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tool_dependencies.xml |
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| diff -r 000000000000 -r 0918c21d2f6d tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Sep 30 08:58:34 2015 -0400 |
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| @@ -0,0 +1,81 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="ncurses" version="5.9"> + <repository changeset_revision="93ce0192b9db" name="package_ncurses_5_9" owner="anmoljh" prior_installation_required="True" toolshed="https://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="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="samtools" version="1.2"> + <install version="1.0"> + <actions_group> + <actions architecture="x86_64" os="linux"> + <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-1.2-Linux-x86_64.tgz</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + </actions> + <actions> + <action type="download_by_url">https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2</action> + <action type="set_environment_for_install"> + <repository changeset_revision="93ce0192b9db" name="package_ncurses_5_9" owner="anmoljh" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="ncurses" version="5.9" /> + </repository> + <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="zlib" version="1.2.8" /> + </repository> + </action> + <action type="shell_command">sed -i.bak 's#/usr/local#$INSTALL_DIR#' Makefile</action> + <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/' Makefile</action> + <action type="shell_command">sed -i.bak -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH -L$NCURSES_LIB_PATH|g" Makefile</action> + <action type="make_install" /> + <action type="move_file"> + <source>samtools</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + </actions> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + <environment_variable action="set_to" name="SAMTOOLS_ROOT_PATH">$INSTALL_DIR</environment_variable> + </action> + </actions_group> + </install> + <readme> +Program: samtools (Tools for alignments in the SAM format) +Version: 1.2 + +Usage: samtools <command> [options] + +Commands: + -- indexing + faidx index/extract FASTA + index index alignment + -- editing + calmd recalculate MD/NM tags and '=' bases + fixmate fix mate information + reheader replace BAM header + rmdup remove PCR duplicates + targetcut cut fosmid regions (for fosmid pool only) + -- file operations + bamshuf shuffle and group alignments by name + cat concatenate BAMs + merge merge sorted alignments + mpileup multi-way pileup + sort sort alignment file + split splits a file by read group + bam2fq converts a BAM to a FASTQ + -- stats + bedcov read depth per BED region + depth compute the depth + flagstat simple stats + idxstats BAM index stats + phase phase heterozygotes + stats generate stats (former bamcheck) + -- viewing + flags explain BAM flags + tview text alignment viewer + view SAM<->BAM<->CRAM conversion + </readme> + </package> +</tool_dependency> |