fjossinet/assemble2 repository overview

⁠Assemble2Docker

A docker image containing the following algorithms fully configured:

• RNAVIEW⁠
• Vienna RNA package⁠
• foldalign⁠
• LocARNA⁠

⁠Installation

First you need to install Docker on your computer. You can find all the details here⁠.

Then, to get our docker image, you need to type:

docker pull fjossinet/assemble2

⁠Usages and Examples

In general, these algorithms need input files. Consequently, you have to mount the file system of your computer (the host) in the Docker container (the guest). This is done with the -v option.

LocARNA algorithm:

 docker run -v /Users/fjossinet/my_files/:/data fjossinet/assemble2 mlocarna /data/my_sequences.fasta

RNAVIEW algorithm:

docker run -v /Users/fjossinet/my_files/:/data fjossinet/assemble2 rnaview -p /data/my_3D.pdb

RNAFold algorithm:

docker run -v /Users/fjossinet/my_files/:/data fjossinet/assemble2 bash -c 'RNAfold < /data/my_sequence.fasta'"