P3 workspace changes #24
Conversation
…ed dependency from workspace scripts
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I’m really not enamored with having the patric login changing the KBase config, as this essentially precludes one from using both PATRIC and KBase at the same time - a position that I find myself and my collaborators in quite often. The problem is, changes to the default config files persist even when one shifts the environment of the shell. Can we have kbase tools in PATRIC configured to point to the patric config file using the environment variable instead? Aren’t all KBase tools already configured to use an environment variable for the config? Couldn’t we make the setting of this environment variable as default part of user-env.sh in the PATRIC build? This seems like a better solution that trying to have two systems with different account types sharing a common config file for login, and thus forcing users to constantly log in and out of both services... Hey - the main point of this commit is to change the behavior of p3-login and p3-logout to update .kbase_config as well as the .p3 config so that the stock KBase tools work properly. There is an old fix in here for the zero-size update bug we ran into last year; I'm not sure why it did not get rolled in before ... You can view, comment on, or merge this pull request online at: Commit Summary Fix zero-size update bug M lib/Bio/P3/Workspace/ScriptHelpers.pm (31) https://github.com/cshenry/Workspace/pull/24.patch |
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BTW, if this is really needed and there’s no reasonable work around, I’m willing to merge this. I just wanted to register my concerns. I’m really not enamored with having the patric login changing the KBase config, as this essentially precludes one from using both PATRIC and KBase at the same time - a position that I find myself and my collaborators in quite often. The problem is, changes to the default config files persist even when one shifts the environment of the shell. Can we have kbase tools in PATRIC configured to point to the patric config file using the environment variable instead? Aren’t all KBase tools already configured to use an environment variable for the config? Couldn’t we make the setting of this environment variable as default part of user-env.sh in the PATRIC build? This seems like a better solution that trying to have two systems with different account types sharing a common config file for login, and thus forcing users to constantly log in and out of both services... Hey - the main point of this commit is to change the behavior of p3-login and p3-logout to update .kbase_config as well as the .p3 config so that the stock KBase tools work properly. There is an old fix in here for the zero-size update bug we ran into last year; I'm not sure why it did not get rolled in before ... You can view, comment on, or merge this pull request online at: Commit Summary Fix zero-size update bug M lib/Bio/P3/Workspace/ScriptHelpers.pm (31) https://github.com/cshenry/Workspace/pull/24.patch |
… like it may fix the public workspace download problem.
3 participants
Hey - the main point of this commit is to change the behavior of p3-login and p3-logout to update .kbase_config as well as the .p3 config so that the stock KBase tools work properly.
There is an old fix in here for the zero-size update bug we ran into last year; I'm not sure why it did not get rolled in before ...