Mercurial > repos > devteam > package_samtools_0_1_16
changeset 1:3cc494fb5a14 draft default tip
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
| author | devteam |
|---|---|
| date | Wed, 25 Sep 2013 10:50:18 -0400 |
| parents | 75367f13eb3c |
| children | |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 44 insertions(+), 9 deletions(-) [+] |
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--- a/tool_dependencies.xml Tue Feb 05 14:17:34 2013 -0500 +++ b/tool_dependencies.xml Wed Sep 25 10:50:18 2013 -0400 @@ -2,18 +2,53 @@ <tool_dependency> <package name="samtools" version="0.1.16"> <install version="1.0"> - <actions> - <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/0.1.16/samtools-0.1.16.tar.bz2</action> - <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action> - <action type="shell_command">make</action> - <action type="move_file"> - <source>samtools</source> - <destination>$INSTALL_DIR/bin</destination> - </action> + <actions_group> + <actions os="linux" architecture="i386"> + <action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/linux/i386/samtools/samtools-0.1.16-linux-i386.tgz</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + </actions> + <actions os="linux" architecture="x86_64"> + <action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.16-linux-x86_64.tgz</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + </actions> + <actions os="darwin" architecture="i386"> + <action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/darwin/i386/samtools/samtools-0.1.16-Darwin-i386.tgz</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + </actions> + <actions os="darwin" architecture="x86_64"> + <action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.16-Darwin-x86_64.tgz</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + </actions> + <actions> + <action type="download_by_url">http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.16.tar.bz2</action> + <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action> + <action type="shell_command">make</action> + <action type="move_file"> + <source>samtools</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>libbam.a</source> + <destination>$INSTALL_DIR/lib</destination> + </action> + </actions> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + <environment_variable name="BAM_LIB_PATH" action="set_to">$INSTALL_DIR/lib</environment_variable> </action> - </actions> + </actions_group> </install> <readme> This is the last version of SAMTools to include the 'pileup' command.