </action> 27 </action>
30 <action type="shell_command">make SAMTOOLS=~/samtools THREADS=2</action> 28 <action type="shell_command">make SAMTOOLS=~/samtools THREADS=2</action>
31 <!-- <action type="shell_command">./INSTALL ~/samtools</action> -->
32
33
34 <action type="move_file"> 29 <action type="move_file">
35 <source>pindel</source> 30 <source>pindel</source>
36 <destination>$INSTALL_DIR/</destination> 31 <destination>$INSTALL_DIR/</destination>
37 </action> 32 </action>
38 <action type="set_environment"> 33 <action type="set_environment">