Mercurial > repos > iuc > package_samtools_0_1_19
view tool_dependencies.xml @ 5:923adc89c666 draft
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author | bgruening |
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date | Tue, 22 Jul 2014 12:04:37 -0400 |
parents | 279806044d60 |
children | 96aab723499f |
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<?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> </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> </install> <readme> Program: samtools (Tools for alignments in the SAM format) Version: 0.1.19 Usage: samtools <command> [options] Command: view SAM<->BAM conversion sort sort alignment file mpileup multi-way pileup depth compute the depth faidx index/extract FASTA tview text alignment viewer index index alignment idxstats BAM index stats (r595 or later) fixmate fix mate information flagstat simple stats calmd recalculate MD/NM tags and '=' bases merge merge sorted alignments rmdup remove PCR duplicates reheader replace BAM header cat concatenate BAMs targetcut cut fosmid regions (for fosmid pool only) phase phase heterozygotes Requirements: libncurses header files </readme> </package> </tool_dependency>