WIP: Toil times - #1958
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cactus-panpatch's main() was missing the standard per-tool boilerplate that every other cactus entry point runs after parsing options: - cactus_override_toil_options(options): sets toil defaults (retryCount, realtime logging, default memory) and exports CACTUS_MAX_MEMORY / CACTUS_DEFAULT_MEMORY. panpatch calls cactus_clamp_memory(), which reads those env vars, so without this it would KeyError. - setupBinaries(options): configures binariesMode/docker so cactus_call works as requested (panpatch runs vg, bgzip, etc. via cactus_call). - set_logging_from_options(options) and enableDumpStack(): consistent logging setup and debug stack dumps. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
…t Slurm partition Newer Toil exposes a per-job `walltime` requirement that its Slurm backend uses to pick a partition (and set --time). This gives Cactus's many small "coordination" jobs a short walltime so Slurm routes them to a fast/short partition, while everything else falls back to Toil's --defaultWalltime. Machinery (src/cactus/shared/common.py): - cactus_fast_walltime(): reads CACTUS_FAST_WALLTIME (mirrors cactus_clamp_memory). - add_cactus_toil_options(): adds --fastWalltime (default 1800 = 30 min, very conservative for these jobs; 0 disables). - cactus_override_toil_options() exports CACTUS_FAST_WALLTIME so it reaches workers. - RoundedJob / ChildTreeJob now forward walltime to Toil. Application: - Wired add_cactus_toil_options(parser) into every tool's main(). - Tagged the small coordination jobs' scheduling call sites with walltime=cactus_fast_walltime() (the FAST set plus a hand-picked subset of the ambiguous ones; compute-heavy jobs left on --defaultWalltime). Docs (doc/progressive.md, doc/pangenome.md): recommend --defaultWalltime (+ the new --fastWalltime) instead of --slurmTime, which is now framed as a global override. IMPORTANT: toil-requirement.txt is temporarily pinned to Toil master because per-job walltime is not in a Toil release yet. Revert to a released toil[aws]==<ver> before merging. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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start trying to have cactus assign times to toil jobs, with the hopes of getting small jobs onto faster partitions.
todo: