| Previous changeset 1:00e17a794a2e (2013-09-17) Next changeset 3:6b6b5498d9a2 (2014-04-29) |
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tool_dependencies.xml |
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| diff -r 00e17a794a2e -r b471600c8a3b tool_dependencies.xml --- a/tool_dependencies.xml Tue Sep 17 11:36:59 2013 -0500 +++ b/tool_dependencies.xml Sun Apr 27 14:28:10 2014 -0400 |
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| @@ -1,32 +1,26 @@ <?xml version="1.0"?> <tool_dependency> + <package name="ncurses" version="5.9"> + <repository changeset_revision="9ed7af129bd3" name="package_ncurses_5_9" 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="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action> + <action type="set_environment_for_install"> + <repository changeset_revision="9ed7af129bd3" name="package_ncurses_5_9" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu"> + <package name="ncurses" version="5.9" /> + </repository> + </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$NCURSES_INCLUDE_PATH/ncurses/ -L$NCURSES_LIB_PATH|g" Makefile</action> <action type="shell_command">make</action> - <action type="shell_command">chmod ugo+rx misc/*.p?</action> - <action type="shell_command">mkdir misc/bin</action> - <action type="shell_command">cp -p `find misc -type f -perm -555` misc/bin/</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>$INSTALL_DIR/bin</destination> - </action> - <action type="move_directory_files"> - <source_directory>misc/bin</source_directory> - <destination_directory>$INSTALL_DIR/bin</destination_directory> - </action> <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> @@ -54,28 +48,7 @@ targetcut cut fosmid regions (for fosmid pool only) phase phase heterozygotes -This also installs bcftools and misc utility commands: - bcftools - vcfutils.pl - ace2sam - bamcheck - blast2sam.pl - bowtie2sam.pl - export2sam.pl - interpolate_sam.pl - maq2sam-long - maq2sam-short - md5fa - md5sum-lite - novo2sam.pl - psl2sam.pl - sam2vcf.pl - samtools.pl - soap2sam.pl - varfilter.py - wgsim - wgsim_eval.pl - zoom2sam.pl +Requirements: libncurses header files </readme> </package> </tool_dependency> |