NanoPack

[boegel]

• link to support ticket: #2024083060000914
• website: http://nanoplot.bioinf.be/
• installation docs: https://github.com/wdecoster/nanopack?tab=readme-ov-file#installation
• toolchain: foss/2023a
• easyblock to use: PythonBundle
• required dependencies:
  • see setup.py
• notes:
  • should be compatible with dorado/0.7.3-foss-2023a-CUDA-12.1.1
• effort: (TBD)
• other install methods
  • conda: no
  • container image: no
  • pre-built binaries (RHEL8 Linux x86_64): no
  • easyconfig outside EasyBuild: no

[PetrKralCZ]

• {bio,math,tools}[foss/2023a] NanoStat v1.6.0, nanoget v1.19.3, nanomath v1.4.0 easybuilders/easybuild-easyconfigs#21367

[PetrKralCZ]

• {bio}[foss/2023a] NanoFilt v2.8.0 easybuilders/easybuild-easyconfigs#21368

[PetrKralCZ]

• {bio}[foss/2023a] NanoLyse v1.2.1 easybuilders/easybuild-easyconfigs#21369

[PetrKralCZ]

• {tools}[foss/2023a] nanoQC v0.9.4 easybuilders/easybuild-easyconfigs#21371

[boegel]

@PetrKralCZ Some clarification by researcher:

In my application I forgot to mention that all tools should be included in the nanopack installation (also the rust apps).
'Pip instal' won't install the rust packages.

Can you look into the Rust tools too, see NanoPack's README?

[PetrKralCZ]

• {bio}[GCC/12.3.0] cramino v0.14.5 easybuilders/easybuild-easyconfigs#21382

[PetrKralCZ]

• {bio}[GCC/12.3.0] chopper v0.9.0 easybuilders/easybuild-easyconfigs#21388

[PetrKralCZ]

• {bio}[GCC/12.3.0] phasius v0.2.0 easybuilders/easybuild-easyconfigs#21389

[PetrKralCZ]

• {bio,math,vis}[foss/2023a] NanoComp v1.24.0, plotly-orca v1.3.1, joypy v0.2.6 easybuilders/easybuild-easyconfigs#21390

[PetrKralCZ]

• {bio}[foss/2023a] NanoPlot v1.43.0 easybuilders/easybuild-easyconfigs#21391

[boegel]

• {bio}[GCC/12.3.0] chopper v0.9.0 easybuilders/easybuild-easyconfigs#21388

Replaced with:

• {bio}[GCCcore/12.3.0] chopper v0.9.0 easybuilders/easybuild-easyconfigs#21418

[boegel]

@PetrKralCZ All open PRs merged, is next step a PR for NanoPack itself?

[PetrKralCZ]

@PetrKralCZ All open PRs merged, is next step a PR for NanoPack itself?

No, the last dependency needed for NanoPack is kyber. Which gives me the following error:

== 2024-09-12 15:53:37,826 build_log.py:171 ERROR EasyBuild crashed with an error (at easybuild/easybuild-framework/easybuild/base/exceptions.py:126 in __init__): cmd " cargo build --profile=release  --tests -j 8 " exited with exit code
 101 and output:
   Compiling autocfg v1.1.0
   Compiling libc v0.2.140
   Compiling cfg-if v1.0.0
   Compiling proc-macro2 v1.0.52
   Compiling quote v1.0.26
   Compiling unicode-ident v1.0.8
   Compiling pkg-config v0.3.26
   Compiling syn v1.0.109
   Compiling scopeguard v1.1.0
   Compiling crossbeam-utils v0.8.15
   Compiling num-traits v0.2.15
   Compiling memoffset v0.8.0
   Compiling crossbeam-epoch v0.9.14
   Compiling num-integer v0.1.45
92 |     feature(proc_macro_span, proc_macro_span_shrink)ous error
   |                              ^^^^^^^^^^^^^^^^^^^^^^..
For more information about this error, try `rustc --explain E0635`.rse_cmd_output)
   Compiling version_check v0.9.4cro2` (lib) due to previous error
   Compiling rayon-core v1.11.0for other jobs to finish... lock /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/.locks/_scratch_gent_vo_001_gvo00117_easybuild_RHEL8_cascadelake-ampere-ib_software_kyber_0.4.0For more information about this error, try `rustc --explain E0635`.rse_cmd_output)
error: could not compile `proc-macro2` (lib) due to previous errort/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/.locks/_scratch_gent_vo_001_gvo00117_easybuild_RHEL8_cascadelake-ampere-ib_software_kyber_0.4.0-GCC-12.3.warning: build failed, waiting for other jobs to finish... lock /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/.locks/_scratch_gent_vo_001_gvo00117_easybuild_RHEL8_cascadelake-ampere-ib_software_kyber_0.4.0 (at easybuild/easybuild-framework/easybuild/tools/run.py:682 in parse_cmd_output)01/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/.locks/_scratch_gent_vo_001_gvo00117_easybuild_RHEL8_cascadelake-ampere-ib_software_kyber_0.4.0

WIP easyconfig:

• https://github.com/vscentrum/vsc-software-stack/blob/wip/407_NanoPack/kyber-0.4.0-GCC-12.3.0.eb

[boegel]

@PetrKralCZ Seems like that should be fixable by using a newer version of proc-macro2, see dtolnay/proc-macro2#356 + rust-lang/rust#113152.

That probably means patching the Cargo.lock file

[PetrKralCZ]

@PetrKralCZ Seems like that should be fixable by using a newer version of proc-macro2, see dtolnay/proc-macro2#356 + rust-lang/rust#113152.

That probably means patching the Cargo.lock file

That old version of proc-macro2 seems to be required by clap_derive.

== 2024-09-17 12:30:13,668 build_log.py:171 ERROR EasyBuild crashed with an error (at easybuild/easybuild-framework/easybuild/base/exceptions.py:126 in __init__): cmd " cargo build --profile=release  --tests -j 8 " exited with exit code 101 and output:
error: failed to select a version for the requirement `proc-macro2 = "^1.0.42"` (locked to 1.0.86)
candidate versions found which didn't match: 1.0.52
location searched: directory source `/tmp/vsc45304/easybuild/build/kyber/0.4.0/GCC-12.3.0/easybuild_vendor` (which is replacing registry `crates-io`)
required by package `clap_derive v4.1.8`
    ... which satisfies dependency `clap_derive = "=4.1.8"` (locked to 4.1.8) of package `clap v4.1.8`
    ... which satisfies dependency `clap = "^4.1.4"` (locked to 4.1.8) of package `kyber v0.4.0 (/tmp/vsc45304/easybuild/build/kyber/0.4.0/GCC-12.3.0/kyber-0.4.0)`
perhaps a crate was updated and forgotten to be re-vendored?
As a reminder, you're using offline mode (--offline) which can sometimes cause surprising resolution failures, if this error is too confusing you may wish to retry without the offline flag.
 (at easybuild/easybuild-framework/easybuild/tools/run.py:682 in parse_cmd_output)

[boegel]

@PetrKralCZ To avoid that problem with clap_derive, we'll need to use clap_derive 4.4.11, which requires proc-macro2 1.0.69 (which should be recent enough to avoid the other problem).

Hopefully that won't lead to other similar issues...

[PetrKralCZ]

• {bio}[GCC/12.3.0,foss/2023a] NanoPack v20230602, kyber v0.4.0 easybuilders/easybuild-easyconfigs#21649

[boegel]

@PetrKralCZ PR merged, software installed, ready for cleanup