Skip to content
Snippets Groups Projects
Commit c625b58a authored by schereme's avatar schereme Committed by chow
Browse files

fix,chore: Fixed support for multiple Python versions. Supported Python...

parent 21208b43
Branches
Tags 1.0.0b2
2 merge requests!29since catboost1.0.0 is no longer pip-installable for older python versions,...,!17fix,chore: Fixed support for multiple Python versions. Supported Python...
......@@ -29,11 +29,18 @@ Users should create a `data` folder in parallel to `src` to store all pre-requis
## Installation
________________________
### Requirements
* Python version >=3.7,<3.10
### As a python library
`pip install git+https://git.mpi-cbg.de/tothpetroczylab/shark.git`
** This allows users to import functionalities as python package
Please note that additionally you need to install all project requirements. Follow the instruction for
installing the project requirements in the next section called "As a cmd utility".
### As a cmd utility
`git clone https://git.mpi-cbg.de/tothpetroczylab/shark.git`
......@@ -45,6 +52,28 @@ ________________________
**[Download required packages]** Preferably within a local python virtual environment
Run in command line: pip install -r requirements.txt
Once you have a copy of the source, you can embed it in your own Python package, or install it into your site-packages easily
```shell
$ git clone https://git.mpi-cbg.de/tothpetroczylab/shark.git
$ cd shark
$ python3.9 -m venv shark-env
$ source shark-env/bin/activate
(shark-venv) % pip install -r requirements.txt
```
### How to install SHARK-Dive using Conda?
There isn't any binary installer available on Conda yet. Though it is possible to install SHARK-Dive within a virtual Conda environment.
```shell
$ conda config --add channels conda-forge
$ conda config --set channel_priority strict
$ conda create -n shark-env python=[3.7, 3.8, 3.9]
$ conda activate shark-env
(shark-env) % pip install -r requirements.txt
```
### External Dependencies
- Substitution matrix file:
- A tab-separated file with rows and columns as amino acids and cell values as similarity score between them.
......@@ -150,7 +179,7 @@ output = predictor.predict() # List of output objects; Each element is for on
_You may use the `sample_fasta_file.fasta` from `data` folder (Owncloud link)_
```
% python dive/prediction.py "<query-fasta-file>.fasta" "<target-fasta-file>.fasta"
% python src/shark_atplab/dive/prediction.py "<query-fasta-file>.fasta" "<target-fasta-file>.fasta"
Read fasta file from path <query-fasta-file>.fasta; Found 4 sequences; Skipped 0 sequences for having X
Read fasta file from path <target-fasta-file>.fasta; Found 6 sequences; Skipped 0 sequences for having X
Output stored at <DATA_DIR>/<path-to-sequence-fasta-file>.fasta.csv
......
requests==2.24.0
matplotlib==3.8.2
pandas==2.1.3
matplotlib>=3.3.4
pandas>=1.3.5
catboost==1.0.0
logomaker==0.8
alfpy==1.0.6
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment