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Make database paths configurable - add GetOrganelle to Galaxy #64
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How about making the databases or a file storing the path under "~/.GetOrganelle" by default? |
Thanks for the feedback. I would prefer a command line parameter ( |
In the latest update (version 1.7.3), sort by priority,
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I just noticed that this is for Galaxy project, my collaborator @wbyu has mentioned many times of adding GetOrganelle to Galaxy. We are very interested in contributing. Please let me know if there's anything else we can help. |
Good to know :) Indeed some "small" test data and an example command line would simplify creating such a tool a bit. |
We have a simulated mini-data along with the command: and a few real test data (also very small ones): |
Downloaded reference data with Trying to get the examples running:
I'm also wondering if you could switch from optparse (which is deprecated) to argparse? For argparse I could auto-generate Galaxy wrappers. For |
Thanks for the feedback. Sorry about the remaining issues - now I believe I have fixed it and tested it in different ways. Sure. Please branch out from the latest master if you haven't started the conversion. Thanks again! |
@bernt-matthias |
@Kinggerm this looks great :) |
1.7.4 is now formally released with all above requirements fulfilled. |
Excellent. I hope that I find the time to wrap this for Galaxy any time soon. |
@bernt-matthias |
Thanks for the reference to the small test data. Is there also a small seed (and label) database? For the IUC Galaxy tool repo we are aiming at <1MB per test file. |
Just back from traveling. Sure, I can prepare a small seed and label database for it ASAP. I will keep you updated. |
Hi @Kinggerm any news on small seed and label databases? |
Hi @bernt-matthias, I created a minimal dataset derived from 0.0.1, named it This
However, please note that the local files will inflate a lot as you format them into Please let me know if these make sense. |
Thanks a lot. We will try to use those for the galaxy tool wrapper tests. |
Seems that we can close this issue. Thanks for the help. |
Seems to me that the databases are currently stored next to the library. This does not work for read-only installations (e.g. containers and multi user installations) and is considered bad practice for conda installations (even if writable).
Ideally this could be done via an environment variable of command line parameter.
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