Installing with Conda

This section uses Conda to install SEISMIC-RNA in a virtual environment. If you are not familiar with virtual environments, read this primer on Virtual Environments. If you do not have a working installation of Conda on your system (or are not sure if you do), then see the section of this tutorial about Prerequisites: Python, pip, and Conda for guidance.

Create and activate your virtual environment

Make a new virtual environment into which you will install SEISMIC-RNA. Give it a short, memorable name, such as seismic, and process Python version 3.10, which is currently the only supported version. The rest of this tutorial assumes that the virtual environment is named seismic, so if you have chosen a different name, then type that name instead:

conda create -n seismic python=3.10

Activate your virtual environment with this command:

conda activate seismic

Note that this environment must be active whenever you install, use, or update SEISMIC-RNA. To deactivate it after you are finished, type:

conda deactivate

Note that you do not need to type seismic after deactivate.

Install the non-Python dependencies

SEISMIC-RNA has four dependencies that are not Python packages. They are all available to install using Conda, but this installation process seems prone to failing on some systems, such as Macbook computers with M1 and M2 processors. If you encounter errors, you can also install each dependency by following its own installation instructions.

The four non-Python dependencies are

  • Samtools ≥ v1.17 (required)

  • FastQC ≥ 0.12.1 (optional: only for FASTQ quality control)

  • Bowtie2 ≥ v2.5.1 (optional: only for FASTQ alignment)

  • RNAstructure ≥ v6.3 (optional: only for RNA structure prediction)

Installing

You can install them all at once by running the following command (note that it is long and you may need to scroll horizontally to see it all):

conda install -y -c bioconda -c conda-forge samtools=1.17 fastqc=0.12.1 bowtie2=2.5.1 rnastructure=6.3

Or, if you do not want to install all of them, then you can choose which to install by running the corresponding individual command(s):

# Samtools
conda install -y -c bioconda -c conda-forge samtools=1.17

# FastQC
conda install -y -c bioconda -c conda-forge fastqc=0.12.1

# Bowtie2
conda install -y -c bioconda -c conda-forge bowtie2=2.5.1

# RNAstructure
conda install -y -c bioconda -c conda-forge rnastructure=6.3

Verifying

To confirm that the dependencies have been installed successfully, type the following commands for each dependency that you want to check:

# Samtools
which samtools

# FastQC
which fastqc

# Bowtie2
which bowtie2

# RNAstructure
which ct2dot

If a dependency has been installed properly, then running its above command will print a message that looks similar to this:

/home/your-name/miniconda3/envs/seismic/bin/name-of-dependency

If it prints an error message that the depdendency was not found, then the program has not been installed.

Troubleshooting

If you encounter errors during installation with Conda, then first double check that you have entered the command exactly, especially that

  • the command includes -c bioconda and -c conda-forge

  • the version of the program in the command is correct

  • there are no extra spaces or missing spaces

  • every word is spelled correctly

If you had mistyped the command, then just re-run the command with the correct spelling. If you have verified that the command is correct and it is still not installing, then try to install the dependency using the instructions on its website (instead of with Conda):

Install SEISMIC-RNA and its Python dependencies

After you have installed your chosen non-Python dependencies, run this command to install SEISMIC-RNA and all its Python dependencies:

pip install --upgrade seismic-rna

The above command will install the latest version of SEISMIC-RNA and its dependencies. If you want to install a specific version instead, then run this command (substituting 1.2.3 with the version you want):

pip install seismic-rna==1.2.3