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Add an AnnData experiment to our local SCXA #340
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I started to work on this ticket. I started to update its description regarding the dataset. |
At my 1st run of the PostgreSQL step I had a couple of missing files error:
and also these lines of errors:
|
@pmb59 told me that for now we can download the missing I discussed it with him that it is in a feature branch and it should be merged ASAP into the repo's main branch ( |
We still have these missing files according to the log:
This is the current state. I still need more info from the curators/bioinformaticians... |
We have the files ready at this location if you join codon:
but Now we are waiting for @pmb59 and/or @irisdianauy to fix the files for |
The cell counts in the various
|
I am going to move this task to the next sprint as I really hope that we are going to get the relevant files from the data prod / curation team in the next 2 weeks. |
I tried to load E-ANND-3 experiment locally by using the files from I got this error:
After @alfonsomunozpomer helped me investigating this error, it looks like that the 3rd column should be numerical in |
I asked @YalanBi and @irisdianauy to look into this issue. |
Data production team need to reanalyse |
@irisdianauy notified me that the files for the test loading of E-ANND-3 are available now in /nfs/production/irene/ma/sc_experiments/E-ANND-3. |
I successfully loaded |
@irisdianauy Fixed the above mentioned |
Hi @ke4, After loading Anndata experiment ('E-ANND-3') into my local DB. I want to highlight a few corrections to the above steps.
Please let me know if you want me to update these steps. |
After a discussion with Pedro the suitable anndata experiment for our local environment is with the accession:
E-ANND-3
.It can be found here:
/nfs/production/irene/ma/anndata-ingest/datasets/tabula_sapiens/E-ANND-3/*
Steps:
scp -r codon-login:/nfs/production/irene/ma/sc_experiments/E-ANND-3 .
You have to do this unfortunately, as these experiments are not available yet on our FTP. This download should be less than 1 hour.As theidf
file is missing from that file bundle for now (@pmb59 said that they are going to fix this), you can download it from here: https://gitlab.ebi.ac.uk/ebi-gene-expression/scxa-metadata/-/blob/feature/add_E-ANND-3/ANND/E-ANND-3/E-ANND-3.idf.txt. Please put it into the root folder of the experiment (E-ANND-3
).Rename theumap.tsv
toE-ANND-3.umap.tsv
.docker container create --name pgvol -v scxa_atlas-data-exp:/atlas-data/exp ubuntu:jammy
docker cp E-ANND-3 pgvol:/atlas-data/exp/magetab/
E-ANND-3
to yourtest-data.env
file underdocker/prepare-dev-environment
folder./docker/prepare-dev-environment/postgres/run.sh -r -l pg-anndata.log
SCHEMA_VERSION=latest \ docker compose --env-file ./docker/dev.env \-f ./docker/docker-compose-postgres.yml \ up
./docker/prepare-dev-environment/solr/run.sh -r -l solr.log
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