Mercurial > repos > davidvanzessen > igblastn_immunerepertoire_igg

comparison tool_dependencies.xml @ 1:7b0d9c107680 draft

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author davidvanzessen
date Thu, 23 Jan 2014 08:29:40 -0500
parents d52f6a986108
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0:d52f6a986108 1:7b0d9c107680
4 </set_environment> 4 </set_environment>
5 5
6 <package name="igBlastn" version="1.0.0"> 6 <package name="igBlastn" version="1.0.0">
7 <install version="1.0"> 7 <install version="1.0">
8 <actions> 8 <actions>
9 <action type="download_by_url" target_filename="ncbi-igblast-1.0.0-x64-linux.tar.gz"> 9 <action type="shell_command">wget ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/1.0.0/ncbi-igblast-1.0.0-x64-linux.tar.gz -P $INSTALL_DIR</action>
10 ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/1.0.0/ncbi-igblast-1.0.0-x64-linux.tar.gz 10 <action type="shell_command">tar zxvf $INSTALL_DIR/ncbi-igblast-1.0.0-x64-linux.tar.gz -C $INSTALL_DIR</action>
11 </action>
12
13
14 <action type="move_directory_files">
15 <source_directory>ncbi-igblast-1.0.0</source_directory>
16 <destination_directory>$INSTALL_DIR/ncbi-igblast-1.0.0</destination_directory>
17 </action>
18 <action type="set_environment">
19 <environment_variable name="IGDATA" action="set_to">$INSTALL_DIR/ncbi-igblast-1.0.0</environment_variable>
20 </action>
21 <action type="set_environment"> 11 <action type="set_environment">
22 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/ncbi-igblast-1.0.0/bin</environment_variable> 12 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/ncbi-igblast-1.0.0/bin</environment_variable>
23 </action> 13 </action>
24
25 <action type="make_directory">$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> 14 </actions>
35 </install> 15 </install>
36 <readme> 16 <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/ 17 Downloads the igblastn-1.0.0 executable from NCBI and uses a fixed database included in this tool.
38 </readme> 18 </readme>
39 </package> 19 </package>
40 </tool_dependency> 20 </tool_dependency>