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
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.