msPurity.spectralMatching - sqllite db

[lecorguille]

Hi,

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

https://github.com/computational-metabolomics/mspurity-galaxy/blob/master/tools/msPurity/macros.xml#L119

Is there a data table mecanism?

[Tomnl]

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:

Here is an example database derived from MoNA https://github.com/computational-metabolomics/msp2db/releases/tag/0.0.5

See the basic library schema here https://github.com/computational-metabolomics/msp2db/blob/master/msp2db/db.py#L21-L96 (but can include XCMS information as well)

[lecorguille]

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

• https://training.galaxyproject.org/training-material/topics/dev/tutorials/tool-integration/slides.html#72
• https://galaxyproject.org/admin/tools/data-tables/

Ping @yguitton
Which database do you need?

Cheers

[yguitton]

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]

@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?)