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Fix pipeline stuck: synthetic FASTQ fallback and demo mode

Download minimap2 at runtime if not found

Remove minimap2 build step, download at runtime instead

Add sequencing pipeline (FASTQ -> QC -> alignment -> variant calling -> report)

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feat: download pre-compiled PhyML from bioconda instead of source build

fix: use valid EBI email (bionexus@example.com)

fix: add missing pipeline_v2.py

fix: remove PhyML source build, graceful missing-binary error

fix: add libtool ca-certificates, remove -j for low-mem

fix: PhyML build — disable-native, split RUN steps, verbose wget

feat: add phylo router (NJ/UPGMA/ML), local PhyML binary

fix: Foldseek alignments are [dict] lists, parse target format

fix: debug alignment structure types

fix: debug Foldseek result structure

fix: Foldseek alignments are dicts, parse with .get() correctly

fix: debug Foldseek alignment format (list vs dict)

fix: add full traceback to Foldseek error

fix: use aiohttp for Foldseek multipart upload

fix: debug Foldseek submit response type

fix: use sync httpx in thread pool for Foldseek submit

fix: restore nested alignments loop, remove debug raw

fix: return raw Foldseek data for debugging

fix: Foldseek returns list directly, no alignments sub-key

fix: move fetch inside httpx async with block

fix: manual multipart for Foldseek, add secrets import

fix: use sync httpx.Client for Foldseek multipart upload

fix: add error detail to Foldseek, use bytes, longer timeout

fix: simplify Foldseek, send full PDB as bytes

fix: primer3 error handling, STRING scores 0-1, Foldseek replace PDBeFold

fix: handle null name in InterPro domain response

Add domains, interactions, primers, structure_analysis routers

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