snakemake / snakemake/snakemake

add connection pooling for remote objects

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enhancement
Dominant language
Python
Stars
2.9k
Forks
656
Avg merge
4d 12h
Merged PRs (30d)
9

Description

Is your feature request related to a problem? Please describe.
I have a workflow for downloading the latest version of RefSeq. However, there are a few thousand protein files to download. Using FTP remote to download the files is untenable. I gave up after waiting a day for the DAG to resolve.

Describe the solution you'd like
I hacked remote/FTP.py to use connection pooling (https://github.com/niciqy/ConnectionPool) and it was able to resolve the DAG in under half an hour.

For a different workflow with only a dozen files, it cut the dry-run time from 30s to 20s.

I've only looked at the FTP module so far, and I only partially understand how the whole Remote system is built, but it could be a way to speed up any workflow using remote resources.

Describe alternatives you've considered
I can make my workflow functional by manually checking the dates and downloading with wget or curl, but that requires more code in the workflow than simply using remotes.

Contributor guide

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with remote/FTP.py and trace how the broader Remote system creates and reuses connections. Compare the existing FTP behavior with the reported connection-pooling approach, then verify that workflows using many remote resources resolve substantially faster without breaking smaller remote workflows.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
networking
Issue type
Feature
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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