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"author": "Roberto Villegas-Diaz",
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"description": "\n# RuNA-seq (ᚱᚢᚾᚨᛋ) */roonas/* Pipeline\n\n![Rule Graph](images/rule-graph.png?raw=true \"Rule Graph\")\n## Requirements\n-\tPython 3.6+ (using [Ana](https://anaconda.org)([mini](https://docs.conda.io/en/latest/miniconda.html))conda)\n\n## Setup\n```bash\ngit clone https://github.com/villegar/runas --branch v2\ncd runas\nconda env create -f environment.yml\npython download.genome.py human-genome.json\n```\n\n## Execution\n### Single node\n```bash\nsnakemake -j CPUS \\ # maximum number of CPUs available to Snakemake\n\t --configfile config.json # configuration file\n```\n\n### Multi-node\n```bash\nsnakemake -j JOBS \\ # maximum number of simultaneous jobs to spawn\n\t --configfile config.json # configuration file\n --latency-wait 1000 \\ # files latency in seconds\n --cluster-config cluster.json \\ # cluster configuration file\n --cluster \"sbatch --job-name={cluster.name} \n --nodes={cluster.nodes} \n --ntasks-per-node={cluster.ntasks} \n --output={cluster.log} \n --partition={cluster.partition} \n --time={cluster.time}\"\n```\n#### Alternatively\n```bash\nbash run_cluster &> log &\n```\n\n#### Cluster configuration (cluster.json)\n```bash\n{\n \"__default__\" :\n {\n \"time\" : \"1-00:00:00\",\n \"nodes\" : 1,\n \"partition\" : \"compute\",\n\t\"ntasks\": \"{threads}\",\n\t\"name\": \"RuNAs-{rule}\",\n\t\"log\": \"RuNAS-{rule}-%J.out\"\n }\n}\n```\n\n#### Pipeline configuration (config.json)\n```bash\n{\n \"genome4phiX\":\n {\n \"PhiX\": \n \"ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/PhiX/Illumina/RTA/PhiX_Illumina_RTA.tar.gz\"\n },\n\n \"genome4star\":\n {\n \"GRCm38.primary_assembly.genome.fa.gz\": \n \"ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M22/GRCm38.primary_assembly.genome.fa.gz\",\n \"gencode.vM22.annotation.gtf.gz\": \n \"ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M22/gencode.vM22.annotation.gtf.gz\"\n },\n\n \"krakenDB\":\n {\n \"minikraken_20171019_8GB.tgz\": \n \"https://ccb.jhu.edu/software/kraken/dl/minikraken_20171019_8GB.tgz\"\n },\n\n \"reads\":\n {\n \"extension\": \"fastq.gz\",\n \"path\": \"/gpfs/scratch/Classes/stat736/p53reads\",\n \"prefix\": \"SRR\"\n },\n\n \"rRNAref\":\n {\n \"txid9606.fasta\": \n \"https://raw.githubusercontent.com/villegar/RuNAs/v2/txid9606.fasta\"\n }\n}\n```\n\n\n",
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