microSplit_scRNAseq/setup.sh at main · nvivanco/microSplit_scRNAseq · GitHub

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#!/bin/bash
# default paths
export RAW_DATA="$OAK/scRNAseq/raw_data"
export PROCESSED_DATA="$OAK/scRNAseq/processed_data"
export ECOLI_REF_GENOME="$RAW_DATA/references/ecoli/GCF_000005845.2_ASM584v2_genomic.fna"
export ECOLI_GTF="$RAW_DATA/references/ecoli/GCF_000005845.2_ASM584v2_genomic.gtf"
export ECOLI_REF_TRNX="$RAW_DATA/references/ecoli/GCF_000005845.2_ASM584v2_cds_from_genomic.fna"

export BSUB_REF_GENOME="$RAW_DATA/references/bsubtilis/GCF_000009045.1_ASM904v1_genomic.fna"
export BSUB_GTF="$RAW_DATA/references/bsubtilis/GCF_000009045.1_ASM904v1_genomic.gtf"
export BSUB_REF_TRNX="$RAW_DATA/references/bsubtilis/GCF_000005845.GCF_000009045.1_ASM904v1_cds_from_genomic.fna"


export BSUB_PY79_REF_GENOME="$RAW_DATA/references/bsubtilis/bacillus_subtilis_py79.reformatted.fna"
export BSUB_PY79_GTF="$RAW_DATA/references/bsubtilis/bacillus_subtilis_py79.gtf"
export BSUB_PY79_GFF="$RAW_DATA/references/bsubtilis/bacillus_subtilis_py79.gff"

#TODO: download cds file
#export BSUB_PY79_REF_TRNX="$RAW_DATA/references/bsubtilis/..."

# run with singularity
export RUN="singularity run $OAK/scRNAseq/envs/scrna_latest.sif"