Mercurial > repos > devteam > package_samtools_0_1_16
comparison tool_dependencies.xml @ 1:cac9b701b6f8 draft default tip
Uploaded tool_dependencies.xml that defines a recipe to get a pre-compiled version if possible.
| author | devteam |
|---|---|
| date | Tue, 24 Sep 2013 16:18:59 -0400 |
| parents | 72432392e81a |
| children |
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| 0:72432392e81a | 1:cac9b701b6f8 |
|---|---|
| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | 2 <tool_dependency> |
| 3 <package name="samtools" version="0.1.16"> | 3 <package name="samtools" version="0.1.16"> |
| 4 <install version="1.0"> | 4 <install version="1.0"> |
| 5 <actions> | 5 <actions_group> |
| 6 <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/0.1.16/samtools-0.1.16.tar.bz2</action> | 6 <actions os="linux" architecture="i386"> |
| 7 <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action> | 7 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/i386/samtools/samtools-0.1.16-linux-i386.tgz</action> |
| 8 <action type="shell_command">make</action> | 8 <action type="move_directory_files"> |
| 9 <action type="move_file"> | 9 <source_directory>.</source_directory> |
| 10 <source>samtools</source> | 10 <destination_directory>$INSTALL_DIR</destination_directory> |
| 11 <destination>$INSTALL_DIR/bin</destination> | 11 </action> |
| 12 </action> | 12 </actions> |
| 13 <actions os="linux" architecture="x86_64"> | |
| 14 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.16-linux-x86_64.tgz</action> | |
| 15 <action type="move_directory_files"> | |
| 16 <source_directory>.</source_directory> | |
| 17 <destination_directory>$INSTALL_DIR</destination_directory> | |
| 18 </action> | |
| 19 </actions> | |
| 20 <actions os="darwin" architecture="i386"> | |
| 21 <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/i386/samtools/samtools-0.1.16-Darwin-i386.tgz</action> | |
| 22 <action type="move_directory_files"> | |
| 23 <source_directory>.</source_directory> | |
| 24 <destination_directory>$INSTALL_DIR</destination_directory> | |
| 25 </action> | |
| 26 </actions> | |
| 27 <actions os="darwin" architecture="x86_64"> | |
| 28 <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.16-Darwin-x86_64.tgz</action> | |
| 29 <action type="move_directory_files"> | |
| 30 <source_directory>.</source_directory> | |
| 31 <destination_directory>$INSTALL_DIR</destination_directory> | |
| 32 </action> | |
| 33 </actions> | |
| 34 <actions> | |
| 35 <action type="download_by_url">http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.16.tar.bz2</action> | |
| 36 <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action> | |
| 37 <action type="shell_command">make</action> | |
| 38 <action type="move_file"> | |
| 39 <source>samtools</source> | |
| 40 <destination>$INSTALL_DIR/bin</destination> | |
| 41 </action> | |
| 42 <action type="move_file"> | |
| 43 <source>libbam.a</source> | |
| 44 <destination>$INSTALL_DIR/lib</destination> | |
| 45 </action> | |
| 46 </actions> | |
| 13 <action type="set_environment"> | 47 <action type="set_environment"> |
| 14 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | 48 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> |
| 49 <environment_variable name="BAM_LIB_PATH" action="set_to">$INSTALL_DIR/lib</environment_variable> | |
| 15 </action> | 50 </action> |
| 16 </actions> | 51 </actions_group> |
| 17 </install> | 52 </install> |
| 18 <readme> | 53 <readme> |
| 19 This is the last version of SAMTools to include the 'pileup' command. | 54 This is the last version of SAMTools to include the 'pileup' command. |
| 20 | 55 |
| 21 Program: samtools (Tools for alignments in the SAM format) | 56 Program: samtools (Tools for alignments in the SAM format) |