Comments (6)
arq5x
commented on August 24, 2024
Yep, good idea. I am currently looking into how best to pull data from Ensembl. Not that easy, unfortunately. Also, if you are interested in adding a recipe to ggd-recipes, that would be great!
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martijnvermaat
commented on August 24, 2024
Could have a look at how https://github.com/hammerlab/pyensembl rolls.
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arq5x
commented on August 24, 2024
Ah, thanks. Will have a look.
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arq5x
commented on August 24, 2024
By my eye, it appears that pyensembl rolls by creating a local instance of a SQLite database by downloading the relevant gzipped GTF, etc. files from Ensembl. This strategy could work, but ideally, I would really like GGD to use the existing APIs to pull data. This is going to be a challenge, however...
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mw55309
commented on August 24, 2024
Aren't the Ensembl APIs in Perl?
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arq5x
commented on August 24, 2024
They have a MYSQL database under the hood as well.
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Related Issues (15)
- Comments on example command HOT 8
- Config file to specify where to install datasets.
- Update config file with installed datasets to detect updates, etc.
- Use checksum to ensure recipe was executed successfully. HOT 1
- Use wildcards to install collections of recipes
- SRA downloader? HOT 3
- Make species the top level in hierarchy HOT 1
- set exit codes on errors.
- allow simpler running of installing single local yaml
- versioning HOT 2
- dependencies on other recipes and on softare HOT 4
- recipe responsible for writing files
- make and get sections
- template variables
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