msPurity.spectralMatching - sqllite db

lecorguille commented 3 years ago

Hi,

As admin of an instance, how can I provide the full sqllite database to my users ?

Is there a data table mecanism?

Tomnl commented 3 years ago

Hi, sorry for the delay in reply - I have been away for a couple of weeks.

This can be set here

https://github.com/computational-metabolomics/mspurity-galaxy/blob/master/tools/msPurity/dbconfig.R

So you have to manually update the toolshed code on the server.

e.g. on our Bham servers this is located as follows (where fecfe8c80e25 changes based on each version of the tool)

shed_tools/toolshed.g2.bx.psu.edu/repos/computational-metabolomics/mspurity_spectralmatching/fecfe8c80e25/mspurity_spectralmatching/dbconfig.R

If you plan on using a local SQLite database just set the l_dbPth value:

l_dbPth <- '/path/2/library_spectra.sqlite'

Also note:

lecorguille commented 3 years ago

Hi, @Tomnl Not really practical to modify the line within the wrapper :/ Can you considering to implement Data tables:

Ping @yguitton Which database do you need?

Cheers

yguitton commented 3 years ago

Hi @lecorguille , Hi @Tomnl

I was thinking of including the mona_nov_parsed_20181120122122.db made by Tom that is available here https://github.com/computational-metabolomics/msp2db/releases

Would be really cool if the include database can be regularly updated with https://github.com/computational-metabolomics/msp2db

Many thanks for your help and time Yann

Tomnl commented 3 years ago

@lecorguille I wasn't aware that I could use sqlite files for the "Data table" implementation. I thought it was only .loc files (i.e. text files?)

computational-metabolomics / mspurity-galaxy