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Installing this software in the future

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