BulkSeq Studio 0.12.2

BulkSeq Studio 0.12.2

Superseded by 0.13.0. A rule guard added in this release has an unescaped-brace bug that Snakemake parses as a format field, aborting 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 environment fixes below are unaffected.

Patch release. The Salmon and HISAT2 aligner routes now work with the core environment.

Fixed

• Salmon and HISAT2 aligner routes failed on a core-only environment. The bulkseq_core.yaml profile installed by Install / repair core environment did not include gffread, salmon, or hisat2; those tools were only in the full R/DESeq2 profile. Choosing the Salmon or HISAT2 aligner with a core (or pre-0.11.0) environment ran through trimming and QC, then failed mid-run with exit status 127 (command not found) at make_transcriptome, salmon_index, or hisat2_index. The three tools are now part of the core profile, so every aligner route works with the core environment.
• Check Environment did not probe the alternative-aligner tools. gffread, salmon, and hisat2 are now probed and shown, so a stale environment is visible instead of failing only at run time. The "core ready" indicator still tracks the default STAR route, so a working STAR setup is not reported as incomplete.
• Clearer failure when an aligner tool is missing. The affected rules now exit with a message that points to Setup, instead of a raw exit status 127 partway through the run.

Upgrading

If you already have a bulkseq environment, open Check Environment → Install / repair core environment so it gains gffread, salmon, and hisat2 (an additive update). On Linux, recreate or update the environment from workflow/envs/bulkseq_core.yaml.

Downloads (Windows)

• BulkSeqStudio-Setup-0.12.2.exe — installer
• BulkSeqStudio-Portable-0.12.2.zip — unzip and run BulkSeqStudio.exe, no install