Statistics pipe #10
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Statistics pipe #10
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ens-ftricomi
requested review from
EreboPSilva,
leannehaggerty,
vianeyBE and
swatiebi
docs/source/conf.py
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| import datetime | ||
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| sys.path.insert(0, os.path.abspath("../../src/python/ensembl/genes/metadata")) | ||
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Is this copied from the transcriptomic pipeline? Should it be ensembl/gene/statistics?
docs/source/conf.py
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| copyright_owner = "EMBL-European Bioinformatics Institute" | ||
| copyright_dates = "[2016-%d]" % datetime.datetime.now().year | ||
| copyright = copyright_dates + " " + copyright_owner | ||
| html_baseurl = 'https://ensembl.github.io/ensembl-genes-metadata/' |
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Should this be the ensembl-genes-nf repo?
docs/source/conf.py
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| "Ensembl-genes-metadata Documentation.", | ||
| "Miscellaneous", | ||
| ), | ||
| ] |
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Statistics documentation rather than metadata?
| "--ncbi_url", | ||
| type=str, | ||
| help="NCBI dataset url", | ||
| default="https://api.ncbi.nlm.nih.gov/datasets/v2alpha/taxonomy/taxon/", |
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This is likely to be updated quite often. Do you think it's better to have a hardcoded default or move it to config?
…ne to run the different scripts and add the metakeys into the core
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The pipeline can run for multiple species at the same time Busco in genome and proteine mode as default or use a specific mode thanks to a parameter. The busco lineage is calculated getting the list of taxon id from ncbi taxonomy and choosing the closest match with the list of taxonomy id available in the busco dataset config file. If the dataset is provided as input parameter this will be used for all the species in the batch.
The genome file is downloaded by ncbi dataset.
The default input is a core db but the user can check the completeness in the genome specifying the gca only.
The pipeline can also run OMARk and the Perl statistics from a core db and upload all the results in the Ensembl Rapid ftp creating the current directory and set the permission for the folder. This might change in the future according to the new structure for Beta ftp.
The script to apply the Busco patches in Beta is still missing