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Inserting transcripts on server

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Dave Lawrence edited this page Jul 6, 2023 · 1 revision

Copy latest files onto cdot_rest machine:

scp -i ~/.ssh/variantgrid-cloud.pem refseq/cdot-0.2.19.refseq.grch37_grch38.json.gz ensembl/cdot-0.2.19.ensembl.grch37_grch38.json.gz  [email protected]:/data/incoming

ssh to machine, then run:

sudo su cdot
cd /opt/cdot_rest
source venv/cdot/bin/activate
python3 -m pip install --upgrade cdot # Latest version
python3 manage.py import_transcript_json /data/incoming/cdot-0.2.19.ensembl.grch37_grch38.json.gz --annotation-consortium=Ensembl
python3 manage.py import_transcript_json /data/incoming/cdot-0.2.19.refseq.grch37_grch38.json.gz --annotation-consortium=RefSeq
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