Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/csbiology/imlp
codebase and dotnet CLI tool for prediction of iMTS-Ls
https://github.com/csbiology/imlp
Last synced: 30 days ago
JSON representation
codebase and dotnet CLI tool for prediction of iMTS-Ls
- Host: GitHub
- URL: https://github.com/csbiology/imlp
- Owner: CSBiology
- License: mit
- Created: 2021-04-09T08:16:13.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2024-01-15T09:00:18.000Z (12 months ago)
- Last Synced: 2024-12-04T12:15:55.149Z (30 days ago)
- Language: F#
- Size: 6.19 MB
- Stars: 3
- Watchers: 5
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Citation: CITATION.cff
Awesome Lists containing this project
README
# iMLP
The imlp cli tool predicts iMTS-L propensity profiles for proteins of interest.
- [General](#general)
- [Installation](#installation)
- [Docker (Recommended)](#docker-recommended)
- [Dotnet tool](#dotnet-tool)
- [External dependencies on linux](#external-dependencies-on-linux)
- [External dependencies on windows](#external-dependencies-on-windows)
- [Docker](#docker)
- [Published binaries](#published-binaries)
- [Usage](#usage)
- [Development](#development)
- [build](#build)
- [test](#test)
- [publish self contained libraries](#publish-self-contained-libraries)
- [docker](#docker)
## General
## Installation
### Docker (Recommended)
This tool is very easy to install and use with docker.
Dependencies: Only [Docker](https://www.docker.com) :whale:!
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! :warning:) you can start/stop/restart or delete this container. In our case we want to open a console inside the **running** container.
2. `docker exec -it da9b7ed591eb bash`, this will pen a console and you can now type to execute commands inside the container.
3. Run imlp with `dotnet imlp --help` :tada:
4. Check out how to use imlp [here](#usage).
#### 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="",target=/data/
```
**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](https://dotnet.microsoft.com/download) 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](https://cntk.azurewebsites.net/BinaryDrop/CNTK-2-7-Linux-64bit-CPU-Only.tar.gz)
- 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](./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](#external-dependencies-on-linux)
## Usage
```shell
USAGE: imlp [--help] [--sequence ] [--inputfile ] [--outputfile ] [--model ] [--plotdirectory ] [--proteinheaderregex ]
[--verbosity ]
OPTIONS:
--sequence, -s
A single, one-letter coded amino acid input sequence. Either --sequence (-s)
or --inputFile (-f) must be specified.
--inputfile, -f
Path to a fasta formatted input file that may contain multiple entries. Either
--sequence (-s) or --inputFile (-f) must be specified.
--outputfile, -o
(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
(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
(optional) Path to a directory to save plots to.
--proteinheaderregex, -pr
(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
(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](#external-dependencies-on-windows)/[linux](#external-dependencies-on-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`