Software Install - 10x Genomics Supernova on Mox (Hyak)

Steven asked me to install Supernova (by 10x Genomics on our Mox node.

First, need to install a dependency: bcl2fastq2.

Followed Illumina bcl2fastq2 manual.

Logged into Mox and initiated a Build node:

srun -p build --time=1:00:00 --pty /bin/bash

Install bclsfastq2 dependency

cd /gscratch/srlab/tmp

wget ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/software/bcl2fastq/bcl2fastq2-v2-20-0-tar.zip

export TMP=/gscratch/srlab/tmp

export SOURCE=${TMP}/bcl2fastq

export BUILD=${TMP}/bcl2fastq2.20-build

export INSTALL_DIR=/gscratch/srlab/programs/bcl2fastq-v2.20

cd ${TMP}

unzip bcl2fastq2-v2-20-0-tar.zip

tar -xvzf bcl2fastq2-v2.20.0.422-Source.tar.gz

cd ${BUILD}

chmod ugo+x ${SOURCE}/src/configure

chmod ugo+x ${SOURCE}/src/cmake/bootstrap/installCmake.sh

${SOURCE}/src/configure --prefix=${INSTALL_DIR}

cd ${BUILD}

make

make install

Install Supernova 2.0.0

Supernova install directions

Note

Due to the requirement to sign a licensing aggreement, the direct URL for downloading Supernova is not proided in the code chunk below.

cd /gscratch/srlab/programs

wget -O supernova-2.0.0.tar.gz "<URL for supernova download>"

tar -xzvf supernova-2.0.0.tar.gz

rm supernova-2.0.0.tar.gz

cd supernova-2.0.0

supernova-cs/2.0.0/bin/supernova sitecheck > sitecheck.txt

supernova-cs/2.0.0/bin/supernova upload samwhite@uw.edu sitecheck.txt

srun -p srlab -A srlab --time=2:00:00 --pty /bin/bash

/gscratch/srlab/programs/supernova-2.0.0/supernova testrun --id=tiny

OK, looks like the test run finished successfully.