Mercurial > repos > fcaramia > methylation_analysis_bismark
comparison tool_dependencies.xml @ 15:d2ba233899b0 draft default tip
Uploaded
| author | fcaramia |
|---|---|
| date | Mon, 17 Jun 2013 21:50:56 -0400 |
| parents | cdb7231da7f2 |
| children |
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| 14:cdb7231da7f2 | 15:d2ba233899b0 |
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| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | 2 <tool_dependency> |
| 3 <set_environment version="1.0"> | 3 <set_environment version="1.0"> |
| 4 <environment_variable name="SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> | 4 <environment_variable name="SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> |
| 5 </set_environment> | 5 </set_environment> |
| 6 <package name="samtools" version="0.1.18"> | |
| 7 <install version="1.0"> | |
| 8 <actions> | |
| 9 <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action> | |
| 10 <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action> | |
| 11 <action type="shell_command">make</action> | |
| 12 <action type="move_file"> | |
| 13 <source>samtools</source> | |
| 14 <destination>$INSTALL_DIR/bin</destination> | |
| 15 </action> | |
| 16 <action type="move_file"> | |
| 17 <source>misc/maq2sam-long</source> | |
| 18 <destination>$INSTALL_DIR/bin</destination> | |
| 19 </action> | |
| 20 <action type="set_environment"> | |
| 21 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | |
| 22 </action> | |
| 23 </actions> | |
| 24 </install> | |
| 25 <readme> | |
| 26 Compiling SAMtools requires the ncurses and zlib development libraries. | |
| 27 </readme> | |
| 28 </package> | |
| 29 | |
| 6 <package name="bowtie2" version="2.0.0-beta7"> | 30 <package name="bowtie2" version="2.0.0-beta7"> |
| 7 <install version="1.0"> | 31 <install version="1.0"> |
| 8 <actions> | 32 <actions> |
| 9 <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.0.0-beta7/bowtie2-2.0.0-beta7-source.zip</action> | 33 <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.0.0-beta7/bowtie2-2.0.0-beta7-source.zip</action> |
| 10 <action type="shell_command">make</action> | 34 <action type="shell_command">make</action> |