docs: Add tutorial for running SACCELERATOR with LSF/Mamba and new Xenium ovarian cancer datasets#356
Draft
Copilot wants to merge 2 commits into
Draft
docs: Add tutorial for running SACCELERATOR with LSF/Mamba and new Xenium ovarian cancer datasets#356Copilot wants to merge 2 commits into
Copilot wants to merge 2 commits into
Conversation
…nium ovarian cancer datasets
Copilot
AI
changed the title
docs: Add tutorial for running SACCELERATOR with LSF/Mamba on example and new Xenium ovarian cancer datasets
docs: Add tutorial for running SACCELERATOR with LSF/Mamba and new Xenium ovarian cancer datasets
May 31, 2026
Copilot created this pull request from a session on behalf of
shwong-tw
May 31, 2026 21:57
View session
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Tutorial for running the pipeline on HPC with LSF (
bsub) and Mamba, including how to manage Snakemake's hashed conda environments and how to add new datasets.Contents (
docs/tutorial_lsf_mamba.md)libd_dlpfcandxenium-breast-cancerwith an LSF Snakemake profile (covers both Snakemake 7.x and 8.x plugin-based configs)--conda-prefixfor shared persistent cachesaccelerator_method_spaGCN, etc.)--conda-create-envs-onlyfor upfront env resolutionExample LSF profile snippet:
Note: The download script templates require users to fill in actual 10x Genomics URLs (gated behind their ToS acceptance page).