Mercurial > repos > jeremie > package_pindel_0_2_5

comparison tool_dependencies.xml @ 26:47817c968422 draft

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author jeremie
date Fri, 20 Jun 2014 10:28:26 -0400
parents 88444ff7009f
children ae37c0fd6590
comparison
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25:88444ff7009f 26:47817c968422
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">
13 echo "$samtools
14 samtools
15 $PATH
16 $INSTALL_DIR"
17 </action>
12 <!-- <action type="shell_command">ls</action> --> 18 <!-- <action type="shell_command">ls</action> -->
13 <!-- <action type="move_directory_files"> 19 <!-- <action type="move_directory_files">
14 <source_directory>.</source_directory> 20 <source_directory>.</source_directory>
15 <destination_directory>$INSTALL_DIR</destination_directory> 21 <destination_directory>$INSTALL_DIR</destination_directory>
16 </action> 22 </action>
23 THREADS= 29 THREADS=
24 COLOUSINGBD15_TIME=60 30 COLOUSINGBD15_TIME=60
25 COLOWOBD15_TIME=80 31 COLOWOBD15_TIME=80
26 SIM1CHRVS20305_TIME=60" > Makefile.local 32 SIM1CHRVS20305_TIME=60" > Makefile.local
27 </action> 33 </action>
28 <action type="shell_command">make SAMTOOLS=~/samtools THREADS=2</action> 34 <action type="shell_command">make SAMTOOLS=$samtools THREADS=2</action>
29 <action type="move_file"> 35 <action type="move_file">
30 <source>pindel</source> 36 <source>pindel</source>
31 <destination>$INSTALL_DIR/</destination> 37 <destination>$INSTALL_DIR/</destination>
32 </action> 38 </action>
33 <action type="set_environment"> 39 <action type="set_environment">