Mercurial > repos > lionelguy > spades
comparison tools/spades_2_5/tool_dependencies.xml @ 3:d82f18c76309 draft
Uploaded spades wrapper 0.6. Supports spades 2.5.1. Also removes the need for the hack at installation time, by fixing the problem with input files. Shows the license for the tool as well.
| author | lionelguy |
|---|---|
| date | Thu, 12 Sep 2013 07:46:54 -0400 |
| parents | 0f8b2da62d7d |
| children | 1b1af74a54ae |
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| 2:b5ce24f34dd7 | 3:d82f18c76309 |
|---|---|
| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | 2 <tool_dependency> |
| 3 <package name="spades" version="2.5.0"> | 3 <package name="spades" version="2.5.0"> |
| 4 <install version="1.0"> | 4 <install version="1.0"> |
| 5 <actions> | 5 <actions> |
| 6 <action type="download_by_url">http://spades.bioinf.spbau.ru/release2.5.0/SPAdes-2.5.0-Linux.tar.gz</action> | 6 <action type="download_by_url">http://spades.bioinf.spbau.ru/release2.5.1/SPAdes-2.5.1-Linux.tar.gz</action> |
| 7 <!-- Copying the whole bin folder --> | 7 <!-- Copying the whole bin folder --> |
| 8 <action type="make_directory">$INSTALL_DIR/bin</action> | 8 <action type="make_directory">$INSTALL_DIR/bin</action> |
| 9 <action type="make_directory">$INSTALL_DIR/share</action> | 9 <action type="make_directory">$INSTALL_DIR/share</action> |
| 10 <action type="move_directory_files"> | 10 <action type="move_directory_files"> |
| 11 <source_directory>bin</source_directory> | 11 <source_directory>bin</source_directory> |
| 14 <action type="move_directory_files"> | 14 <action type="move_directory_files"> |
| 15 <source_directory>share</source_directory> | 15 <source_directory>share</source_directory> |
| 16 <destination_directory>$INSTALL_DIR/share</destination_directory> | 16 <destination_directory>$INSTALL_DIR/share</destination_directory> |
| 17 </action> | 17 </action> |
| 18 <!-- This is required to have spades accept .dat files --> | 18 <!-- This is required to have spades accept .dat files --> |
| 19 <action type="shell_command">sed -i -e "s/\('\.fa', '\.fasta', '\.fq', '\.fastq', '\.gz'\)/\\1, '.dat'/" $INSTALL_DIR/share/spades/spades_pipeline/support.py</action> | 19 <!-- <action type="shell_command">sed -i -e "s/\('\.fa', '\.fasta', '\.fq', '\.fastq', '\.gz'\)/\\1, '.dat'/" $INSTALL_DIR/share/spades/spades_pipeline/support.py</action> --> |
| 20 <action type="set_environment"> | 20 <!-- <action type="set_environment"> --> |
| 21 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | 21 <!-- <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> --> |
| 22 </action> | 22 <!-- </action> --> |
| 23 </actions> | 23 </actions> |
| 24 </install> | 24 </install> |
| 25 <readme> | 25 <readme> |
| 26 This installs SPAdes 2.5.0. | 26 This installs SPAdes 2.5.1. |
| 27 | 27 |
| 28 See manual here http://spades.bioinf.spbau.ru/release2.5.0/manual.html | 28 See manual here http://spades.bioinf.spbau.ru/release2.5.1/manual.html |
| 29 See also here http://bioinf.spbau.ru/en/spades | 29 See also here http://bioinf.spbau.ru/en/spades |
| 30 </readme> | 30 </readme> |
| 31 </package> | 31 </package> |
| 32 </tool_dependency> | 32 </tool_dependency> |
| 33 | 33 |