[BUG] PGAP fails install when running on singularity.

Ge0rges commented 9 months ago

Running on Rocky Linux. Installed successfully by doing pgap.py --update -D /Accounts/gkanaan/.conda/envs/methylate/bin/singularity as my system does not support docker.

I then run PGAP by doing pgap.py --container-path /researchdrive/gkanaan/tools/pgap/pgap_2023-10-03.build7061.sif -D /Accounts/gkanaan/.conda/envs/methylate/bin/singularity -r -o annotation/$genome_name/ -g $genome -s $genome_name --taxcheck --auto-correct-tax

I get the following error and output:

PGAP version 2023-10-03.build7061 is up to date.
installation directory: /Accounts/gkanaan/.pgap
Sys. de fichiers              blocs de 1K     Utilisé Disponible Uti% Monté sur
137.22.86.56:/liverpool_users 20401094656 13224792576 7176302080  65% /Accounts
Skipping already installed tarball: https://s3.amazonaws.com/pgap/input-2023-10-03.build7061.tgz
Downloading and extracting tarball: https://s3.amazonaws.com/pgap/input-2023-10-03.build7061.ani.tgz
Downloading (as needed) Docker image docker:///researchdrive/gkanaan/tools/pgap/pgap_2023-10-03.build7061.sif
FATAL:   While making image from oci registry: error fetching image to cache: failed to get checksum for docker:///researchdrive/gkanaan/tools/pgap/pgap_2023-10-03.build7061.sif: unable to parse image name docker:///researchdrive/gkanaan/tools/pgap/pgap_2023-10-03.build7061.sif: invalid reference format
None
Traceback (most recent call last):926 bytes (100.00%)
  File "/researchdrive/gkanaan/tools/pgap/pgap.py", line 1067, in <module>
    main()
  File "/researchdrive/gkanaan/tools/pgap/pgap.py", line 994, in main
    params = Setup(args)
  File "/researchdrive/gkanaan/tools/pgap/pgap.py", line 558, in __init__
    self.update()
  File "/researchdrive/gkanaan/tools/pgap/pgap.py", line 718, in update
    raise Exception(f'installation of some or all of components failed. Please remove {self.data_path}, {self.install_dir}/test_genomes, {self.test_genomes_path} directories and try again.')
Exception: installation of some or all of components failed. Please remove /Accounts/gkanaan/.pgap/input-2023-10-03.build7061, /Accounts/gkanaan/.pgap/test_genomes, /Accounts/gkanaan/.pgap/test_genomes-2023-10-03.build7061 directories and try again.

azat-badretdin commented 9 months ago

Thank you, Gio, for your report! This looks like something specific happens on your computer system related to singularity setup.

What is the version of singularity you are using?

Ge0rges commented 9 months ago

It seems like removing the --container-path argument fixed it.

ncbi / pgap

[BUG] PGAP fails install when running on singularity. #272