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tool_dependencies.xml |
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| diff -r 923adc89c666 -r 96aab723499f tool_dependencies.xml --- a/tool_dependencies.xml Tue Jul 22 12:04:37 2014 -0400 +++ b/tool_dependencies.xml Thu Feb 26 14:21:15 2015 -0500 |
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| @@ -1,38 +1,57 @@ <?xml version="1.0"?> <tool_dependency> - <package name="ncurses" version="5.9"> - <repository changeset_revision="71e3f4bfd1a9" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> - </package> - <package name="zlib" version="1.2.8"> - <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> - </package> <package name="samtools" version="0.1.19"> <install version="1.0"> - <actions> - <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/0.1.19/samtools-0.1.19.tar.bz2</action> - <action type="set_environment_for_install"> - <repository changeset_revision="71e3f4bfd1a9" name="package_ncurses_5_9" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu"> - <package name="ncurses" version="5.9" /> - </repository> - <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu"> - <package name="zlib" version="1.2.8" /> - </repository> + <actions_group> + <actions os="linux" architecture="x86_64"> + <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> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + </actions> + <actions os="darwin" architecture="x86_64"> + <action type="download_by_url" target_filename="samtools-0.1.19.tgz">http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.19-Darwin-x86_64.tgz</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + </actions> + <actions> + <action type="download_by_url">http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.19.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>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bcftools/bcftools</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bcftools/vcfutils.pl</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>libbam.a</source> + <destination>$INSTALL_DIR/lib</destination> + </action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR/include/bam</destination_directory> + </action> + </actions> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + <environment_variable name="BAM_LIB_PATH" action="set_to">$INSTALL_DIR/lib</environment_variable> + <environment_variable name="BAM_ROOT" action="set_to">$INSTALL_DIR</environment_variable> </action> - <action type="shell_command">sed -i 's/-lcurses/-lncurses/' Makefile</action> - <action type="shell_command">sed -i -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH -L$NCURSES_LIB_PATH|g" Makefile</action> - <action type="shell_command">make</action> - <action type="move_file"> - <source>samtools</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> + </actions_group> </install> <readme> Program: samtools (Tools for alignments in the SAM format) -Version: 0.1.19 +Version: 0.1.19-44428cd Usage: samtools <command> [options] @@ -51,10 +70,10 @@ rmdup remove PCR duplicates reheader replace BAM header cat concatenate BAMs + bedcov read depth per BED region targetcut cut fosmid regions (for fosmid pool only) phase phase heterozygotes - -Requirements: libncurses header files + bamshuf shuffle and group alignments by name </readme> </package> </tool_dependency> |