Primary software containers are stored in /fs/project/PAS1046/software/containers. If you wish to use one of these software, add the binaries to your $PATH by adding the following line to your ~/.bash_profile:
#Singularity containers
export PATH=$PATH:/fs/project/PAS1046/software/containers/.sifs
Then, identify the .sif file for the software you want and call it open to access the software:
<CONTAINER>.sif
To close, press CTRL + D or command exit.
There are multiple methods for installing software, but a singularity container is the easiest when available. Quay.io is a website that has prepackaged bioinformatics containers, and there is a solid chance your software of interest is located there. Your first option is to use a search engine, such as Qwant/google, to search for your software of interest - just add "quay" to your search. If the software exists open the quay.io URL, click the tags section, click "fetch tag" on the far right of the latest version, and pull down "Docker Pull (by tag)". Take note of the quay.io/biocontainers.... URL.
Now, on OSC, make a directory in /fs/project/PAS1046/software/containers/ with your software name (preferably lower case). Navigate into the directory you created and run the following command with the URL you just retrieved:
#pull the container
singularity pull <URL>
#test it
./<CONTAINER_NAME>.sif
#close it
exit
If you exported the .sifs folder to your path as described above, new containers will not show up until you run bash /fs/project/PAS1046/software/containers/.addlinks.sh or contact Zach to do it.