Testing out macrophage solutions with install script
I am trying to create some instructions that can be used by folks outside the team: https://gitlab.com/album-app/album/-/wikis/zebrafish-xenograft-solution-suite
All of this testing is happening on the MDC max cluster, which will be the same system that our collaborators use.
Album is installed with the script: https://gitlab.com/album-app/album/-/raw/installer-scripts/install/install_album_linux64.sh
Previously I was able to install and run this solution with an album that I installed using the method of: create conda env for album w/ python3.8 then pip install the main
branch of album
$ ./album/album install https://gitlab.com/album-app/catalogs/capture-knowledge-dev/-/raw/macrophage-brain-vasculature-update/macrophage-brain-vasculature/find-points-3d-from-2d/solution.py
2021-10-26 11:57:41,431 - root - INFO - Running album version 0.1.0
Kyle Harrington, Jan Philipp Albrecht, Deborah Schmidt - contact via album@kyleharrington.com
Traceback (most recent call last):
File "/fast/project/PG_VascularImageAnalysis/zebrafish_xenograft_model_scripts/album/miniconda3/envs/album/bin/album", line 8, in <module>
sys.exit(startup())
File "/home/kharrin/PG_VascularImageAnalysis/zebrafish_xenograft_model_scripts/album/miniconda3/envs/album/lib/python3.6/site-packages/album/__main__.py", line 14, in startup
main()
File "/home/kharrin/PG_VascularImageAnalysis/zebrafish_xenograft_model_scripts/album/miniconda3/envs/album/lib/python3.6/site-packages/album/argument_parsing.py", line 22, in main
__handle_args(args, parser)
File "/home/kharrin/PG_VascularImageAnalysis/zebrafish_xenograft_model_scripts/album/miniconda3/envs/album/lib/python3.6/site-packages/album/argument_parsing.py", line 28, in __handle_args
__run_subcommand(args, parser)
File "/home/kharrin/PG_VascularImageAnalysis/zebrafish_xenograft_model_scripts/album/miniconda3/envs/album/lib/python3.6/site-packages/album/argument_parsing.py", line 44, in __run_subcommand
args[0].func(args[0]) # execute entry point function
File "/home/kharrin/PG_VascularImageAnalysis/zebrafish_xenograft_model_scripts/album/miniconda3/envs/album/lib/python3.6/site-packages/album/core/commandline.py", line 56, in install
InstallManager().install(args.path, sys.argv)
File "/home/kharrin/PG_VascularImageAnalysis/zebrafish_xenograft_model_scripts/album/miniconda3/envs/album/lib/python3.6/site-packages/album/core/controller/install_manager.py", line 38, in install
resolve_result = self.collection_manager.resolve_download_and_load(str(path_or_id))
File "/home/kharrin/PG_VascularImageAnalysis/zebrafish_xenograft_model_scripts/album/miniconda3/envs/album/lib/python3.6/site-packages/album/core/controller/collection/collection_manager.py", line 148, in resolve_download_and_load
resolve_result = self._resolve(str_input)
File "/home/kharrin/PG_VascularImageAnalysis/zebrafish_xenograft_model_scripts/album/miniconda3/envs/album/lib/python3.6/site-packages/album/core/controller/collection/collection_manager.py", line 283, in _resolve
solution_entry = self._search_for_local_file(path)
File "/home/kharrin/PG_VascularImageAnalysis/zebrafish_xenograft_model_scripts/album/miniconda3/envs/album/lib/python3.6/site-packages/album/core/controller/collection/collection_manager.py", line 325, in _search_for_local_file
solution_entry = self.catalog_collection.get_solution_by_catalog_grp_name_version(
AttributeError: 'NoneType' object has no attribute 'get_solution_by_catalog_grp_name_version'
Edited by Kyle Harrington