Metadata-Version: 2.1
Name: metapi
Version: 0.7.0
Summary: a pipeline to construct a genome catalogue from metagenomics data
Home-page: https://github.com/ohmeta/metapi
Author: Jie Zhu
Author-email: zhujie@genomics.cn
License: GPLv3
Description: #+TITLE: metapi
        
        * Install
        #+BEGIN_SRC bash
        conda install metapi
        #+END_SRC
        
        * Run
        ** help
        #+BEGIN_SRC bash
        $ metapi --help
        
        .___  ___.  _______ .___________.    ___      .______    __
        |   \/   | |   ____||           |   /   \     |   _  \  |  |
        |  \  /  | |  |__   `---|  |----`  /  ^  \    |  |_)  | |  |
        |  |\/|  | |   __|      |  |      /  /_\  \   |   ___/  |  |
        |  |  |  | |  |____     |  |     /  _____  \  |  |      |  |
        |__|  |__| |_______|    |__|    /__/     \__\ | _|      |__|
        
        Omics for All, Open Source for All
        
        A pipeline to construct a genome catalogue from metagenomics data
        
        optional arguments:
        -h, --help     show this help message and exit
        -v, --version  print software version and exit
        
        available subcommands:
        
        init         init project
        denovo_wf    denovo_wf pipeline
        #+END_SRC
        ** init
        #+BEGIN_SRC bash
        $ metapi init --help
        
        usage: metapi init [-h] [-d WORKDIR] [-s SAMPLES]
                           [-b {simulate,trimmingrmhost,assembly}]
        
        arguments:
          -h, --help            show this help message and exit
          -d WORKDIR, --workdir WORKDIR
                                project workdir
          -s SAMPLES, --samples SAMPLES
                                samples list, tsv format required if begin from
                                trimming, rmhost, or assembly: if it is fastq: the
                                header is [id, fq1, fq2], else it is sra: the header
                                is [id, sra] else begin from simulate: the header is
                                [id, genome, abundance, reads_num, model]
        -b {simulate,trimming,rmhost,assembly}, --begin {simulate,trimming,rmhost,assembly}
                                pipeline starting point
        #+END_SRC
        
        ** denovo_wf
        #+BEGIN_SRC bash
        $ metapi denovo_wf --help
        
        usage: metapi denovo_wf [-h] [-d WORKDIR] [--cores CORES] [--jobs JOBS]
                                [--list] [--run] [--debug] [--dry_run] [--qsub]
                                [--wait WAIT] [--snake [SNAKEMAKEARGS]]
                                [TASK]
        
        positional arguments:
          TASK                  pipeline end point. Allowed values are simulate_all,
                                prepare_reads_all, raw_fastqc_all, rmhost_bwa_all,
                                rmhost_bowtie2_all, rmhost_all, assebmly_megahit_all,
                                assembly_idba_ud_all, assembly_metaspades_all,
                                assembly_spades_all, assembly_metaquast_all,
                                assembly_report_all, assembly_all,
                                alignment_base_depth_all, alignment_all,
                                binning_metabat2_all, binning_maxbin2_all,
                                binning_all, predcit_scafitgs_gene_all,
                                predict_bins_gene_all, predcit_all, checkm_link_bins,
                                checkm_all, dereplicate_drep_all, dereplicate_all,
                                classify_short_reads_kraken2_all,
                                classify_hmq_bins_gtdbtk_all, classify_all,
                                profiling_metaphlan2_all, profiling_jgi_all,
                                profiling_humann2_all, profiling_all,
                                upload_sequencing_all, upload_assembly_all,
                                upload_all, all
        
        arguments:
          -h, --help            show this help message and exit
          -d WORKDIR, --workdir WORKDIR
                                project workdir, default: ./
          --cores CORES         CPU cores
          --jobs JOBS           qsub job numbers
          --list                list pipeline rules
          --run                 run pipeline
          --debug               debug pipeline
          --dry_run             dry run pipeline
          --qsub                qsub pipeline
          --wait WAIT           wait given seconds
          --snake [SNAKEMAKEARGS]
                                other snakemake command options, if want --touch, just
                                --snake touch
        #+END_SRC
        
        ** input requirements
        Please supply samples.tsv format like below:
        | id | fq1           | fq2           |
        |----+---------------+---------------|
        | s1 | s1.1.fq.gz    | s1.2.fq.gz    |
        | s2 | s2.1.fq.gz    | s2.2.fq.gz    |
        | s2 | s21.1.fq.gz   | s21.2.fq.g    |
        | s3 | hello.1.fq.gz | hello.2.fq.gz |
        The header must be: id fq1 fq2.
        If id is same, the fq1 and fq2 belong to one sample, and will be merged to
        process.
        
        * License
        - Omics for all, Open Source for all.
        - GPLv3+
        
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.5
Description-Content-Type: text/markdown
