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

2018
Miscellaneous
Author

Sam White

Published

January 22, 2018

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

First, need to install a dependency: bcl2fastq2.

Followed Illumina bcl2fastq2 manual (PDF)

Logged into Mox and initiated a Build node:

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

Install bclsfastq2 dependency

Illumina bcl2fastq2 manual (PDF)

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

cd /gscratch/srlab/programs

wget -O supernova-2.0.0.tar.gz "https://cf.10xgenomics.com/releases/assembly/supernova-2.0.0.tar.gz?Expires=1516707075&Policy;=eyJTdGF0ZW1lbnQiOlt7IlJlc291cmNlIjoiaHR0cDovL2NmLjEweGdlbm9taWNzLmNvbS9yZWxlYXNlcy9hc3NlbWJseS9zdXBlcm5vdmEtMi4wLjAudGFyLmd6IiwiQ29uZGl0aW9uIjp7IkRhdGVMZXNzVGhhbiI6eyJBV1M6RXBvY2hUaW1lIjoxNTE2NzA3MDc1fX19XX0_&Signature;=XJR7c9UlSkueydP304nKJrqomLXBH9~DWsenwlvBrplFMojbO-DPMghO09Sk6Wi5ApZSPwKB3sl1Wrnjy3qBLwr7dCoT~9oStyBpqlF~Xl2nBY6odnTzUaq3IpLyu8icIkt7DJM0GMXQTTp6rYu1PlLG31hMM5b5HZI3Tjzrhk8URbSrsG~7mm6m5-28afYHX00kT2Xfor7xr-ZSjjLe2jr99SEIARfzZjt6kUEnDMbl~3FXCHsSxXzKrkYXobGmfQhYBrey0iRyCAc9yNF7eSuBHAsqRGsP2yURVcYf3BB5nB1ZuEUo0qLgc5GlZJDQdsqDNC69HkyLCJamkJSnVg__&Key-Pair-Id;=APKAI7S6A5RYOXBWRPDA"

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.