update and simplify requirements

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
 

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
 

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