Comments (1)
hi @indianewok, thank you for your interest and support !
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Thanks for bringing up the potential issue about the environmental variables. There is a mechanism to deal with that currently, which is to specify the
igblast_db
option manually in the function: https://sc-dandelion.readthedocs.io/en/latest/modules/dandelion.preprocessing.reannotate_genes.html#dandelion.preprocessing.reannotate_genes -
For the database packaging, currently the way this is being managed is through the singularity image which simplifies this as it then just becomes 2 lines to type in the command line to pull and set up the image and run the entire preprocessing https://sc-dandelion.readthedocs.io/en/latest/notebooks/Q1-singularity-preprocessing.html.
I've also recently updated the scripts in the container folder to now have two python scripts that will download and prepare the databases too: https://github.com/zktuong/dandelion/tree/master/container/scripts.
One can simply invokepython prepare_imgt_database.py
and it should take care of everything. that's what i do with the container build too https://github.com/zktuong/dandelion/blob/master/container/sc-dandelion.def -
yes the 3.12 update is still just a draft. a couple of dependencies are not possible to install just yet and i'm just using to run the CI/CD to check periodically.
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Related Issues (20)
- CI failing because can't download the demo.h5ad from kp9's folder HOT 2
- Mouse VDJ Data
- Dandelion singularity (v0.2.4) cannot quantify mutation HOT 6
- Singularity - C call correction local variable referenced before assignment HOT 4
- speed up minimum spanning tree step HOT 1
- generate network in 0.3.4dev is not working the same way as 0.3.3
- Number of PASS and FAIL in output of the function ddl.pp.reannotate_genes HOT 3
- Singularity Container Preprocessing Error HOT 1
- Bugs in 'pp.check_contigs' HOT 1
- mouse TRA contigs not passing pre-processing HOT 1
- Incompatibility with latest matplotlib HOT 2
- No such file or directory: 'MakeDb_gentle.py' HOT 3
- Singularity Error: raise ValueError(f"cannot insert {column}, already exists") HOT 2
- Igblastn error for Human and not Mouse HOT 1
- TypeError: clone_overlap() got an unexpected keyword argument 'colorby' HOT 1
- Singularity Container Preprocessing Error from container HOT 1
- error dandelion/utilities/_core.py KeyError: 'trbc*'. HOT 3
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