Comments (2)
I'd recommend you to create a bioconda recipe. Once you have that you get a container for free through biocontainers.
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Singularity container for v0.1.0 all set up and ready for testing!
https://cloud.sylabs.io/library/kt16/default/sc-dandelion
singularity pull library://kt16/default/sc-dandelion:latest
singularity shell sc-dandelion.sif
Just earmarking some not-so-distant plans:
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streamline preprocessing
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@ktpolanski proposed to streamline the pre-processing step to something like a module/wrapper so that a user can essentially do something like:
container run dandelion-preprocess -o [OPTIONS] on/this/folder/here
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This should solve some of the installation issues that required 'advanced' knowledge of how to set up a working R, python environment that pointed to the dependencies and reference databases.
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Reference databases and environmental variables are also set-up so no need to mess around with profile scripts.
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Can add in a option to specify user-supplied database to overwrite the container's
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This needs a clever system to do multi-sample preprocessing, especially for the
reassign_alleles
step -
current proposal is to have a text file containing columns specifying the sample id, prefixes/suffixes to add to the fasta and a column indicating if a sample is meant to be combined for
reassign_alleles
or not. -
trim back on softwares
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the image might be too big (1.5gb) and i should look into removing some potentially unnecessary softwares for the build.
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I think it probably won't change much though because gcc is required to build the R packages.
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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
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- speed up minimum spanning tree step HOT 1
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- Number of PASS and FAIL in output of the function ddl.pp.reannotate_genes HOT 3
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- Bugs in 'pp.check_contigs' HOT 1
- mouse TRA contigs not passing pre-processing HOT 1
- IGDATA vs. IGBLAST_DB Confusion + Other Installation kerfuffles HOT 1
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- 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
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