quantms icon indicating copy to clipboard operation
quantms copied to clipboard
verified publisher icon bigbio

Conda Support

Open ypriverol opened this issue 9 months ago • 3 comments

Description of feature

The current DIA workflow does not support the Conda platform. Only the ID, DDA-LFQ, and DDA-TMT can be run in the three platforms Conda, Docker, and Singularity. However, this tree workflow heavily depends on the OpenMS platform to do the releases for us to do the release.

OpenMS team @timosachsenberg has mentioned that the most difficult for OpenMS to release is the Conda platform. They can nightly release docker and singularity. This situation prompts the following issues:

  • Delay our releases waiting for OpenMS's big release.
  • When a bug is found and @timosachsenberg (OpenMS) team fixes it, we have to wait a year to get it.

Multiple pipelines in nf-core are not supporting anymore Conda (https://nfcore.slack.com/archives/C04QR0T3G3H/p1744360287778109) and we do in fact not support it for DIA. Knowing this. I will propose the following flow:

  • Enable a CI/CD that enables to pull from (ghcr.io/openms/openms-tools-thirdparty-sif:latest) OpenMS Docker and Singularity container and tag it with the date: Y.M.D, push the containers to quantms ghcr.io space.
  • Have a mechanism to disable on specific releases Conda. The idea is that we can have released with Conda support and others without Conda support (when OpenMS is available). The other option is to disable the Conda until more people/users complain about this issue.

Would be good to have a feedback here, with comments.

ypriverol avatar Apr 12 '25 07:04 ypriverol

Honestly, I basically don't use the conda myself. Not sure how often conda is used for other users. I agree with disable the Conda for now, until more feedback

daichengxin avatar Apr 13 '25 05:04 daichengxin

Containers are now here: https://github.com/orgs/bigbio/packages?repo_name=quantms-containers. quantms PR ongoing here: #515

ypriverol avatar Apr 13 '25 08:04 ypriverol

This issue is related to conda support and DSL https://github.com/nf-core/proteomicslfq/issues/172#issue-1037218369

XXX@XXX: conda activate quantms_env (quantms_env) XXX@XXX:~$ nextflow -version Error: cannot find Java or it's a wrong version -- please make sure that Java 7 or higher it's installed Note: Nextflow is trying to use the Java VM defined by the following environment variables: JAVA_CMD: /opt/miniconda3/envs/env_nf/lib/jvm/bin/java JAVA_HOME: /opt/miniconda3/envs/env_nf/lib/jvm

XXX@XXX: conda activate proteomicslfq_env (proteomicslfq_env) XXX@XXX: nextflow ... XXX@XXX: N E X T F L O W ~ version 25.04.6

Nextflow DSL1 is no longer supported — Update your script to DSL2, or use Nextflow 22.10.x or earlier

nayanvs avatar Jul 07 '25 07:07 nayanvs