Leafcutter

[laraPPr]

• link to support ticket: #2023071760000372 + #2023072860000173
• website: http://davidaknowles.github.io/leafcutter/index.html
• installation docs: http://davidaknowles.github.io/leafcutter/articles/Installation.html
• toolchain: foss/2022b
• easyblock to use: ...
• required dependencies:
  • samtools
  • regtools
  • python
  • R
• optional dependencies:
  • ...
• notes:
  • ...
• effort: (TBD)
• other install methods
  • conda: yes (http://davidaknowles.github.io/leafcutter/articles/Installation.html#using-conda)
  • container image: no
  • pre-built binaries (RHEL8 Linux x86_64): no
  • easyconfig outside EasyBuild: no

[laraPPr]

made easyconfig for newer RegTools

[laraPPr]

Added a the easyconfig for leafcutter to WIP. When running it I get the following error: ERROR: no packages specified

[boegel]

You probably need to instruct EasyBuild to run the installation command for the R package from the leafcutter subdirectory, since that's where the [DESCRIPTION](https://github.com/davidaknowles/leafcutter/blob/master/leafcutter/DESCRIPTION) file is located:

start_dir = 'leafcutter'

[laraPPr]

Now I hit the following error:

Error: object evalWithTimeout is not exported by 'namespace:R.utils'
Execution halted
ERROR: lazy loading failed for package leafcutter

I also had another question. On their website it says that the latest version is 0.2.9 but I can only find 0.2.7 and older.

[boegel]

Seems like you will need to create a patch so it uses withTimeout instead, see also nuno-agostinho/psichomics#383

W.r.t. version: the DESCRIPTION file says it's 0.2.9, so I would download the commit that set the version to 0.2.9 in that file, and download that as leafcuffer-0.2.9.tar.gz?

[boegel]

Note: duplicate of #162 (so we have 3 open install requests for Leafcutter)

[laraPPr]

easybuilders/easybuild-easyconfigs#18615