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smith-chem-wisc / Spritz

Software for RNA-Seq analysis to create sample-specific proteoform databases from RNA-Seq data
https://smith-chem-wisc.github.io/Spritz/
MIT License
7 stars 11 forks source link

Conda/dotnet not properly detecting openssl within minimamba docker container; probable conda issue #222

Closed acesnik closed 2 years ago

acesnik commented 2 years ago

The Docker build has been working pretty consistently, but without any change in dotnet version, openssl version, or seemingly miniconda Docker image version, it stopped recently. https://github.com/smith-chem-wisc/Spritz/actions

I tracked this down to the issue of No usable version of the libssl was found starting to pop up for running dotnet SpritzModifications.dll.

I confirmed this is also an issue with smithlab/spritz:0.3.4 from DockerHub, which is downloaded by the GUI. This eliminates the possibility that this is due to a change in Docker images. Therefore, it's likely that conda has changed slightly that makes dotnet not detect openssl in the same way

The correct version of openssl does show up:

image

Here's an attempt of fixing this, but to no avail yet: https://github.com/smith-chem-wisc/Spritz/compare/dockerfix?expand=1.

acesnik commented 2 years ago

Part of the issue with conda runs in docker is that they're done without initializing conda like in a normal commandline setup. Plus, the dependability of containerization can be defeated by changes in conda.

acesnik commented 2 years ago

I found that the mamba version changed between the unbroken and broken versions. Fixing that didn't fix the issue, apparently. https://github.com/smith-chem-wisc/Spritz/pull/223

acesnik commented 2 years ago

https://github.com/smith-chem-wisc/Spritz/pull/223