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fix: pin mikado python dependencies to fix issues with installation #444
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gemygk committed May 13, 2024
1 parent c27d7e0 commit f37c595
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57 changes: 29 additions & 28 deletions environment.yml
Original file line number Diff line number Diff line change
Expand Up @@ -5,34 +5,35 @@ channels:
- defaults
- anaconda
dependencies:
- biopython>=1.78
- cython>=0.29.13
- docutils
- drmaa
- hypothesis
- msgpack-python>=1.0.0
- networkx>=2.3
- numpy>=1.17.2
- pandas>=1.0
- python>=3.9,<3.11
- cython==0.29.32
- biopython==1.79
- docutils==0.19
- drmaa==0.7.9
- hypothesis==6.56.2
- msgpack-python==1.0.4
- networkx==2.8.7
- numpy==1.23.3
- pandas==1.5.0
- pysam==0.19.1
- pyyaml==6.0.1
- scipy==1.9.2
- snakemake==6.15.5
- sqlalchemy==1.4.41
- sqlalchemy-utils==0.38.3
- tabulate==0.9.0
- pytest==7.1.3
- python-rapidjson==1.9
- toml==0.10.2
- pyfaidx==0.5.9.5
- marshmallow==3.14.1
- marshmallow-dataclass==8.5.3
- typeguard==2.13.3
- sqlite
- pip
- pyfaidx>=0.5.8
- wheel
- samtools>=1.11
- htslib>=1.11
- pysam>=0.15.3
- python>=3.6,<3.10
- pyyaml>=5.1.2
- scipy>=1.3.1
- gmap==2021.08.25
- snakemake-minimal>=5.7.0
- sqlalchemy>1.4.0,<2
- sqlalchemy-utils==0.34.1
- sqlite
- tabulate>=0.8.5
- wheel
- pytest>=5.4.1
- python-rapidjson>=1.0
- marshmallow==3.14.1
- marshmallow-dataclass==8.5.3
- typeguard>=2.9.1
- conda-forge::toml>=0.10.0
- bioconda::pyfaidx>=0.5.8
- prodigal==2.6.3
- diamond==2.0.11
- portcullis==1.2.4
47 changes: 23 additions & 24 deletions requirements.txt
Original file line number Diff line number Diff line change
@@ -1,24 +1,23 @@
biopython>=1.78
docutils
drmaa
hypothesis
msgpack>=1.0.0
networkx>=2.3
numpy>=1.17.2
pandas>=1.0
pip
pysam>=0.15.3
pyyaml>=5.1.2
scipy>=1.3.1
snakemake>=5.7.0
sqlalchemy>1.4.0,<2
sqlalchemy-utils==0.37
tabulate>=0.8.5
pytest>=5.4.1
python-rapidjson>=1.0.0
toml>=0.10.0
pyfaidx>=0.5.8
dataclasses; python_version < '3.7'
marshmallow>=3.14.1
marshmallow-dataclass>=8.5.3
typeguard # Necessary for mashmallow apparently
cython==0.29.32
biopython==1.79
docutils==0.19
drmaa==0.7.9
hypothesis==6.56.2
msgpack==1.0.4
networkx==2.8.7
numpy==1.23.3
pandas==1.5.0
pysam==0.19.1
pyyaml==6.0.1
scipy==1.9.2
snakemake==6.15.5
sqlalchemy==1.4.41
sqlalchemy-utils==0.38.3
tabulate==0.9.0
pytest==7.1.3
python-rapidjson==1.9
toml==0.10.2
pyfaidx==0.5.9.5
marshmallow==3.14.1
marshmallow-dataclass==8.5.3
typeguard==2.13.3

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