Installing Sircel on MARCC

install_run_sircel.sh

#!/bin/bash

# this module is specific to MARCC
module load anaconda-python/3.6

# create anaconda environment and use it
conda create -y -n sircel python
source activate sircel

# install kallisto, redis
conda install -y -c bioconda kallisto
conda install -y redis

# install sircel to same conda environment
git clone https://github.com/pachterlab/sircel
cd sircel
python3 setup.py install --kallisto $(command -v kallisto)  --prefix "$HOME"/.conda/envs/"$CONDA_DEFAULT_ENV"
cd ..

# get to the example
cd sircel/example

# set up tmpdir to relative tmp (should be in scratch), otherwise it will try to use /tmp and there's not enough space
mkdir -p tmp
export TMPDIR="$PWD"/tmp

# launch redis-server on port 6379 in the background
redis-server &
redis-cli ping # should emit PONG

# run sircel
READFQ=SRR1873277_1m_r1.fastq.gz
BARCFQ=SRR1873277_1m_r2.fastq.gz
sircel --threads 10 --dropseq --output_dir sircel_test --reads "$READFQ" --barcodes "$BARCFQ"

# shutdown redis
redis-cli shutdown

Updated to 10 threads. This script should be running on a compute node.

Added snippet to shut down redis