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computational-metabolomics / mspurity-galaxy

Galaxy tools for msPurity package: includes precursor ion purity calculations and spectral matching
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Error Galaxy msPurity.spectralMatching with mona_nov_parsed_20181120122122.db #39

Closed yguitton closed 3 years ago

yguitton commented 3 years ago

Hi Tom, Hi Ralf, I hope that your both fine,

I'm using msPurity under workflow4metabolomics.usegalaxy.fr and everything was fine, with all default parameters, until I tried to upload the complete mona_nov_parsed_20181120122122.db

I have the following error

Loading required package: Rcpp Running msPurity spectral matching function for LC-MS(/MS) data Error in if (is.na(l_dbPth)) { : argument is of length zero Calls: Execution halted

It seems that the db is not found, If you have some time to investigate, my history is here https://workflow4metabolomics.usegalaxy.fr/u/yguitton44/h/qva-iterative-dda

Many thanks Yann

Tomnl commented 3 years ago

Hi Yann,

Sorry about this.. seems like a bug in the Galaxy wrapper when choosing the SQLite input. I will look into it now

In the meantime - If you have access to update the toolshed file on the Galaxy server - it should work by updating the local config (defined here) just set l_dbPth <- "/path/2/sqlite/library.db" and l_dbType <- "sqlite"

yguitton commented 3 years ago

Hi Tom, Thanks for the quick reply.

If it's a wrapper issue, I can wait until the upload of a new version on the toolshed. Just let us know when this small beug is corrected and I can ask @lecorguille to update the wrapper.

In the mean time I will try to work within Rstudio on my own PC Best Yann

Tomnl commented 3 years ago

OK. Thanks for letting me know. I've hopefully fixed it now.

I just need to make sure all the tests pass, merge and push it to the toolshed

Tomnl commented 3 years ago

Hi @yguitton - the fix should now be in the most recent version on the toolshed so I am going to close now. Let me know if you still have any other issues