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DRL / blobtools

Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
GNU General Public License v3.0
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add an output options to the nodesdb tools #120

Open ArthurPERE opened 2 years ago

ArthurPERE commented 2 years ago

Hello

Can you please add an option to the nodesdb tools to redirect the output nodesDB.txt in an another place ? It's for continue to use the tools even if we can't write inside the /usr directory.

Thank, Regards

ceanothus commented 2 years ago

Hi, just chiming in that I also would like this feature. I am getting "Permission denied" when trying to create my own nodesDB file because it is being created in my cluster's software folders.

ceanothus commented 2 years ago

Hey @ArthurPERE , take a look at issue 95 . If you do blobtools create with

--names path/to/names.dmp --nodes path/to/nodes.dmp --db same/path/as/names&nodes/nodesDB.txt

it will create nodesDB.txt in the folder with your names.dmp and nodes.dmp folder instead of wherever it's trying to write where it doesn't have permissions.

ArthurPERE commented 2 years ago

Hey @ceanothus

I saw that, but it will be better if they add this feature, and it will remove some error. Because in the code if there is already the nodesDB.txt, and you give --names, --nodes and --db nodesDB.txt, you will have an error. For a pipeline, it's not impossible, but it's harder. And the fact that when you do the same command twice and the first is good the second is in error is frustrating.

Also it's not a very difficult feature to add.

Thanks, Regards