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environment.yml
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environment.yml
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# note if you're running macOS M1 - miniconda doesn't have direct support for that, but using x64 with a translation layer should work fine
# to enable run
# conda config --env --set subdir osx-64
name: vgconda
channels:
- conda-forge
- bioconda
- anaconda
- defaults
dependencies:
- python=3.11
- pip
- py-bgzip
- setuptools=68.0
- more-itertools=9.1 # was 8.12.0
- beautifulsoup4=4.12 # was 4.10.0
- biopython=1.81
- celery=5.2
- configargparse=1.5
- coreapi=2.3
# - cyvcf2=0.30.28 (claims it doesn't work with python 3.11)
# - htseq=2.0.5 (claims it doesn't work with python 3.11)
- ijson=3.1
- ipython=8.15
- kombu=5.3 # was kombu==5.2.3
- levenshtein==0.21 # was levenshtein==0.20.9
- markdown=3.2 # was 3.1
- matplotlib=3.8.4
- networkx=2.7.1
- nltk=3.8 # was 3.7
- numpy=1.25 # was 1.22
- oauthlib=3.1
- pandas=2.2.2
- psycopg2=2.9.9
- pypdf2=2.11 # was 2.6
# - pysam=0.22.1 # was 0.18
- python-dateutil=2.8
- pyvcf3=1.0.3
- redis=3.5 # was redis==3.5.3
- reportlab=3.6 # increased patch version from requirements.txt
- requests=2.32
- requests-oauthlib=1.3
- scipy=1.11 # was scipy==1.8.0
- sqlparse=0.5
- toposort=1.10 # was toposort==1.7
- Unidecode=1.3
- boto3=1.26
- pyspellchecker=0.6
- pydantic=2.4.0
- deepdiff=6.5.0
- gdal=3.9 # needed for geo
- lxml=5.2.1
#- setuptools-rust=1.9.0
- pip:
- deprecation==2.1.0
- django-auditlog==3.0.0
- setuptools_rust==1.9.0
- fastobo==0.12.3
- cyvcf2==0.30.28
- htseq==2.0.5
- pysam==0.22.1
- cdot==0.2.21
- stream-zip==0.0.47
# - bgzip==0.4.0 (using py-bgzip in conda instead)
- Django==4.2.11
- django-amazon-ses==4.0.1
- django-storages==1.12.3
- django_autocomplete_light==3.9.1
- django-avatar==8.0.0
- django_cache_memoize==0.1.10
- django-compressor==4.3.1
- django_crispy_forms==2.0
- django_dag==1.4.3
- django_datetime_utc==1.0.3
- django_debug_toolbar==4.2.0
- django_downloadview==2.3.0
- django-extensions==3.1.5
- django-geojson==3.2.0
- django_glrm==1.1.3
- django-guardian==2.4.0
- django_htmlmin==0.11.0
- django-leaflet==0.28.2
- django_model_utils==4.2.0
- django-postgres-extra==2.0.5
- django-registration-redux==2.9
- django_termsandconditions==2.0.12
- django-reversion-compare==0.15.0
- django_threadlocals==0.10
- djangorestframework==3.14.0
- crispy-bootstrap4==2022.1
- mozilla_django_oidc==2.0.0
- easy_thumbnails==2.8.5
- fontawesomefree==6.4.0
- django_json_widget==2.0.1
- git+https://github.com/davmlaw/django-jfu#egg=django-jfu
- git+https://github.com/davmlaw/django-messages/#egg=django-messages
- git+https://github.com/davmlaw/django-starfield#egg=django_starfield
- django-js-reverse==0.10.2
- git+https://github.com/SACGF/hgvs#egg=pyhgvs
- git+https://github.com/biocommons/hgvs#egg=hgvs
- nameparser==1.1.1 # nameparser hasn't been updated in conda since 1.0.5
- rollbar==0.16.3
- frozendict==2.3.4
- pronto==2.5.7 # pronto causes a lot of dependancy issues that we're going to sweep under pip's rug
- django_recaptcha==4.0.0