Mercurial > repos > jeremie > package_pindel_0_2_5
comparison tool_dependencies.xml @ 26:47817c968422 draft
Uploaded
author | jeremie |
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date | Fri, 20 Jun 2014 10:28:26 -0400 |
parents | 88444ff7009f |
children | ae37c0fd6590 |
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25:88444ff7009f | 26:47817c968422 |
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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"> |