- Aria2c 1.34.0+
- BEDtools 2.29+
- Bowtie2 2.3.5+
- BWA (alignment via Burrows-Wheeler transformation) 0.7.17+
- FastQC 0.11.8+
- FeatureCounts 1.6.4+
- KrakenUniq 0.5.8+
- MultiQC 1.7+
- Python 3.6+ (using Ana(mini)conda)
- Samtools 1.9+
- Snakemake 5.7+
- SRA Toolkit 2.9.6+
- STAR 2.7.3+
- Trimmomatic 0.39+
git clone https://github.com/villegar/runas
cd runas
conda env create -f environment.yml
conda activate RuNAs or source activate RuNAs
python download.genome.py human-genome.json
snakemake -j CPUS \ # maximum number of CPUs available to Snakemake
--configfile config.json # configuration file
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}"
bash run_cluster &> log &
{
"__default__" :
{
"time" : "1-00:00:00",
"nodes" : 1,
"partition" : "compute",
"ntasks": "{threads}",
"name": "RuNAs-{rule}",
"log": "RuNAS-{rule}-%J.log"
}
}
{
"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"
},
"_comment" :
"Below READS section shows the configuration for a directory containing reads in the format:
/{PATH}/SRR{LIBRARY}_1.fastq",
"reads":
{
"extension": "fastq.gz",
"path": "/gpfs/scratch/Classes/stat736/p53reads",
"prefix": "SRR"
},
"rRNAref":
{
"txid9606.fasta":
"https://raw.githubusercontent.com/villegar/RuNAs/v2/txid9606.fasta"
}
}