pegi3s/i-tasser_server

Sponsored OSS

By i3S

Updated 4 months ago

I-TASSER (https://zhanglab.ccmb.med.umich.edu/I-TASSER/) docker image.

Image
Data Science
Machine Learning & AI

447

This image belongs to a larger project called Bioinformatics Docker Images Project (http://pegi3s.github.io/dockerfiles)

(Please note that the original software licenses still apply)

This image facilitates the usage of I-TASSER (Iterative Threading ASSEmbly Refinement) Online Server, a hierarchical approach to protein structure prediction and structure-based function annotation.

Using the I-TASSER Server image in Linux

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/i-tasser_server bash -c "/opt/run /data/inputFolder /data/outputFolder"

In this command, you should replace:

  • /your/data/dir to point to the directory that contains the input folder with the multi FASTA file with the residues you want to analyze, as well as a file with your I-TASSER account information. Additionally, this will be the same directory where a folder with the results will be created.
  • /inputFolder to point to the folder that contains the multi FASTA file and the file with your I-TASSER access credentials (see Note 2 further below).
  • /outputFolder to point to the folder where the sub-folders with the results for each submitted job will be saved. For each sequence present in the input file you provided, a new folder will be created where these results will be.
Note 1

You have the option to run the image without specifying the /inputFolder and the /outputFolder. If that is the case, this image will assume you have your input data in a folder named /input inside /your/data/dir and additionally will save the results in a new folder, named /Results_I-TASSER. For this, adapt and run the command:

docker run --rm -v /your/data/dir:/data pegi3s/i-tasser_server bash -c "/opt/run"

Note 2

In order to successfully submit each job, you need to create a file called parameters.itasser filled with the following information:

-F REPLY-E-MAIL="your_email_address" -F password="your_password"

which must be in the same folder as your input FASTA file. Registration is mandatory for submission and can be done here.

Note 3

For Developers: To see Formfind information, just run: cat ./opt/info.

Docker Pull Command

docker pull pegi3s/i-tasser_server