Mercurial > repos > lionelguy > spades
diff tools/spades_2_5/tool_dependencies.xml @ 1:0f8b2da62d7d draft
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
| author | lionelguy |
|---|---|
| date | Mon, 19 Aug 2013 09:06:17 -0400 |
| parents | |
| children | d82f18c76309 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/spades_2_5/tool_dependencies.xml Mon Aug 19 09:06:17 2013 -0400 @@ -0,0 +1,33 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="spades" version="2.5.0"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://spades.bioinf.spbau.ru/release2.5.0/SPAdes-2.5.0-Linux.tar.gz</action> + <!-- Copying the whole bin folder --> + <action type="make_directory">$INSTALL_DIR/bin</action> + <action type="make_directory">$INSTALL_DIR/share</action> + <action type="move_directory_files"> + <source_directory>bin</source_directory> + <destination_directory>$INSTALL_DIR/bin</destination_directory> + </action> + <action type="move_directory_files"> + <source_directory>share</source_directory> + <destination_directory>$INSTALL_DIR/share</destination_directory> + </action> + <!-- This is required to have spades accept .dat files --> + <action type="shell_command">sed -i -e "s/\('\.fa', '\.fasta', '\.fq', '\.fastq', '\.gz'\)/\\1, '.dat'/" $INSTALL_DIR/share/spades/spades_pipeline/support.py</action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> +This installs SPAdes 2.5.0. + +See manual here http://spades.bioinf.spbau.ru/release2.5.0/manual.html +See also here http://bioinf.spbau.ru/en/spades + </readme> + </package> +</tool_dependency> +