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CCRGeneticsBranch / Oncogenomics_v2

Oncogenomics portal version 2
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AVIA file exchange implementation #7

Open hsienchao opened 1 year ago

hsienchao commented 1 year ago

  1. Implemented two scripts: export_new_variants.pl and import_new_variants.pl

  2. At 1am every day, the sync script will invoke export_new_variants.pl to generate the variant list to be annotated:

    /mnt/projects/CCR-JK-oncogenomics/static/site_data/dev/avia/hg19/new_variants.tsv

  3. Anney should take this file and move it to "archives" folder and generate the Open Cravat annotation file to:

    /mnt/projects/CCR-JK-oncogenomics/static/site_data/dev/avia/hg19/annotation.tsv

  4. The cronjob will read this file and insert data to database and move the file to "archives" folder

hsienchao commented 1 year ago

I've created a new hg19_annot_oc table to replace hg19_annot_oc@aviad_lnk. I also found there are duplicate records in hg19_annot_oc@aviad_lnk. See the attachment.

h19_oc_duplicate.txt

cheanney commented 1 year ago

Created a script to annotate /mnt/projects/CCR-JK-oncogenomics/static/site_data/dev/avia/hg19/new_variants.tsv/new_variants.tsv from Hsien-Chao's script.

A cron job is set up to run everyday at 6am