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running OmaStandalone without network access #5
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Hi Eric, the uniprot taxonomy is only needed in very special config settings, e.g. with
This should create all the necessary files in the Cheers Adrian |
Hi Adiran. many thanks for the input. best regards Eric |
hi Adiran. I have few more question
if I understand right when
best regards Eric |
Hi Eric, indeed, when you set AuxDataPath in the parameter file, this superseeds the default datadirname. The two files (and two symlinks) are the only files that are used from this folder. So in principle I think it would be ok to set the an absolute path for However, maybe it would be more sensible to have an environment variable that can be set as default. then, we could have set the path to these auxiliary data like:
would that make sense from your point and would simplify setting up the package on an HPC system? Cheers Adrian |
thanks Adrian, the "default" and on OMA_DATA path we provide the and it seems to work can you provide me some information about the and finaly are you the author of Darwin ? best regards Eric |
Hi Eric, yes, that seems like a good setup. regarding your darwin questions: yes, I am a co-author of that language. The darwinlib/TaxTools functionality isn't needed by OmaStandalone at all, so you won't need to download that data. about hardcoded /tmp dir - where did you find that? I don't think that this is used anywhere. The GetTmpDir() function actually already uses the |
Adrian, thanks for your feedback regarding the use of hardcoded
I guess some of this library files are not used by OMA. but some are ;-) regards Eric |
Hi Eric, indeed, there are quite a few places in the darwinlib, but in OmaStandalone, only the function in Best wishes |
Hello,
our cluster compute nodes does not have access to internet, so oma fails while trying to download at first http://purl.obolibrary.org/obo/go.obo
I may execute a run on a machine that have internet access and provide the
$HOME/.cache/oma/GOdata.drw
or for our usersbut I saw that
darwinlib/Taxonomy
also perform a download fromhttp://www.uniprot.org/taxonomy/?query=*&compress=yes&format=tab
is there a way that I can download and process (ConvertRawFile) this file and provide the resulting
UniProtTaxonomy.drw
file to our users in order to be abble to run oma without internet access.this way oma will be really Standalone ;-)
regards
Eric
edit typo
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