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Added enformer predictor #2
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02d834e
added enformer pipeline
gtsitsiridis 0739ca0
added enformer pipeline
gtsitsiridis 56014f6
added enformer pipeline
gtsitsiridis 9ffe6bd
added enformer pipeline
gtsitsiridis 17301b0
added enformer pipeline
gtsitsiridis 0eee3a2
added enformer pipeline
gtsitsiridis 602f2c8
added enformer pipeline
gtsitsiridis dea4bbd
added enformer pipeline
gtsitsiridis e4f1878
added enformer pipeline
gtsitsiridis 719c116
added enformer defaults in config
gtsitsiridis 61044ef
added enformer defaults in config
gtsitsiridis 567612a
added enformer defaults in config
gtsitsiridis c03dc4d
added enformer defaults in config
gtsitsiridis b36bf25
added enformer defaults in config
gtsitsiridis 9d31278
download enformer reference logic
gtsitsiridis a77ebf2
download enformer reference logic
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download enformer reference logic
gtsitsiridis 58f6fe5
download enformer reference logic
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download enformer reference logic
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download enformer reference logic
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download enformer reference logic
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download enformer reference logic
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download enformer reference logic
gtsitsiridis bc46e3e
enformer refactoring
gtsitsiridis ee124d9
enformer refactoring
gtsitsiridis 2f30730
enformer refactoring
gtsitsiridis 1178fcd
renamed enformer run config
gtsitsiridis 2c8bd58
renamed enformer run config
gtsitsiridis 3ea517b
renamed enformer run config
gtsitsiridis f1c271c
removed duplicate gtf2parquet rule
gtsitsiridis 99ca6b2
enformer protein_coding_only flag
gtsitsiridis 0b2b1e9
enformer chromosomes flag
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,22 @@ | ||
name: abexp-enformer-gpu | ||
channels: | ||
- conda-forge | ||
- bioconda | ||
dependencies: | ||
- python>=3.11 | ||
- attrs<=21.4.0 # because of kipoi | ||
- cyvcf2>=0.30.28 | ||
- numpy>=1.26.4 | ||
- pandas>=2.2.1 | ||
- pyarrow>=16.1.0 | ||
- pyranges>=0.0.129 | ||
- polars>=0.20.19 | ||
- scikit-learn>=1.4.1.post1 | ||
- lightgbm>=4.3.0 | ||
- zarr>=2.15.0 | ||
- xarray>=2024.5.0 | ||
- tensorflow-hub==0.16.1 | ||
- tensorflow==2.16.1 | ||
- tensorflow-gpu==2.16.1 | ||
- pip: | ||
- "git+https://github.com/gtsitsiridis/kipoi_veff_analysis.git@master" | ||
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,21 @@ | ||
name: abexp-enformer | ||
channels: | ||
- conda-forge | ||
- bioconda | ||
dependencies: | ||
- python>=3.11 | ||
- attrs<=21.4.0 # because of kipoi | ||
- cyvcf2>=0.30.28 | ||
- numpy>=1.26.4 | ||
- pandas>=2.2.1 | ||
- pyarrow>=16.1.0 | ||
- pyranges>=0.0.129 | ||
- polars>=0.20.19 | ||
- scikit-learn>=1.4.1.post1 | ||
- lightgbm>=4.3.0 | ||
- zarr>=2.15.0 | ||
- xarray>=2024.5.0 | ||
- tensorflow-hub==0.16.1 | ||
- tensorflow==2.16.1 | ||
- pip: | ||
- "git+https://github.com/gtsitsiridis/kipoi_veff_analysis.git@master" | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. move to gagneurlab |
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We need to move this repo to the gagneurlab team