Mercurial > repos > fcaramia > contra
comparison tool_dependencies.xml @ 25:c361b3fb806e
added Nicola Path 2.0
| author | Franco Caramia <franco.caramia@petermac.org> |
|---|---|
| date | Tue, 03 Jun 2014 17:31:28 +1000 |
| parents | 2770f49cb0dc |
| children | 0bf826f62f04 |
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| 24:6bcf47cc272a | 25:c361b3fb806e |
|---|---|
| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | 2 <tool_dependency> |
| 3 | |
| 4 <package name="R" version="3.0.3"> | |
| 5 <repository name="package_r_3_0_3" owner="iuc" /> | |
| 6 </package> | |
| 7 | |
| 3 <package name="samtools" version="0.1.18"> | 8 <package name="samtools" version="0.1.18"> |
| 4 <install version="1.0"> | 9 <repository name="package_samtools_0_1_18" owner="devteam" /> |
| 5 <actions> | |
| 6 <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action> | |
| 7 <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action> | |
| 8 <action type="shell_command">make</action> | |
| 9 <action type="move_file"> | |
| 10 <source>samtools</source> | |
| 11 <destination>$INSTALL_DIR/bin</destination> | |
| 12 </action> | |
| 13 <action type="move_file"> | |
| 14 <source>misc/maq2sam-long</source> | |
| 15 <destination>$INSTALL_DIR/bin</destination> | |
| 16 </action> | |
| 17 <action type="set_environment"> | |
| 18 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | |
| 19 </action> | |
| 20 </actions> | |
| 21 </install> | |
| 22 <readme> | |
| 23 Compiling SAMtools requires the ncurses and zlib development libraries. | |
| 24 </readme> | |
| 25 </package> | 10 </package> |
| 26 | |
| 27 | 11 |
| 28 <package name="bedtools" version="2.17.0"> | 12 <package name="bedtools" version="2.17.0"> |
| 29 <install version="1.0"> | 13 <install version="1.0"> |
| 30 <actions> | 14 <actions> |
| 31 <action type="download_by_url" target_filename="bedtools-2.17.0.tar.gz" >http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz</action> | 15 <action type="download_by_url" target_filename="bedtools-2.17.0.tar.gz" >http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz</action> |
| 32 <action type="shell_command">make all</action> | 16 <action type="shell_command">make all</action> |
| 33 <action type="make_directory">$INSTALL_DIR/bin</action> | 17 <action type="make_directory">$INSTALL_DIR/bin</action> |
| 34 <action type="move_directory_files"> | 18 <action type="move_directory_files"> |
| 35 <source_directory>bin</source_directory> | 19 <source_directory>bin</source_directory> |
| 36 <destination_directory>$INSTALL_DIR/bin</destination_directory> | 20 <destination_directory>$INSTALL_DIR/bin</destination_directory> |
| 37 </action> | 21 </action> |
| 38 <action type="set_environment"> | 22 <action type="set_environment"> |
| 39 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | 23 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> |
| 40 </action> | 24 </action> |
| 41 </actions> | 25 </actions> |
| 42 </install> | 26 </install> |
| 43 <readme> | 27 <readme> |
| 44 GCC version 4.1 or greater is recommended. 3.x versions will typically not compile BEDTools. g++ required | 28 GCC version 4.1 or greater is recommended. 3.x versions will typically not compile BEDTools. g++ required |
| 45 </readme> | 29 </readme> |
| 46 </package> | 30 </package> |
| 47 <package name="contra" version="2.0.4"> | 31 <package name="contra" version="2.0.4"> |
| 48 <install version="1.0"> | 32 <install version="1.0"> |
| 49 <actions> | 33 <actions> |
| 50 <action type="download_by_url">http://downloads.sourceforge.net/project/contra-cnv/CONTRA.V2.0/CONTRA.v2.0.4.tar.gz</action> | 34 <action type="download_by_url">http://downloads.sourceforge.net/project/contra-cnv/CONTRA.V2.0/CONTRA.v2.0.4.tar.gz</action> |
| 51 <action type="shell_command">rm -rf bedtools_installation_guide.txt</action> | 35 <action type="move_file"> |
| 52 <action type="shell_command">rm -rf BEDTools-User-Manual.v4.pdf</action> | |
| 53 <action type="shell_command">rm -rf BEDTools.v2.11.2.tar.gz</action> | |
| 54 <action type="shell_command">rm -rf CONTRA_User_Guide.2.0.pdf</action> | |
| 55 <action type="make_directory">$INSTALL_DIR/bin</action> | |
| 56 <action type="make_directory">$INSTALL_DIR/bin/scripts</action> | |
| 57 <action type="move_file"> | |
| 58 <source>contra.py</source> | 36 <source>contra.py</source> |
| 59 <destination>$INSTALL_DIR/bin</destination> | 37 <destination>$INSTALL_DIR/bin</destination> |
| 60 </action> | 38 </action> |
| 61 <action type="move_file"> | 39 <action type="move_file"> |
| 62 <source>baseline.py</source> | 40 <source>baseline.py</source> |
| 63 <destination>$INSTALL_DIR/bin</destination> | 41 <destination>$INSTALL_DIR/bin</destination> |
| 64 </action> | 42 </action> |
| 65 <action type="move_directory_files"> | 43 <action type="move_directory_files"> |
| 66 <source_directory>scripts</source_directory> | 44 <source_directory>scripts</source_directory> |
| 67 <destination_directory>$INSTALL_DIR/bin/scripts</destination_directory> | 45 <destination_directory>$INSTALL_DIR/bin/scripts</destination_directory> |
| 68 </action> | 46 </action> |
| 69 <action type="set_environment"> | 47 <action type="set_environment"> |
| 70 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | 48 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> |