Re: PyEnsembl - how does that help us?
Quick update - I have package all dependencies fo xpore (and of
pyensembl with it) , packages are tagged orange on the spreadsheet's
"Nanopore" tab
(https://docs.google.com/spreadsheets/d/1tApLhVqxRZ2VOuMH_aPUgFENQJfbLlB_PFH_Ah_q7hM/edit#gid=1806578173)
- but, no idea how you are feeling about it all, but I think this better
waits till after the release.
@Nilesh, I want to run pyensembl locally to ensure that it works - it is
not too far from a gigabyte that is downloaded if I am interpreting the
URLs right and am not erroneous, which just for testing purposes is a
bit too much.
Best,
Steffen
Am 18.05.21 um 15:15 schrieb Nilesh Patra:
>
> On 5/18/21 6:16 PM, Steffen Möller wrote:
>> Hello,
>>
>> I just packaged xpore, which points to
>> https://github.com/openvax/pyensembl to get various sorts of sequencing
>> data, also complete genomes. I like that and address its packaging now.
>> New packages are uploaded to PyPi, not release tagged, but, well, ... .
> Nice.
>
>> In my reading this is a way to get test data for various applications of
>> ours in a reproducible way. Since this packages only the routines to
>> retrieve the data, not the data itself, we cannot use that for package
>> autotests. However, we can still use it for testing our workflows if our
>> workflow-test-environment is allowed to have internet access, which I
>> think it should have.
> If internet access is the only bottle-neck, there's a needs-internet
> restriction[1] which can get this moving.
>
> [1]: https://people.debian.org/~eriberto/README.package-tests.html
>
> Nilesh
>
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