Mercurial > repos > iuc > package_samtools_0_1_19
comparison tool_dependencies.xml @ 7:c9bd782f5342 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_0_1_19 commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
| author | iuc |
|---|---|
| date | Sat, 25 Jun 2016 17:21:35 -0400 |
| parents | 96aab723499f |
| children |
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| 6:96aab723499f | 7:c9bd782f5342 |
|---|---|
| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | 2 <tool_dependency> |
| 3 <package name="samtools" version="0.1.19"> | 3 <package name="samtools" version="0.1.19"> |
| 4 <install version="1.0"> | 4 <install version="1.0"> |
| 5 <actions_group> | 5 <actions_group> |
| 6 <actions os="linux" architecture="x86_64"> | 6 <actions architecture="x86_64" os="linux"> |
| 7 <action type="download_by_url" target_filename="samtools-0.1.19.tgz">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.19-Linux-x86_64.tgz</action> | 7 <action type="download_by_url" sha256sum="3cc457cd66e077b70887155435d8f563154371a61e7ac6714bc10b6aa19841bd" target_filename="samtools-0.1.19.tgz">https://depot.galaxyproject.org/software/samtools/samtools_0.1.19_linux_x64.tar.gz</action> |
| 8 <action type="move_directory_files"> | 8 <action type="move_directory_files"> |
| 9 <source_directory>.</source_directory> | 9 <source_directory>.</source_directory> |
| 10 <destination_directory>$INSTALL_DIR</destination_directory> | 10 <destination_directory>$INSTALL_DIR</destination_directory> |
| 11 </action> | 11 </action> |
| 12 <action type="set_environment"> | |
| 13 <environment_variable name="BAM_INCLUDE" action="set_to">$INSTALL_DIR/include</environment_variable> | |
| 14 </action> | |
| 12 </actions> | 15 </actions> |
| 13 <actions os="darwin" architecture="x86_64"> | 16 <actions architecture="x86_64" os="darwin"> |
| 14 <action type="download_by_url" target_filename="samtools-0.1.19.tgz">http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.19-Darwin-x86_64.tgz</action> | 17 <action type="download_by_url" sha256sum="01e0a2cb38b1bcd433461cef43ff6555755a30dfbe83cb9c0a24cb028b104ac7" target_filename="samtools-0.1.19.tgz">https://depot.galaxyproject.org/software/samtools/samtools_0.1.19_darwin_x64.tar.gz</action> |
| 15 <action type="move_directory_files"> | 18 <action type="move_directory_files"> |
| 16 <source_directory>.</source_directory> | 19 <source_directory>.</source_directory> |
| 17 <destination_directory>$INSTALL_DIR</destination_directory> | 20 <destination_directory>$INSTALL_DIR</destination_directory> |
| 18 </action> | 21 </action> |
| 22 <action type="set_environment"> | |
| 23 <environment_variable name="BAM_INCLUDE" action="set_to">$INSTALL_DIR/include</environment_variable> | |
| 24 </action> | |
| 19 </actions> | 25 </actions> |
| 20 <actions> | 26 <actions> |
| 21 <action type="download_by_url">http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.19.tar.bz2</action> | 27 <action type="download_by_url" sha256sum="d080c9d356e5f0ad334007e4461cbcee3c4ca97b8a7a5a48c44883cf9dee63d4">https://depot.galaxyproject.org/software/samtools/samtools_0.1.19_src_all.tar.bz2</action> |
| 22 <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action> | 28 <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action> |
| 23 <action type="shell_command">make</action> | 29 <action type="shell_command">make</action> |
| 24 <action type="move_file"> | 30 <action type="move_file"> |
| 25 <source>samtools</source> | 31 <source>samtools</source> |
| 26 <destination>$INSTALL_DIR/bin</destination> | 32 <destination>$INSTALL_DIR/bin</destination> |
| 38 <destination>$INSTALL_DIR/lib</destination> | 44 <destination>$INSTALL_DIR/lib</destination> |
| 39 </action> | 45 </action> |
| 40 <action type="move_directory_files"> | 46 <action type="move_directory_files"> |
| 41 <source_directory>.</source_directory> | 47 <source_directory>.</source_directory> |
| 42 <destination_directory>$INSTALL_DIR/include/bam</destination_directory> | 48 <destination_directory>$INSTALL_DIR/include/bam</destination_directory> |
| 49 </action> | |
| 50 <action type="set_environment"> | |
| 51 <environment_variable name="BAM_INCLUDE" action="set_to">$INSTALL_DIR/include/bam</environment_variable> | |
| 43 </action> | 52 </action> |
| 44 </actions> | 53 </actions> |
| 45 <action type="set_environment"> | 54 <action type="set_environment"> |
| 46 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | 55 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> |
| 47 <environment_variable name="BAM_LIB_PATH" action="set_to">$INSTALL_DIR/lib</environment_variable> | 56 <environment_variable name="BAM_LIB_PATH" action="set_to">$INSTALL_DIR/lib</environment_variable> |