Mercurial > repos > jeremie > package_breakdancer_1_2_6
changeset 35:fff5d75555e2 draft
Uploaded
author | jeremie |
---|---|
date | Fri, 27 Jun 2014 06:02:46 -0400 |
parents | 145d09fbd014 |
children | 8fe9a0856399 |
files | tool_dependencies.xml |
diffstat | 1 files changed, 36 insertions(+), 9 deletions(-) [+] |
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--- a/tool_dependencies.xml Fri Jun 27 05:59:25 2014 -0400 +++ b/tool_dependencies.xml Fri Jun 27 06:02:46 2014 -0400 @@ -2,19 +2,46 @@ <tool_dependency> <package name="breakdancer" version="1.2.6"> <install version="1.0"> - <actions> - <action type="download_by_url" target_filename="bin.tar.gz">https://www.dropbox.com/s/6fpm0vqmn0vu5m2/1_2_6.tar.gz?dl=1</action> - <action type="move_directory_files"> - <source_directory>.</source_directory> - <destination_directory>$INSTALL_DIR/bin</destination_directory> - </action> + <actions_group> + <actions architecture="i386" os="linux"> + <action type="download_by_url">http://depot.galaxyproject.org/package/linux/i386/freebayes/freebayes-0.9.6_9608597d-Linux-i686.tgz</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR/bin</destination_directory> + </action> + </actions> + <actions architecture="x86_64" os="linux"> + <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/freebayes/freebayes-0.9.6_9608597d-Linux-x86_64.tgz</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR/bin</destination_directory> + </action> + </actions> + <actions architecture="x86_64" os="darwin"> + <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/freebayes/freebayes-0.9.6_9608597d-Darwin-x86_64.tgz</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR/bin</destination_directory> + </action> + </actions> + <actions> + <action type="shell_command">git clone --recursive git://github.com/ekg/freebayes.git</action> + <action type="shell_command">git checkout 9608597d12e127c847ae03aa03440ab63992fedf</action> + <action type="shell_command">git submodule update --recursive</action> + <action type="shell_command">make || ( make clean && sed -i.bak -e 's:LIBS = -lz -lm -L./ -L../vcflib/tabixpp/ -L$(BAMTOOLS_ROOT)/lib -ltabix:LIBS = -lm -L./ -L../vcflib/tabixpp/ -L$(BAMTOOLS_ROOT)/lib -ltabix -lz:g' src/Makefile && make )</action> + <action type="move_directory_files"> + <source_directory>bin</source_directory> + <destination_directory>$INSTALL_DIR/bin</destination_directory> + </action> + </actions> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> - </actions> + </actions_group> </install> <readme> +FreeBayes requires g++ and the standard C and C++ development libraries. +Additionally, cmake is required for building the BamTools API. </readme> </package> -</tool_dependency> - +</tool_dependency> \ No newline at end of file