Mercurial > repos > bonsai > sortmerna
diff tool_dependencies.xml @ 0:2e7f0da431e3 draft default tip
Uploaded version 1.0
author | bonsai |
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date | Tue, 30 Apr 2013 13:12:35 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Apr 30 13:12:35 2013 -0400 @@ -0,0 +1,42 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="sortmerna" version="1.7"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://bioinfo.lifl.fr/RNA/sortmerna/code/sortmerna-1.7.tar.gz</action> + <action type="shell_command">./configure</action> + <action type="shell_command">make</action> + <action type="shell_command">make check</action> + <action type="move_file"> + <source>sortmerna</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>buildtrie</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>scripts/merge-paired-reads.sh</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_directory_files"> + <source_directory>rRNA_databases</source_directory> + <destination_directory>$INSTALL_DIR/rRNA_databases</destination_directory> + </action> + <action type="move_directory_files"> + <source_directory>automata</source_directory> + <destination_directory>$INSTALL_DIR/automata</destination_directory> + </action> + <action type="set_environment"> + <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR</environment_variable> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> +SortMeRNA requires g++ 4.3 or later. Installation may take a moment since ribosomal databases have to be indexed. + </readme> + </package> +</tool_dependency>