---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2018-01-22 23:46:35+00:00
layout: post
slug: software-install-10x-genomics-supernova-on-mox-hyak
title: Software Install - 10x Genomics Supernova on Mox (Hyak)
categories:
  - 2018
  - Miscellaneous
tags:
  - 10x genomics
  - bcl2fastq2
  - hyak
  - mox
  - supernova
---

[Steven asked me to install Supernova (by 10x Genomics on our Mox node](https://github.com/RobertsLab/resources/issues/159).

First, need to install a dependency: [bcl2fastq2](https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html).

Followed [Illumina bcl2fastq2 manual (PDF)](https://support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/bcl2fastq/bcl2fastq2_guide_15051736_v2.pdf)

Logged into Mox and initiated a [Build node](https://github.com/RobertsLab/hyak_mox/wiki/Node-Types#build-node):



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




### Install bclsfastq2 dependency



[Illumina bcl2fastq2 manual (PDF)](https://support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/bcl2fastq/bcl2fastq2_guide_15051736_v2.pdf)


```shell
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](https://support.10xgenomics.com/de-novo-assembly/software/pipelines/latest/installation)

```shell
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
```

![](https://owl.fish.washington.edu/Athaliana/20180122_mox_supernova_install.png)

OK, looks like the test run finished successfully.
