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App::Egaz - Backend of Easy Genome Aligner SYNOPSIS egaz [-?h] [long options...] --help (or -h) show help aka -? Available commands: commands: list the application's commands help: display a command's help screen blastlink: link sequences by blastn blastmatch: matched positions by blastn in genome sequences blastn: blastn wrapper between two fasta files exactmatch: exact matched positions in genome sequences fas2vcf: list variations in blocked fasta file formats: formats of files use in this project lastz: lastz wrapper for two genomes or self alignments lav2axt: convert .lav files to .axt lav2psl: convert .lav files to .psl lpcnam: the pipeline of pairwise lav-psl-chain-net-axt-maf maskfasta: soft/hard-masking sequences in a fasta file multiz: multiz step by step normalize: normalize lav files partition: partitions fasta files by size prepseq: preparing steps for lastz raxml: raxml wrapper to construct phylogenetic trees repeatmasker: RepeatMasker wrapper template: create executing bash filesRun egaz help command-name for usage information. DESCRIPTIONApp::Egaz is the backend of Easy Genome Aligner. Caution: egaz lpcnam implement UCSC's chain-net pipeline, but some parts, e.g. axtChain don't work correctly under macOS. Use egaz lastz's build in chaining mechanism (C=2) instead. INSTALLATION cpanm --installdeps https://github.com/wang-q/App-Egaz/archive/0.2.5.tar.gz curl -fsSL https://raw.githubusercontent.com/wang-q/App-Egaz/master/share/check_dep.sh | bash cpanm -nq https://github.com/wang-q/App-Egaz/archive/0.2.5.tar.gz # cpanm -nq https://github.com/wang-q/App-Egaz.git CONTAINERegaz has tons of dependencies, so the simplest way to use it is using a container system. Singularity 3.x is the preferred one. # Pull and build the image singularity pull docker://wangq/egaz:master # Run a single command singularity run egaz_master.sif egaz help # Interactive shell # Note: # * .sif is immutable # * $HOME, /tmp, and $PWD are automatically loaded # * All actions affect the host paths # * Singularity Desktop for macOS isn't Fully functional. # * https://github.com/hpcng/singularity/issues/5215 singularity shell egaz_master.sif # With Docker docker run -it --rm -v "$(pwd)"/egaz:/egaz wangq/egaz:master EXAMPLE Multiple genome alignments of Saccharomyces cerevisiae strains and other Saccharomyces species Detailed steps https://github.com/wang-q/App-Egaz/blob/master/doc/Scer.md#detailed-steps egaz template steps https://github.com/wang-q/App-Egaz/blob/master/doc/Scer.md#template-steps Self alignments of S. cerevisiae reference strain S288c Detailed steps https://github.com/wang-q/App-Egaz/blob/master/doc/Scer-self.md#detailed-steps egaz template steps https://github.com/wang-q/App-Egaz/blob/master/doc/Scer-self.md#template-steps AUTHORQiang Wang [email protected] LICENSEThis software is copyright (c) 2018 by Qiang Wang. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. CITATIONYan Wang, Xiaohui Liang, Yuqian Jiang, Danjiang Dong, Cong Zhang, Tianqiang Song, Ming Chen, Yong You, Han Liu, Min Ge, Haibin Dai, Fengchan Xi, Wanqing Zhou, Jian-Qun Chen, Qiang Wang, Qihan Chen, Wenkui Yu. Novel fast pathogen diagnosis method for severe pneumonia patients in the intensive care unit: randomized clinical trial. eLife. 2022; 11: e79014. DOI: https://doi.org/10.7554/eLife.79014 |
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