Metadata-Version: 2.1
Name: RuNAs
Version: 0.0.1
Summary: RNAseq pipeline
Home-page: https://github.com/villegar/runas/tree/v2
Author: Roberto Villegas-Diaz
Author-email: villegas.roberto@hotmail.com
License: UNKNOWN
Description: 
        # R<sub>u</sub>NA-s<sub>eq</sub> (&#5809;<sub>&#5794;</sub>&#5822;&#5800;&#5835;) */roonas/* Pipeline
        
        ![Rule Graph](images/rule-graph.png?raw=true "Rule Graph")
        ## Requirements
        -	Python 3.6+ (using [Ana](https://anaconda.org)([mini](https://docs.conda.io/en/latest/miniconda.html))conda)
        
        ## Setup
        ```bash
        git clone https://github.com/villegar/runas --branch v2
        cd runas
        conda env create -f environment.yml
        python download.genome.py human-genome.json
        ```
        
        ## Execution
        ### Single node
        ```bash
        snakemake -j CPUS \ # maximum number of CPUs available to Snakemake
        	  --configfile config.json # configuration file
        ```
        
        ### Multi-node
        ```bash
        snakemake -j JOBS  \ # maximum number of simultaneous jobs to spawn
        	  --configfile config.json # configuration file
                  --latency-wait 1000 \ # files latency in seconds
                  --cluster-config cluster.json \ # cluster configuration file
                  --cluster "sbatch --job-name={cluster.name} 
                                    --nodes={cluster.nodes} 
                                    --ntasks-per-node={cluster.ntasks} 
                                    --output={cluster.log} 
                                    --partition={cluster.partition} 
                                    --time={cluster.time}"
        ```
        #### Alternatively
        ```bash
        bash run_cluster &> log &
        ```
        
        #### Cluster configuration (cluster.json)
        ```bash
        {
            "__default__" :
            {
                "time" : "1-00:00:00",
                "nodes" : 1,
                "partition" : "compute",
        	"ntasks": "{threads}",
        	"name": "RuNAs-{rule}",
        	"log": "RuNAS-{rule}-%J.out"
            }
        }
        ```
        
        #### Pipeline configuration (config.json)
        ```bash
        {
            "genome4phiX":
            {
                "PhiX": 
                    "ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/PhiX/Illumina/RTA/PhiX_Illumina_RTA.tar.gz"
            },
        
            "genome4star":
            {
                "GRCm38.primary_assembly.genome.fa.gz": 
                    "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M22/GRCm38.primary_assembly.genome.fa.gz",
                "gencode.vM22.annotation.gtf.gz": 
                    "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M22/gencode.vM22.annotation.gtf.gz"
            },
        
            "krakenDB":
            {
                "minikraken_20171019_8GB.tgz": 
                    "https://ccb.jhu.edu/software/kraken/dl/minikraken_20171019_8GB.tgz"
            },
        
            "reads":
            {
                "extension": "fastq.gz",
                "path": "/gpfs/scratch/Classes/stat736/p53reads",
                "prefix": "SRR"
            },
        
            "rRNAref":
            {
                "txid9606.fasta": 
                    "https://raw.githubusercontent.com/villegar/RuNAs/v2/txid9606.fasta"
            }
        }
        ```
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
