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BulkSeq Studio 0.12.3

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@tunabirgun tunabirgun released this 26 Jun 15:13
v0.12.3
4ca98c4

BulkSeq Studio 0.12.3

Superseded by 0.13.0. This release inherits the 0.12.2 rule-guard bug (unescaped braces parsed by Snakemake as a format field), which aborts the Salmon and HISAT2 routes with a NameError even when the environment is correct. Use 0.13.0 or newer for those aligners. The STAR route and the fixes below are unaffected.

Patch release. Two dependency-coverage gaps found by auditing the rest of the pipeline for the same class as the 0.12.2 aligner-tool fix.

Fixed

  • DESeq2 log-fold-change shrinkage could fail with a missing-package error. run_deseq2.R falls back to lfcShrink(type="ashr") for contrasts apeglm cannot shrink, and ashr is also selectable via deseq2.shrinkage_method, but the ashr R package was in no environment profile. A config that requested ashr (or a default apeglm run that hit the contrast fallback) aborted after the model fit. r-ashr is now in the full environment and the pinned lock, and deseq2.shrinkage_method is restricted to apeglm, ashr, or normal so an unsupported value is rejected when the config loads rather than mid-run. Default (apeglm) runs are unchanged.
  • GO enrichment for yeast, Arabidopsis, C. elegans, and zebrafish fell back to g:Profiler. The enrichment step maps these organisms to the Bioconductor OrgDbs org.Sc.sgd.db, org.At.tair.db, org.Ce.eg.db, and org.Dr.eg.db, but those packages were not installed, so the native clusterProfiler GO route (GO over-representation, GO GSEA, and disease ontology) was skipped and the run quietly used the g:Profiler over-representation fallback instead. The four OrgDbs are now in the full environment and the lock, restoring the full GO route for these organisms.

Upgrading

If you already have a bulkseq environment, open Check Environment → Install full R/DESeq2 stack (or re-run it) so it gains r-ashr and the four OrgDbs. On Linux, update the environment from workflow/envs/bulkseq_full.yaml.

Downloads

Windows:

  • BulkSeqStudio-Setup-0.12.3.exe — installer
  • BulkSeqStudio-Portable-0.12.3.zip — unzip and run BulkSeqStudio.exe, no install

Linux (x86-64, glibc 2.39+):

  • BulkSeqStudio-0.12.3-x86_64.AppImage — mark executable and run
  • BulkSeqStudio-linux-0.12.3.tar.gz — extract and run BulkSeqStudio
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