Mercurial > repos > davidvanzessen > igblast_human

comparison tool_dependencies.xml @ 54:ddc765e7142c draft

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author davidvanzessen
date Tue, 03 Dec 2013 04:33:59 -0500
parents fe9acb633402
children 99541760fdfe
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53:fe9acb633402 54:ddc765e7142c
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="make_directory">$INSTALL_DIR/ncbi-igblast-1.0.0</action>
10 <action type="make_directory">$INSTALL_DIR/ncbi-igblast-1.0.0/bin</action>
11 <action type="download_by_url" target_filename="ncbi-igblast-1.0.0-x64-linux.tar.gz"> 9 <action type="download_by_url" target_filename="ncbi-igblast-1.0.0-x64-linux.tar.gz">
12 ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/1.0.0/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
13 </action> 11 </action>
14 12
15 13
21 <environment_variable name="IGDATA" action="set_to">$INSTALL_DIR/ncbi-igblast-1.0.0</environment_variable> 19 <environment_variable name="IGDATA" action="set_to">$INSTALL_DIR/ncbi-igblast-1.0.0</environment_variable>
22 </action> 20 </action>
23 <action type="set_environment"> 21 <action type="set_environment">
24 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/ncbi-igblast-1.0.0/bin</environment_variable> 22 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/ncbi-igblast-1.0.0/bin</environment_variable>
25 </action> 23 </action>
24
26 <action type="make_directory">$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data</action> 25 <action type="make_directory">$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data</action>
27 <action type="make_directory">$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</action> 26 <action type="make_directory">$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</action>
28 27
29 <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> 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>
30 29
31 <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> 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>
32 31
33 <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> 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>
34 33
35
36 </actions> 34 </actions>
37 </install> 35 </install>
38 <readme> 36 <readme>
39 Downloads igBlast with an older version of the NCBI database. 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/
40 </readme> 38 </readme>
41 </package> 39 </package>
42 </tool_dependency> 40 </tool_dependency>