Closed BenSamy2020 closed 1 year ago
Hi Ben,
Thanks for your interest in inSPIRE!
We have actually just added support for MSFragger pepXML output in inSPIRE 1.5 so good timing! The decoys PSMs should be labelled with 'rev_' at the start of the protein ID (I believe this is the default for fragpipe) and under advanced output options you should set Output max expect to 100.
Also for running inSPIRE please set rescoreMethod to percolatorSeparate in the config file.
Unfortunately inSPIRE 1.5 is not published on pip yet but you can still install it right away with the following steps:
Uninstall your existing installation:
pip uninstall inspirems
Clone the GitHub repo:
git clone https://github.com/QuantSysBio/inSPIRE.git
Change directory into inSPIRE:
cd inSPIRE
Install the cloned repo:
python setup.py install
Best wishes, John.
Hi Ben,
I'm closing this issue as the version containing the fix (inSPIRE 1.5) is now published on pip meaning it can now be installled via the standard:
pip install inspirems==1.5
This does not impact you if you successfully installed inSPIRE manually via the instructions above.
Thank you for your help improving inSPIRE. We hope to hear from you again!
Best wishes, John.
Greeting,
Sure thank you publishing the fixed version on pip.
Regards, Ben
Greetings,
I would like to thank you for providing this cool and useful pipeline. I would like to check if this tool would be compatiable with FragPipe (MSfragger) output?
Regards, Ben