diff --git a/README.md b/README.md index 272229c..3d7db93 100644 --- a/README.md +++ b/README.md @@ -18,8 +18,9 @@ If you would like to make changes to WebSTR, you must: 1. Set up python3 and virtualenv on your machine: [For Mac, follow instructions here.](https://gist.github.com/pandafulmanda/730a9355e088a9970b18275cb9eadef3) -2. Create a new virtual env with python3 and install all the requirements with the following command: -`pip install -r requirements.txt` +2. Create a new conda environment with python3 and install all the requirements with the following command: + +`conda env create -f environment.yml` 3. Copy data files to data directory diff --git a/WebSTR/WebSTR.py b/WebSTR/WebSTR.py index d3ba3f2..36ac205 100755 --- a/WebSTR/WebSTR.py +++ b/WebSTR/WebSTR.py @@ -6,9 +6,7 @@ # Package imports import argparse from flask import Flask, redirect, render_template, request, session, url_for, jsonify -import numpy as np import os -import pandas as pd import pyfaidx import sys diff --git a/environment.yml b/environment.yml new file mode 100644 index 0000000..59ab5dc --- /dev/null +++ b/environment.yml @@ -0,0 +1,90 @@ +name: webstr +channels: + - bioconda + - defaults +dependencies: + - _libgcc_mutex=0.1=main + - _openmp_mutex=5.1=1_gnu + - ansi2html=1.9.1=py312h06a4308_0 + - biopython=1.78=py312h5eee18b_0 + - blas=1.0=mkl + - blinker=1.6.2=py312h06a4308_0 + - bottleneck=1.3.7=py312ha883a20_0 + - brotli-python=1.0.9=py312h6a678d5_8 + - bzip2=1.0.8=h5eee18b_6 + - ca-certificates=2024.9.24=h06a4308_0 + - certifi=2024.8.30=py312h06a4308_0 + - charset-normalizer=3.3.2=pyhd3eb1b0_0 + - click=8.1.7=py312h06a4308_0 + - dash=2.14.2=py312h06a4308_0 + - expat=2.6.3=h6a678d5_0 + - flask=3.0.3=py312h06a4308_0 + - flask-compress=1.13=py312h06a4308_0 + - idna=3.7=py312h06a4308_0 + - importlib-metadata=7.0.1=py312h06a4308_0 + - intel-openmp=2023.1.0=hdb19cb5_46306 + - itsdangerous=2.2.0=py312h06a4308_0 + - jinja2=3.1.4=py312h06a4308_0 + - ld_impl_linux-64=2.40=h12ee557_0 + - libffi=3.4.4=h6a678d5_1 + - libgcc-ng=11.2.0=h1234567_1 + - libgomp=11.2.0=h1234567_1 + - libstdcxx-ng=11.2.0=h1234567_1 + - libuuid=1.41.5=h5eee18b_0 + - markupsafe=2.1.3=py312h5eee18b_0 + - mkl=2023.1.0=h213fc3f_46344 + - mkl-service=2.4.0=py312h5eee18b_1 + - mkl_fft=1.3.10=py312h5eee18b_0 + - mkl_random=1.2.7=py312h526ad5a_0 + - ncurses=6.4=h6a678d5_0 + - nest-asyncio=1.6.0=py312h06a4308_0 + - numexpr=2.8.7=py312hf827012_0 + - numpy=1.26.4=py312hc5e2394_0 + - numpy-base=1.26.4=py312h0da6c21_0 + - openssl=3.0.15=h5eee18b_0 + - packaging=24.1=py312h06a4308_0 + - pandas=2.2.2=py312h526ad5a_0 + - pip=24.2=py312h06a4308_0 + - plotly=5.24.1=py312he106c6f_0 + - pyfaidx=0.8.1.2=pyhdfd78af_0 + - pysocks=1.7.1=py312h06a4308_0 + - python=3.12.7=h5148396_0 + - python-dateutil=2.9.0post0=py312h06a4308_2 + - python-tzdata=2023.3=pyhd3eb1b0_0 + - pytz=2024.1=py312h06a4308_0 + - pyvcf3=1.0.3=pyhdfd78af_0 + - readline=8.2=h5eee18b_0 + - requests=2.32.3=py312h06a4308_0 + - retrying=1.3.3=pyhd3eb1b0_2 + - setuptools=75.1.0=py312h06a4308_0 + - six=1.16.0=pyhd3eb1b0_1 + - sqlite=3.45.3=h5eee18b_0 + - tbb=2021.8.0=hdb19cb5_0 + - tk=8.6.14=h39e8969_0 + - typing_extensions=4.11.0=py312h06a4308_0 + - tzdata=2024b=h04d1e81_0 + - urllib3=2.2.3=py312h06a4308_0 + - werkzeug=3.0.3=py312h06a4308_0 + - wheel=0.44.0=py312h06a4308_0 + - xz=5.4.6=h5eee18b_1 + - zipp=3.17.0=py312h06a4308_0 + - zlib=1.2.13=h5eee18b_1 + - pip: + - attrs==24.2.0 + - colour==0.1.5 + - dash-bio==1.0.2 + - geoparse==2.0.4 + - joblib==1.4.2 + - jsonschema==4.23.0 + - jsonschema-specifications==2024.10.1 + - parmed==4.2.2 + - periodictable==1.7.1 + - pyparsing==3.1.4 + - referencing==0.35.1 + - rpds-py==0.20.0 + - scikit-learn==1.5.2 + - scipy==1.14.1 + - tenacity==9.0.0 + - threadpoolctl==3.5.0 + - tqdm==4.66.5 +prefix: /home/mgymrek/miniconda3/envs/webstr diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index fd5c532..0000000 --- a/requirements.txt +++ /dev/null @@ -1,23 +0,0 @@ -certifi==2024.7.4 -charset-normalizer==2.1.1 -click==8.1.3 -Flask==2.2.2 -idna==3.4 -importlib-metadata==5.1.0 -itsdangerous==2.1.2 -Jinja2==3.1.2 -MarkupSafe==2.1.1 -numpy==1.23.5 -pandas==1.5.2 -plotly==5.11.0 -pyfaidx==0.7.1 -python-dateutil==2.8.2 -pytz==2022.6 -requests==2.31.0 -six==1.16.0 -tenacity==8.1.0 -urllib3==1.26.13 -Werkzeug==2.2.2 -zipp==3.11.0 -gunicorn==20.1.0 -dash_bio==1.0.2 \ No newline at end of file