Mercurial > repos > iuc > package_bcftools_1_2
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planemo upload for repository https://github.com/davebx/tools-iuc/blob/master/packages/package_bcftools_1_2/tool_dependencies.xml commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
author | iuc |
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date | Tue, 19 May 2015 14:57:05 -0400 |
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<?xml version="1.0"?> <tool_dependency> <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="bcftools" 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/bcftools/bcftools-1.2-Linux-x86_64.tgz</action> <action type="move_directory_files"> <source_directory>.</source_directory> <destination_directory>$INSTALL_DIR</destination_directory> </action> </actions> <actions> <action type="set_environment_for_install"> <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> <package name="zlib" version="1.2.8" /> </repository> </action> <action type="download_by_url">https://github.com/samtools/bcftools/releases/download/1.2/bcftools-1.2.tar.bz2</action> <action type="shell_command">sed -i.bak 's#/usr/local#$INSTALL_DIR#' Makefile</action> <action type="make_install" /> </actions> <action type="set_environment"> <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> <environment_variable action="set_to" name="BCFTOOLS_ROOT_PATH">$INSTALL_DIR</environment_variable> </action> </actions_group> </install> <readme> Program: bcftools (Tools for variant calling and manipulating VCFs and BCFs) Version: 1.2 (using htslib 1.2.1) Usage: bcftools <command> <argument> Commands: -- Indexing index index VCF/BCF files -- VCF/BCF manipulation annotate annotate and edit VCF/BCF files concat concatenate VCF/BCF files from the same set of samples convert convert VCF/BCF files to different formats and back isec intersections of VCF/BCF files merge merge VCF/BCF files files from non-overlapping sample sets norm left-align and normalize indels plugin user-defined plugins query transform VCF/BCF into user-defined formats reheader modify VCF/BCF header, change sample names view VCF/BCF conversion, view, subset and filter VCF/BCF files -- VCF/BCF analysis call SNP/indel calling consensus create consensus sequence by applying VCF variants filter filter VCF/BCF files using fixed thresholds gtcheck check sample concordance, detect sample swaps and contamination roh identify runs of autozygosity (HMM) stats produce VCF/BCF stats Most commands accept VCF, bgzipped VCF, and BCF with the file type detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most but not all situations. </readme> </package> </tool_dependency>