Installing this software in the future

In the future, if you want to run the tutorials on your own, you'll need to set up conda in your own account - see instructions).

To install all the tools we used in the future, we can 1. install from an environment yaml file, or 2. install everything manually.

Option 1: Installing from a file

At the end of the course, we exported info from the tara environment using:

conda env export -n tara -f $PROJECT/tara_conda_environment.yaml

You can find download this file here

To make a new conda env like this, download that file, then run:

conda env create -f tara_conda_environment.yaml

you shuld then be able to:

source activate tara

and you remember you can exit this environment with source deactivate

Option 2: Installing Manualling

Then create an environment to work in:

conda create -n tara

and activate it:

source activate tara

Now, install the software!

conda install fastqc multiqc trimmomatic khmer busco megahit sourmash salmon r dammit cd-hit

To make sure you have access to these conda-installed programs, try to execute some of them:

sourmash

Conda works for most of the software we'll use in the workshop. However, there are some exceptions: notably, transrate.

To install transrate, follow the instructions here.

You can also try the following:

cd <location-to-put-transrate>
wget https://bintray.com/artifact/download/blahah/generic/transrate-1.0.3-linux-x86_64.tar.gz
tar xvf transrate-1.0.3-linux-x86_64.tar.gz

To put transrate in your path, you can execute:

echo 'export PATH=/LUSTRE/apps/workshop/transrate-1.0.3-linux-x86_64:$PATH' >> ~/.bashrc
source ~/.bashrc

Then check that transrate is properly installed with

transrate -h