Conda
You dont want to ask us to install the new software you want? That is cool! I was like that too. And conda should be one of your best friend, or maybe docker and singularity images. If you have enough storage space, go ahead. Say I want to install a software called trimmomatic. Get more info about the conda channels that contain this software. By googling, I know it is in bioconda. So, from the login node, just straight:
# Im creating a new conda environment, named it trimmo.
# Softwares usually contain dependencies, and usually conda-forge channel have them. Just a habit of mine.
conda create -n trimmo -c bioconda -c conda-forge trimmomatic
A bit of test-driving here:
# Activate the environment to acces the software
conda activate trimmo
# Test it out, can you find trimmomatic?
$ trimmomatic
Usage:
PE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-summary <statsSummaryFile>] [-quiet] [-validatePairs] [-basein <inputBase> | <inputFile1> <inputFile2>] [-baseout <outputBase> | <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U>] <trimmer1>...
or:
SE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-summary <statsSummaryFile>] [-quiet] <inputFile> <outputFile> <trimmer1>...
or:
-version
# Deactivate the environment once you done with it
# You will notice the conda env name is not in your prompt
conda deactivate
# Can you access trimmomatic without activating the trimmo env?
-bash: trimmomatic: command not found