Slurm profile for CTMR UCP environment #159
Merged
Conversation
This file contains 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
boulund
added a commit
that referenced
this pull request
Feb 2, 2021
* Update version to 0.4.1-dev * Update CircleCI badge in README to monitor develop branch * Add Singularity deffile for stag-mwc env * Add Singularity image for main env up to kraken2 * Add link to Singularity bind docs * Add stag-mwc-main singularity image to all rules that require it * Add Singularity images for biobakery and assembly * Set rule threads from cluster_config if defined * Update CHANGELOG * Docs: Update module intro paragraph, closes #151 * Add {cluster.extra} to slurm-submit.py script call * Update CHANGELOG * Fix typo in kraken2 rules * the host removal script was ignoring it's flag in config.yaml * Update CHANGELOG * Update CHANGELOG * Tweak docs, update changelog, prepare for release * Amrplusplus (#156) * amrplusplus * amrplusplus scripts * added scripts * changed input in config.yaml Co-authored-by: Fredrik Boulund <boulund@users.noreply.github.com> * default db empty Co-authored-by: Fredrik Boulund <boulund@users.noreply.github.com> * db -> megares Co-authored-by: Fredrik Boulund <boulund@users.noreply.github.com> * annotation --> megares_annotation Co-authored-by: Fredrik Boulund <boulund@users.noreply.github.com> * added amrplusplus to circleci * updated CHANGELOG.md * updated amrplusplus in config.yaml * added amrplusplus to modules.rst * updated amrplusplus.smk * added license and removed bin dir * updated modules.rst * added align_to_amr * fixed default database * amrplusplus db empty in conf * indentations * clarification regarding database * Update docs/source/modules.rst Co-authored-by: Fredrik Boulund <boulund@users.noreply.github.com> * Update rules/antibiotic_resistance/amrplusplus.smk Co-authored-by: Fredrik Boulund <boulund@users.noreply.github.com> * Update docs/source/modules.rst grammar Co-authored-by: Fredrik Boulund <boulund@users.noreply.github.com> * Update CHANGELOG.md Co-authored-by: Fredrik Boulund <boulund@users.noreply.github.com> * added bwa to stag-mwc.yaml * added conda environment * amrplusplus exectuable with conda * amrplusplus executable with conda * samtools version 1.10 * amrplusplus conda executable * added amrplusplus.yaml to not break stag-mwc.yaml dependencies * removed amrplusplus dependencies because they broke it * now using amrplusplus.yaml for conda instead of stag-mwc.yaml Co-authored-by: Fredrik Boulund <boulund@users.noreply.github.com> Co-authored-by: Aron Arzoomand <aron@debian.ki.se> * Change report generation call (#161) * Change report generation call Ignore additional arguments to snakemake when creating report, Intended to avoid shell escaping issue with complex arguments to e.g. Singularity, issue #160 * removed snakemake_call * added report generation workaround * report generation Co-authored-by: Fredrik Boulund <boulund@users.noreply.github.com> * report generation Co-authored-by: Fredrik Boulund <boulund@users.noreply.github.com> * indentation Co-authored-by: Aron Arzoomand <51719360+AroArz@users.noreply.github.com> * Slurm profile for CTMR UCP environment (#159) * First draft for CTMR UCP cluster profile * Remove references to rackham profile, remove account check * Updated resource requests for all rules * Final tweaks * Rename ctmr_ucp profile to ctmr_gandalf * Fix yml-yaml typo * Fix incorrectly named singularity images * Remove --use prefix for argument to metawrap * Add missing singularity container to create_kaiju_krona_plot * added dbdir and threads for align_to_amr * Disable area plot for Kaiju * Minor updates to docs (#162) * Update badge URL in README Co-authored-by: Kristaps <kbebris@gmail.com> Co-authored-by: Aron Arzoomand <51719360+AroArz@users.noreply.github.com> Co-authored-by: Aron Arzoomand <aron@debian.ki.se> Co-authored-by: AroArz <aron_arzoomand@live.se>
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.
The CTMR UCP Slurm environment is a bit special, we have no accounts and all people currently use the same (default) partition
ctmr.Currently, using the profile throws continuous error messages like
because we haven't implemented Slurm accounts and accounting yet. It still runs, however.