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iMLP

The imlp cli tool predicts iMTS-L propensity profiles for proteins of interest.

General

Installation

Docker (Recommended)

This tool is very easy to install and use with docker.

Dependencies: Only Docker 🐳!

Steps to run only once:

  1. docker pull csbdocker/imlp, this step might take a few minutes, as the image is around 5GB.
  2. docker run -i -d csbdocker/imlp, start a container from the just downloaded image and run it in the background.

Done! You now have a docker container from the csbdocker/imlp image. You can find the id of the container and more with:

  1. docker ps -l

Output:

CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES
da9b7ed591eb csbdocker/imlp "/bin/bash" 10 minutes ago Up 10 minutes loving_moser

With this container id (Yours will differ! ⚠️) you can start/stop/restart or delete this container. In our case we want to open a console inside the running container.

  1. docker exec -it da9b7ed591eb bash, this will pen a console and you can now type to execute commands inside the container.
  2. Run imlp with dotnet imlp --help 🎉
  3. Check out how to use imlp here.

Using the docker container with mounted directories

The usual use-case is using an input file in fasta format. Obviously, this file must be accessible in the container that you execute the tool in.

A simple way of doing this is mounting the directory on creation of the container. Note that you should target a subfolder of data in the container, as the container starts in /data per default.

docker run -it csbdocker/imlp --mount type=bind,source="<your-path-here>",target=/data/<container-path-here>

Example:

Suppose you have a file test.fasta in C:/my-folder:

bind C:/my-folder to /data/fastas:

docker run -it csbdocker/imlp --mount type=bind,source="C:/my-folder",target=/data/fastas

inside the container, you can use the container path you just bound to access the file, e.g.:

dotnet imlp -f ./fastas/test.fasta -o ./fastas/output.txt

which will run imlp with the fasta input and generate an output file in the same folder, which will also be available on the containers host OS afterwards.

Dotnet tool

imlp is packaged as dotnet tool. To use it:

  • install the .NET SDK for your system
  • run either dotnet tool install imlp (after initializing a local manifest via dotnet new tool-manifest) for a local or dotnet tool install -g imlp for a global installation
  • you can now run the tool via dotnet imlp ... (for a local installation) or imlp ... (for a global installation)

External dependencies on linux

CNTK has some external dependencies that can not be published with the packaged tool.

  • the necessary cntk binaries can be downloaded here
  • for installation of OpenMPI, please follow this guide
  • finally, apply this fix:
    • navigate to the location where you unpacked the cntk binaries
    • run cp ./cntk/lib/Cntk.Core.CSBinding-2.7.so ./cntk/lib/libCntk.Core.CSBinding-2.7.dll

all steps can be seen executed in out Dockerfile

External dependencies on windows

CNTK has some external dependencies that can not be published with the packaged tool.

Download the CNTK package here: https://cntk.ai/dlwc-2.7.html and add the extracted ./cntk/cntk folder to your path variable.

Published binaries

Download links to self-contained binaries can be found under releases. Linux users have to apply the same fixes as laid out under the dotnet tool section

Usage

USAGE: imlp [--help] [--sequence <sequence>] [--inputfile <inputFile>] [--outputfile <outputFile>] [--model <plant|nonplant>] [--plotdirectory <plotDirectory>] [--proteinheaderregex <proteinHeaderRegex>]
            [--verbosity <verbosity>]

OPTIONS:

    --sequence, -s <sequence>
                          A single, one-letter coded amino acid input sequence. Either --sequence (-s) 
                          or --inputFile (-f) must be specified.
    --inputfile, -f <inputFile>
                          Path to a fasta formatted input file that may contain multiple entries. Either 
                          --sequence (-s) or --inputFile (-f) must be specified.
    --outputfile, -o <outputFile>
                          (optional) Path to the desired output file, which will be tab separated (tsv). 
                          If not specified, output will be printed to stdout instead.
    --model, -m <plant|nonplant>
                          (optional) Model to use for prediction. Choose the one that is closest to your 
                          organism of interest: Either 'plant' or 'nonplant'. (default:nonplant)
    --plotdirectory, -p <plotDirectory>
                          (optional) Path to a directory to save plots to.
    --proteinheaderregex, -pr <proteinHeaderRegex>
                          (optional) Regular expression to extract protein names from fasta headers for 
                          the naming of plot output files. if not provided, plot files will be 'protein_{i}.html', 
                          where i is the index in the input.
    --verbosity, -v <verbosity>
                          (optional) The verbosity of the logging process. 0(Silent) | 1(Error) | 2(Warn) | 3(Info) 
                          | >=4 : Debug | (default:1)
    --help                display this list of options.

Development

build

  • dotnet tool restore (once)
  • dotnet fake build

test

  • dotnet tool restore (once)
  • dotnet fake build -t testpackagedtool (You need to have external dependencies (win/linux) installed)

publish self contained libraries

  • dotnet tool restore (once)
  • dotnet fake build -t publishbinaries will publish both win-x64 and linux-x64 binaries.

docker

  • set the correct imlp version in the containers IMLP_VERSION argument
  • docker build . -t imlp