Microbial 'omics


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This article describes some recipes for the installation of softwre used by anvi’o but developed by other groups.

If you are an end-user and trying to install anvi’o, you shouldn’t be on this page. Instead, please find our installation instructions and follow them.

But the article is limited to those tools that we do not install through our conda recipes. Please see our GitHub repository to see a complete list of third-party software that are required for anvi’o to install or critical but not required for its runtime (i.e., they are critical if you want to do anything comprehensive with anvi’o, but without them you still can install and run anvi’o).

Table of Contents

If you find a mistake on this page or would you like to update something in it, please feel free to edit its source by clicking the edit button at the top-right corner (which you will see if you are logged in to GitHub) 😇

DSSP

DSSP (Dictionary of Secondary Structure Prediction) is a program for annotating amino acids in protein structures with structural information, such as secondary structure (alpha, helix, etc.) and solvent accessibility.

Citation: https://www.ncbi.nlm.nih.gov/pubmed/6667333

Citation: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013697/

Do you already have DSSP? Go to your terminal, and type mkdssp --version. If you do not get an error, read ahead to make sure your DSSP is operational. If you get an error, you need to install DSSP.

Use this command line to install DSSP with conda:

conda install -c salilab dssp

If you get a command not found error, you have to install conda, and easy install instructions can be found on their website

Test your DSSP installation by running the following commands your terminal:

wget http://files.rcsb.org/view/1H97.cif #download myoglobin structure
mkdssp -i 1H97.cif -o myoglobin_DSSP.txt

If no error is produced, DSSP is working (you can open up myoglobin_DSSP.txt to see what the output looks like).

MODELLER

MODELLER is a program for homology or comparative modeling of protein three-dimensional structures using a reference database.

Citation: https://www.ncbi.nlm.nih.gov/pubmed/18428767

Citation: https://www.ncbi.nlm.nih.gov/pubmed/10940251

Citation: https://www.ncbi.nlm.nih.gov/pubmed/8254673

Go to your terminal and type mod and then attempt to autocomplete the command by pressing the tab key twice. If something like mod9.xx pops up, where xx is some number, you have MODELLER. If xx is lower than 19, you should reinstall MODELLER using the following instructions.

If you don’t have any version of MODELLER, their website has excellent cross-platform intallation instructions. If you are using conda, you can just run:

conda install -c salilab modeller

Regardless of your method of installation, check it worked by typing mod into your terminal and seeing that it autocompletes after pressing the tab key twice.

Along with an installation, you will need a license key (which is free for academic use). You can go ahead and register for a license key on their website and put the key where they tell you, or you can just pretend you have one and anvi’o will give you precise instructions on how to get one and what to do with it when the time comes.