Via the command line/terminal, navigate to the folder where you would like Slinker installed and execute:

git clone [email protected]:Oshlack/Slinker.git or git clone https://github.com/Oshlack/Slinker.git

Depending on whether you have setup SSH keys.

Slinker has both internal and external dependencies that need to be installed. But before we get to that, let's install Anaconda!

The Slinker installation process heavily relies on https://www.anaconda.com/. This simplifies the process of ensuring that the correct versions of dependent packages are installed. If these versions deviate, there is a risk that the output will differ from what was intended.

1. Download and Install Anaconda
   

   Installation instructions for Anaconda can be found here.

2. Activate bioconda

   Enter the below in order (!important)

   1. conda config --add channels conda-forge
   2. conda config --add channels defaults
   3. conda config --add channels bioconda
3. Create a new environment using the supplied yaml file
   

   Navigate to where you cloned the Slinker package and then execute conda env create -f env/slinker.yml.
   This will create the "slinker" environment which you will need to activate each time you wish to use Slinker.

4. Activate environment
   

   Depending on your Anaconda version, either of these should do the trick.
   source activate slinker or conda activate slinker.

If you already have references you wish to use your own, use the gtf and fasta parameters to input them into the pipeline, i.e. use yours, not the below, save yourself this download if you want.

Rather than bundling some giant annotations in this repository, I thought it would be easier to just point you to the source.

From the clone root:

./dependencies_linux64.sh if you DON'T want to download references.

./dependencies_linux64.sh download if you DO want to download references.

NOTE: If you run into any permissions issues, just do a chmod 774 dependencies_linux64.sh

If all goes according to plan, your workflows/tools.groovy file will be completely populated. If not, apologise, but you will have to manually install those missed. Refer to the manual instructions in the Wiki.

• SLINKERDIR (Mandatory):

  export SLINKERDIR=<slinker_installation_folder>

• Bpipe (optional):
  

  export PATH=<slinker_installation_folder>/tools/bpipe-0.9.9.9/bin/:$PATH

  Otherwise you will need to call the <slinker_installation_folder>/tools//bpipe-0.9.9.9/bin/bpipe everytime you wish to run it (using this installed version of course!

Adjust your bpipe.config to reflect your system.

Sorry to see you go! Uninstalling should be really easy with Anaconda after you have deactivated (conda deactivate slinker).

conda remove --name slinker --all

Follow the relevant documentation on the https://www.anaconda.com/ website to uninstall conda, if required.

Then simply delete the cloned folder, including all downloaded dependencies.