Mercurial > repos > davidvanzessen > igblastn_immunerepertoire_igg
diff tool_dependencies.xml @ 1:7b0d9c107680 draft
Uploaded
author | davidvanzessen |
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date | Thu, 23 Jan 2014 08:29:40 -0500 |
parents | d52f6a986108 |
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--- a/tool_dependencies.xml Thu Jan 23 08:22:28 2014 -0500 +++ b/tool_dependencies.xml Thu Jan 23 08:29:40 2014 -0500 @@ -6,35 +6,15 @@ <package name="igBlastn" version="1.0.0"> <install version="1.0"> <actions> - <action type="download_by_url" target_filename="ncbi-igblast-1.0.0-x64-linux.tar.gz"> - ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/1.0.0/ncbi-igblast-1.0.0-x64-linux.tar.gz - </action> - - - <action type="move_directory_files"> - <source_directory>ncbi-igblast-1.0.0</source_directory> - <destination_directory>$INSTALL_DIR/ncbi-igblast-1.0.0</destination_directory> - </action> - <action type="set_environment"> - <environment_variable name="IGDATA" action="set_to">$INSTALL_DIR/ncbi-igblast-1.0.0</environment_variable> - </action> + <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> + <action type="shell_command">tar zxvf $INSTALL_DIR/ncbi-igblast-1.0.0-x64-linux.tar.gz -C $INSTALL_DIR</action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/ncbi-igblast-1.0.0/bin</environment_variable> </action> - - <action type="make_directory">$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data</action> - <action type="make_directory">$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</action> - - <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> - - <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> - - <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> - </actions> </install> <readme> - 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/ + Downloads the igblastn-1.0.0 executable from NCBI and uses a fixed database included in this tool. </readme> </package> -</tool_dependency> +</tool_dependency> \ No newline at end of file