Mercurial > repos > davidvanzessen > combined_immune_repertoire_pipeline

comparison tool_dependencies.xml @ 0:4e3df2384422 draft

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author davidvanzessen
date Wed, 20 Nov 2013 10:00:28 -0500
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-1:000000000000 0:4e3df2384422
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <set_environment version="1.0">
4 </set_environment>
5
6 <package name="igBlastn" version="1.0.0">
7 <install version="1.0">
8 <actions>
9 <action type="download_by_url" target_filename="ncbi-igblast-1.0.0-x64-linux.tar.gz">
10 ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/1.0.0/ncbi-igblast-1.0.0-x64-linux.tar.gz
11 </action>
12
13
14 <action type="move_directory_files">
15 <source_directory>ncbi-igblast-1.0.0</source_directory>
16 <destination_directory>$INSTALL_DIR/ncbi-igblast-1.0.0</destination_directory>
17 </action>
18 <action type="set_environment">
19 <environment_variable name="IGDATA" action="set_to">$INSTALL_DIR/ncbi-igblast-1.0.0</environment_variable>
20 </action>
21 <action type="set_environment">
22 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/ncbi-igblast-1.0.0/bin</environment_variable>
23 </action>
24
25 <action type="make_directory">$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data</action>
26 <action type="make_directory">$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</action>
27
28 <action type="shell_command">wget -r -np -nH --cut-dirs=4 -R index.html -P $INSTALL_DIR/ncbi-igblast-1.0.0 "ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data"</action>
29
30 <action type="shell_command">wget -r -np -nH --cut-dirs=4 -R index.html -P $INSTALL_DIR/ncbi-igblast-1.0.0 "ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/database"</action>
31
32 <action type="shell_command">wget -r -np -nH --cut-dirs=4 -R index.html -P $INSTALL_DIR/ncbi-igblast-1.0.0 "ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/optional_file"</action>
33
34 </actions>
35 </install>
36 <readme>
37 Downloads igBlast with the latest database provided by NCBI, output may change depending on the database available at ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/
38 </readme>
39 </package>
40 </tool_dependency>