Mercurial > repos > davidvanzessen > igblast_human

comparison tool_dependencies.xml @ 45:02de9290e324 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author davidvanzessen
date Fri, 22 Nov 2013 07:20:20 -0500
parents 46fbf2f2d1aa
children 9ed2773166cf
comparison
equal deleted inserted replaced
44:cf56df9e5dab 45:02de9290e324
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>
9 <action type="download_by_url" target_filename="ncbi-igblast-1.0.0-x64-linux.tar.gz"> 11 <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 12 ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/1.0.0/ncbi-igblast-1.0.0-x64-linux.tar.gz
11 </action> 13 </action>
12 14
13 15
19 <environment_variable name="IGDATA" action="set_to">$INSTALL_DIR/ncbi-igblast-1.0.0</environment_variable> 21 <environment_variable name="IGDATA" action="set_to">$INSTALL_DIR/ncbi-igblast-1.0.0</environment_variable>
20 </action> 22 </action>
21 <action type="set_environment"> 23 <action type="set_environment">
22 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/ncbi-igblast-1.0.0/bin</environment_variable> 24 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/ncbi-igblast-1.0.0/bin</environment_variable>
23 </action> 25 </action>
24 26 <action type="shell_command">unzip database.zip -d $INSTALL_DIR/ncbi-igblast-1.0.0/</action>
25 <action type="make_directory">$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data</action> 27
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 28
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> 29 </actions>
35 </install> 30 </install>
36 <readme> 31 <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/ 32 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> 33 </readme>
39 </package> 34 </package>
40 </tool_dependency> 35 </tool_dependency>