Mercurial > repos > bgruening > bismark
comparison tool_dependencies.xml @ 18:862fb59a9a25 draft
Uploaded
| author | bgruening |
|---|---|
| date | Mon, 14 Apr 2014 16:42:38 -0400 |
| parents | 13f458d69c9b |
| children | 30caca800c9b |
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| 17:73508c5b4273 | 18:862fb59a9a25 |
|---|---|
| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | 2 <tool_dependency> |
| 3 <package name="samtools" version="0.1.19"> | |
| 4 <repository changeset_revision="36aa94676939" name="package_samtools_0_1_19" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> | |
| 5 </package> | |
| 3 <set_environment version="1.0"> | 6 <set_environment version="1.0"> |
| 4 <environment_variable name="SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> | 7 <environment_variable action="set_to" name="SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable> |
| 5 </set_environment> | 8 </set_environment> |
| 6 <package name="bowtie2" version="2.0.0-beta7"> | 9 <package name="bowtie2" version="2.1.0"> |
| 7 <install version="1.0"> | 10 <install version="1.0"> |
| 8 <actions> | 11 <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> | 12 <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.1.0/bowtie2-2.1.0-source.zip</action> |
| 10 <action type="shell_command">make</action> | 13 <action type="shell_command">make</action> |
| 11 <action type="move_file"> | 14 <action type="move_file"> |
| 12 <source>bowtie2</source> | 15 <source>bowtie2</source> |
| 13 <destination>$INSTALL_DIR/bin</destination> | 16 <destination>$INSTALL_DIR/bin</destination> |
| 14 </action> | 17 </action> |
| 20 <source>bowtie2-build</source> | 23 <source>bowtie2-build</source> |
| 21 <destination>$INSTALL_DIR/bin</destination> | 24 <destination>$INSTALL_DIR/bin</destination> |
| 22 </action> | 25 </action> |
| 23 <action type="shell_command">chmod +x $INSTALL_DIR/bin/bowtie2</action> | 26 <action type="shell_command">chmod +x $INSTALL_DIR/bin/bowtie2</action> |
| 24 <action type="set_environment"> | 27 <action type="set_environment"> |
| 25 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | 28 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> |
| 26 </action> | 29 </action> |
| 27 </actions> | 30 </actions> |
| 28 </install> | 31 </install> |
| 29 <readme> | 32 <readme> |
| 30 Compiling bowtie2 requires zlib and libpthread to be present on your system. | 33 Compiling bowtie2 requires zlib and libpthread to be present on your system. |
| 46 <action type="move_file"> | 49 <action type="move_file"> |
| 47 <source>bowtie-build</source> | 50 <source>bowtie-build</source> |
| 48 <destination>$INSTALL_DIR/bin</destination> | 51 <destination>$INSTALL_DIR/bin</destination> |
| 49 </action> | 52 </action> |
| 50 <action type="set_environment"> | 53 <action type="set_environment"> |
| 51 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | 54 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> |
| 52 </action> | 55 </action> |
| 53 </actions> | 56 </actions> |
| 54 </install> | 57 </install> |
| 55 <readme> | 58 <readme> |
| 56 </readme> | 59 </readme> |
| 57 </package> | 60 </package> |
| 58 </tool_dependency> | 61 </tool_dependency> |
| 59 | |
| 60 | |
| 61 |