| Previous changeset 9:d291dc763c4c (2013-06-05) Next changeset 11:e9ebed0c12f6 (2014-02-17) |
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Commit message:
Uploaded updated tool dependency definition. |
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modified:
tool_dependencies.xml |
| b |
| diff -r d291dc763c4c -r 07d55d9ea9a4 tool_dependencies.xml --- a/tool_dependencies.xml Wed Jun 05 15:00:03 2013 -0400 +++ b/tool_dependencies.xml Mon Dec 16 16:31:57 2013 -0500 |
| b |
| @@ -1,47 +1,9 @@ <?xml version="1.0"?> <tool_dependency> <package name="freebayes" version="0.9.6_9608597d12e127c847ae03aa03440ab63992fedf"> - <install version="1.0"> - <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>$INSTALL_DIR/bin</destination_directory> - </action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme> -FreeBayes requires g++ and the standard C and C++ development libraries. -Additionally, cmake is required for building the BamTools API. - </readme> + <repository changeset_revision="7615ee9e216d" name="package_freebayes_0_9_6_9608597d" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> <package name="samtools" version="0.1.18"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action> - <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action> - <action type="shell_command">make</action> - <action type="move_file"> - <source>samtools</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="move_file"> - <source>misc/maq2sam-long</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme> -Compiling SAMtools requires the ncurses and zlib development libraries. - </readme> + <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |