EPI-2023/002-computing.Rmd at main · cbw-dev/EPI-2023 · GitHub

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# Data and Compute Setup

#### Course data downloads

:::: {.callout type="blue" title="Note"}

Some of these files are quite large. If you have issues downloading them, contact us at support@bioinformatics.ca.

::::

- [Module 123]()
- [Module 4]()

#### Compute setup

##### AWS Module

Connecting and properly using a cloud computing cluster at the CBW [here](https://bioinformaticsdotca.github.io/AWS_EPI23)

##### AMI

We have made our AWS AMI (Amazon Machine Image) publicly available. To launch your own instance, follow the instructions provided by Amazon on [how to launch an EC2 instance from a custom Amazon Machine Image](https://repost.aws/knowledge-center/launch-instance-custom-ami). Please note that you will need an AWS account to proceed, and that you will need to upload the CourseData files yourself.

Here are the details of the AMI:

- AWS Region: us-east-1 (N. Virgina)
- AMI type: public image
- AMI name: CBW_EPI_231005
- AMI ID: ami-0ae28d3f8e57ba8cf

If you want to create and activate a new AWS account, please follow the [instructions](https://aws.amazon.com/premiumsupport/knowledge-center/create-and-activate-aws-account/) provided by Amazon.

##### Software

###### conda
Install Miniconda by following the instructoion at [Miniconda official site](https://docs.conda.io/en/main/miniconda.html)

###### bedtools
```{}
wget https://github.com/arq5x/bedtools2/releases/download/v2.30.0/bedtools.static.binary
mv bedtools.static.binary bedtools
chmod +x bedtools
```

###### bwa
```{}
wget https://newcontinuum.dl.sourceforge.net/project/bio-bwa/bwa-0.7.17.tar.bz2
tar -jxvf bwa-0.7.17.tar.bz2
cd bwa-0.7.17/
```

###### make
```{}
#### FastQC
wget https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.12.1.zip
unzip fastqc_v0.12.1.zip
```

###### samtools
```{}
wget https://github.com/samtools/samtools/releases/download/1.17/samtools-1.17.tar.bz2
tar -jxvf samtools-1.17.tar.bz2
cd samtools-1.17
make
sudo make install
```

###### picard
```{}
wget https://github.com/broadinstitute/picard/releases/download/3.1.0/picard.jar
```

###### deeptools
```{}
pip install deeptools
```

###### MACS2
```{}
pip install MACS2
```

###### Homer
```{}
wget http://homer.ucsd.edu/homer/configureHomer.pl
perl ./configureHomer.pl -install
perl ./configureHomer.pl -install hg19
perl ./configureHomer.pl -install hg38
```

###### UCSC tools'
```{}
rsync -aP hgdownload.soe.ucsc.edu::genome/admin/exe/linux.x86_64/ ./
```

###### Biamark
```{}
wget https://github.com/FelixKrueger/Bismark/archive/refs/tags/v0.24.2.tar.gz
tar -zxf v0.24.2.tar.gz
```