The following scripts will install two Anaconda virtual environments (omics-env and qiime2-env) on your computer or server. The two environments include the following software (open the appropriate *.yml file above to see a full list of software and dependencies):
omics-env:
- R 3.5 and several common R packages for data analysis
- Python 3.6 and common python libraries for data analysis
- DADA2 R package
- Anvio
- BWA
- Bowtie2
- Centrifuge
- MCL
- Muscle
- Trimal
- Diamond
- HMMER
- Megahit
- Prodigal
- Spades
- Phyloseq R package
- Vegan R package
- DESeq2 R package
- EdgeR R package
- Fastp
- Quast
- BLAST
qiime2-env:
- QIIME2 and associated dependencies
Installing the above software plus the dependencies will take ~7GB of storage and ~20 minutes. This can be installed on an external storage device as well. If you have any of these tools already installed on your computer, the miniconda installation script will not overwrite any existing software. During the installation, the miniconda3 directory will be created in the current working directory where you run the script.
In order to download the shell script used for installation, you will need the curl command line tool. I believe this comes installed on every Mac though. I suggest running the following commands to download and run the installation script from whichever directory you wish to install the software.
curl -Lo conda_install_mac.sh https://tinyurl.com/conda-omics-mac
bash conda_install_mac.shThe above commands will download a few files necessary for installation and software associated with the two environments will begin to be installed into the miniconda3 directory over the next ~20 minutes.
If you are new to using the terminal, the gif of me running the commands on my computer may help so you are aware of the expected outputs to the screen. I stopped the recording once the installation began:
Once the installation is complete, two environments (omics-env and qiime2-env) have been installed in the miniconda3 directory. In order to check which environments have been installed, you can run:
miniconda3/bin/conda info --envsIn order to utilize the software, you must activate the environment you want to use. Run the following command to activate the omics-env:
source miniconda3/bin/activate omics-envYou will note that the name of the activated environment appears to the left of your terminal prompt. Now, the software installed in this environment is available to you. To list all the software available, run:
miniconda3/bin/conda listThe installed software is in your path, meaning you don't need to include the full path to the location of the software. Below is an example of showing the help screen for an Anvio command:
anvi-profile -hTwo environments cannot be activated at the same time. First, you must deactivate the current environment:
source miniconda3/bin/deactivateThen, you can activate another environment:
source miniconda3/bin/activate qiime2-envOnce activated, you can view the QIIME2 plugins that have been installed:
qiime --helpOnce you are done with your current session, you should deactivate the environment or close the terminal.
source miniconda3/bin/deactivateBelow is another gif demonstrating the activating and deactivating of both environments:
The installation process will be nearly identical to those above for Mac users. The only difference is downloading a different shell script specific for installing on a Linux operating system (must be 64-bit architecture). In order to download the shell script used for installation, you will need the wget command line tool. I believe this comes installed on most Linux distributions. I suggest running the following commands to download and run the installation script from whichever directory you wish to install the software.
wget https://tinyurl.com/conda-omics-linux -O conda_install_linux.sh
bash conda_install_linux.shThe above commands will download a few files necessary for installation and software associated with the two environments will begin to be installed into the miniconda3 directory over the next ~20 minutes.
If you are new to using the navigating the terminal, the gif of me running the commands on my computer above help so you are aware of the expected outputs to the screen.
Once the installation is complete, two environments (omics-env and qiime2-env) have been installed in the miniconda3 directory. In order to check which environments have been installed, you can run:
miniconda3/bin/conda info --envsIn order to utilize the software, you must activate the environment you want to use. Run the following command to activate the omics-env:
source miniconda3/bin/activate omics-envYou will note that the name of the activated environment appears to the left of your terminal prompt. Now, the software installed in this environment is available to you. To list all the software available, run:
miniconda3/bin/conda listThe installed software is in your path, meaning you don't need to include the full path to the location of the software. Below is an example of showing the help screen for an Anvio command:
anvi-profile -hTwo environments cannot be activated at the same time. First, you must deactivate the current environment:
source miniconda3/bin/deactivateThen, you can activate another environment:
source miniconda3/bin/activate qiime2-envOnce activated, you can view the QIIME2 plugins that have been installed:
qiime --helpOnce you are done with your current session, you should deactivate the environment or close the terminal.
source miniconda3/bin/deactivateFor Windows users, we suggest setting up a Linux environment on your computer, using another computer in your lab or department, or using a server available at your institution. Most bioinformatic tools tend not to be compatible with Windows operating systems and while Windows is supported by Anaconda, many of the common bioinformatic packages do not have recipes for Windows. This appears to be a good resource to help you get started: https://github.com/kapsakcj/win10-linux-conda-how-to.
For those seeking smaller installations or to install more software within the provided environments, I encourage you to read the excellent Anaconda documentation to install Anaconda / miniconda and learn to set up virtual environments - https://conda.io/projects/conda/en/latest/user-guide/getting-started.html and https://docs.anaconda.com/anaconda/ are good places to get started. If you are still experiencing issues after going through the documentation, file an issue and I can try to help.
If you are having issues installing the environments, activating them, or running the software, please file an issue in this repository and I will try to help! Some users have experienced losing an internet connection with the Anaconda repository while downloading the software, leading to an error. This error occurred <5% of the time I tested the installation, so I recommend deleting the miniconda3 directory that was created and re-running the installation script.