A docker image containing the fully configured RNAcmap predictor:
RNAcmap predictor requires only a standard computer with around 32 GB RAM to support the in-memory operations for RNAs sequence length less than 500.
Please install docker-engine for any given OS or distro from link shown below:
- Docker-Linux-Platforms: Ubuntu, Centos, Debian, Fedora
- Docker-Mac
- Docker-Windows
In additions, need to download NCBI's nt database file from the links shown below:
- NCBI's nucleotide database (ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/)
Download the file 'nt.gz' from the link above and unzip without renaming it. Make sure, your system have enough space as it is of size around 270 GBs after unzip.
After docker installation and nt database downlaod, RNAcmap is good to run.
Docker can be easily installed for Windows and Mac OS by downloading and running '.exe' and '.dmg' file from the link mentioned above. For Linux, the following steps can be used to install docker on Ubuntu Xenial 16.04 (LTS), Ubuntu Bionic 18.04 (LTS), and Ubuntu Eoan 19.10 distro.
-
sudo apt-get remove docker docker-engine docker.io containerd runc -
sudo apt-get update -
sudo apt-get install apt-transport-https ca-certificates curl gnupg-agent software-properties-common -
curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add - -
sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/ubuntu $(lsb_release -cs) stable" -
sudo apt-get update -
sudo apt-get install docker-ce docker-ce-cli containerd.io -
sudo groupadd docker -
sudo usermod -aG docker $USER
To brings changes into effect, you need to logout and then login to your system.
To verify the correct installation, you can run the following command:
docker run hello-world
The output of the above should give a message about the correct installation.
To install docker for other Linux distro, please follows the steps on the links provided above.
To run RNAcmap, you need provide path to the input sequence file and nt database to the Docker container. Therefore, you have to mount the file system of your computer (the host) in the Docker container (the guest). For prediction, please run the following command by replacing 'path_to_directory_with_input_sequence_file' with absolute path to directory contains input sequence fasta file and 'path_to_directory_with_nt_database_file' with absolute path to directory contains nt database file in the following command:
docker run --rm -ti -v path_to_directory_with_input_sequence_file/:/mnt -v path_to_directory_with_nt_database_file/:/nt_database jaswindersingh2/rnacmap:latest RNAcmap mnt/sequences.fasta RNAfold GREMLIN
Above command saves predicted secondary structure files (.ct, .bpseq, .prob etc) in the 'outputs' folder within the directory 'path_to_directory_with_input_sequence_file'.
If you create file system for RNAcmap in your /home/$USER/ directory as follows:
/home/$USER ("$ mkdir RNAcmap_data; cd RNAcmap_data")
|
|___RNAcmap_data ("$ mkdir database outputs" and copy your input sequences (for example seq1.fasta, seq2.fasta, etc) in this directory)
|
|___seq1.fasta
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|___seq2.fasta
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|___database/ (copy the unzipped nt database file named 'nt' (don't rename) in this directory. If database is not downloaded, RNAcmap provide option for download during running.)
|
|___nt
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|___outputs/ (RNAcmap results will be saved in this directory)
then, the following command can be used for the prediction without any change on your system:
docker run --rm -ti -v /home/$USER/RNAcmap_data/database/:/nt_database -v /home/$USER/RNAcmap_data/:/mnt jaswindersingh2/rnacmap:latest RNAcmap mnt/seq1.fasta RNAfold GREMLIN
You can provide any other input sequence, Secondary Structure Predictor (RNAfold or SPOT-RNA), and DCA predictor (GREMLIN or plmc) but the order of the arguments should remain the same.
If you are running RNAcmap without pre-downloading of the nt database, then it can take a couple of hours for first time prediction.