singleM

[laraPPr]

• link to support ticket: #2023102460000111
• website: https://github.com/wwood/singlem
• installation docs: https://wwood.github.io/singlem/Installation
• toolchain: foss 2023a
• easyblock to use: PythonBundle
• required dependencies:
  • polars
  • Biopython
  • DIAMOND
  • hmmer
  • orfm
  • mfqe
  • extern (as extension)
  • graftm (as extension)
  • krona (krona-tools)
  • pplacer
  • sra-tools
  • ncbi-ngs-sdk
  • sqlite (in Python)
  • mafft
  • seqmagick
  • expressbetadiversity
  • cd-hit (available for 2022b)
  • fasttree
  • fastalite (as extension)
  • jinja2 (as extension)
  • sqlalchemy (as extension)
  • smafa
  • pyranges (as extension)
  • prodigal (available for 2022b)
  • tqdm
  • pyarrow (as Arrow in EC)
• optional dependencies:
  • ...
• notes:
  • ...
• effort: (TBD)
• other install methods
  • conda: yes (link?)
  • container image: yes (link?)
  • pre-built binaries (RHEL8 Linux x86_64): no
  • easyconfig outside EasyBuild: yes

[boegel]

Let's make sure we use foss/2023a for this, even though easyconfigs are missing for 13 dependencies, to make sure we can also install this on our latest cluster shinx (which has AMD Genoa CPUs).

Priority for this is "lowest", so this can be put on hold for now until later...

[boegel]

@pavelToman For the polars, I've opened an issue for the problem with generates contents for crates when using CargoPythonPackage, see easybuilders/easybuild-easyblocks#3078

[lexming]

FYI I opened a PR for polars in 2023a (worked on it for other reasons than singleM):

• {data}[gfbf/2023a] polars v0.19.19 easybuilders/easybuild-easyconfigs#19770

It's for v0.19.19 instead of 0.20.x because the latter needs features in Rust that are not available in Rust v1.75

[pavelToman]

PR

• {bio}[GCC/12.3.0] SingleM v0.16.0, smafa v0.8.0, psycopg v3.2.1, ... easybuilders/easybuild-easyconfigs#21016

[laraPPr]

Am now installing polars centrally. so reopening to make sure I don't forget

[laraPPr]

installed and and ready for clean-up