# Install environment

## 1) Get depad-utils and configure environment

Login and navigate to your home folder

```bash
cd ${HOME}
```

download and unzip [these files](https://github.com/molgenis/molgenis-pipelines/tree/68b42f429224f1d8ee4aa635c4da8e6bd7b22792/docs/pipelines/attachments/depad-utils.zip) ***(There are hidden files/directories)***

***Note:*** Make sure that the etc/skel/.bashrc from the zip file was already deployed as root and that /etc/skel/.bashrc was copied to your home dir when it was created( cp /etc/skel/.bashrc \~ ). If your .bashrc does not have the stuff from the template, you can add it manually and notify an admin to deploy the template in /etc/skel/.

create folder where the modules will be

```bash
mkdir /apps/modules/

###copy all files in the folder /apps/modules/ from the zip to the server (if /apps/modules is not possible, NB the copying of these files should go somewhere else)

cp -r depad-utils/apps/modules/* depad-utils/.lmod/ /apps/modules/
```

***NB: Lmod must already have been deployed as root using your Linux distro's package manager.*** ***NB2: if apps modules is not possible then \~/.bashrc should also be changed*** 

If lmod is not installed, please do the following (admins-only) in our case for CentOS use

```
$root>: yum install lmod
```

To verify /apps/modules/modules.bashrc gets sourced: logout + login. When ${HPC\_ENV\_PREFIX} is set your are good to continue to the next step.

```bash
echo ${HPC_ENV_PREFIX}
```

## 2) Create main folders for our HPC environment.

```bash
mkdir -m 2775 ${HPC_ENV_PREFIX}/data/
mkdir -m 2775 ${HPC_ENV_PREFIX}/software/
mkdir -m 2775 ${HPC_ENV_PREFIX}/sources/
mkdir -m 2770 ${HPC_ENV_PREFIX}/.tmp/
```

## 3) Download EasyBuild bootstrap script

```bash
export EASYBUILD_VERSION=2.8.1
mkdir -p /${HPC_ENV_PREFIX}/sources/EasyBuild/
cd /${HPC_ENV_PREFIX}/sources/EasyBuild
curl -O https://raw.githubusercontent.com/hpcugent/easybuild-framework/develop/easybuild/scripts/bootstrap_eb.py
mv bootstrap_eb.py bootstrap_eb_${EASYBUILD_VERSION}.py
```

## 4) Bootstrap EasyBuild in apps dir.

```bash
python /${HPC_ENV_PREFIX}/sources/EasyBuild/bootstrap_eb_${EASYBUILD_VERSION}.py ${HPC_ENV_PREFIX}
```

## 5) Sanity check

logout and login again

```bash
module load EasyBuild
module list
eb --version
```

## 6) Install toolchain

```bash
eb foss-2015b.eb -–robot
```

***Note: some sources should be downloaded manually***** (see below)**

```bash
scp gcc-4.9.3.tar.bz2 /${HPC_ENV_PREFIX}/sources/g/GCC/
scp gmp-6.0.0a.tar.bz2 /${HPC_ENV_PREFIX}/sources/g/GCC/
scp mpc-1.0.2.tar.gz /${HPC_ENV_PREFIX}/sources/g/GCC/
scp mpfr-3.1.2.tar.gz /${HPC_ENV_PREFIX}/sources/g/GCC/
```

## 7) Installing additional packages

The following packages should be on the cluster/VM (this can only done with root access:

```bash
yum install libibverbs-devel
yum install openssl-devel
yum install unzip
yum install libX11-devel
yum install libXrender-devel
yum install libXext-devel
yum install mesa-libGL-devel
yum install mesa-libGLU-devel
```

## 8a) Get molgenis-easybuild repo

Now that easybuild is installed we have to have the molgenis easybuild configs because it contains a lot of custom easyconfigs that are (sometimes were at the moment we began with this) not in the original easybuild repo from Ghent University: <https://github.com/molgenis/easybuild-easyconfigs>

There are 2 options:

* Fork this repo to your own repo and then do a git clone (on the cluster, then you can skip 8b)
* Download the latest zip or tar.gz at

<https://github.com/molgenis/easybuild-easyconfigs/releases/> (proceed to 8b)

## 8b) Put the new repo on the cluster/VM

```bash
scp -r easybuild-easyconfigs yourusername@yourcluster.nl:${root}/${pathToMYeasybuildconfigs}
```


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