| Previous changeset 3:d82f18c76309 (2013-09-12) Next changeset 5:2f7860a0017b (2013-09-12) |
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Commit message:
Fixed the version number in tool_deps |
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added:
tool_dependencies.xml |
| b |
| diff -r d82f18c76309 -r a0ea0f7ae029 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Sep 12 07:48:30 2013 -0400 |
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| @@ -0,0 +1,33 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="spades" version="2.5.1"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://spades.bioinf.spbau.ru/release2.5.1/SPAdes-2.5.1-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 2.5.1. + +See manual here http://spades.bioinf.spbau.ru/release2.5.1/manual.html +See also here http://bioinf.spbau.ru/en/spades + </readme> + </package> +</tool_dependency> + |