Package: inspire-interact
inSPIRE-interactiveEasy GUI/webserver access for the inSPIRE platform.Set UpBefore DownloadingWe recommend working with inSPIRE through conda. On windows systems you may also needSetting up your environment:For basic inSPIRE-Interactive use.To start with create a new conda environment with python version 3.11:conda create --name inspire python=3.11Activate this environmentconda activate inspireYou will then need to install the inSPIRE-interactive package (this also installs inSPIRE):pip install inspire-interactTo check your installation, run the following command (it is normal for this call to hang for a few seconds on first execution)inspire-interact -hYou will require Percolator for rescoring. On Linux, Percolator can be installed via conda with the command below. Otherwise seehttps://github.com/percolator/percolator.conda install -c bioconda percolatorOnce you have successfully installed inSPIRE-Interactive you should run it specifying your pipeline and the mode of execution. The core execution of inSPIRE will take the form:inspire-interact --config_file path-to-config-file --mode localwhere the config file is a yaml file specifying configuration of your inSPIRE-Interactive server and the mode is either "server" if you are setting up inSPIRE-Interactive for use throughout your lab, or "local" if you are only using inSPIRE-Interactive on your own machine.On local mode you can then access the webserver home by pasting the following address on your browser:http://127.0.0.1:5000/interact-page/homeAdditional FeaturesIn order to use raw files on Linux or Mac O.S. you will require the use of mono (mono project) which is required by the ThermoRawFileParser. (The ThermoRawFileParser itself is open source and downloaded by inSPIRE.)In order to use NetMHCpan for binding affinity prediction you should download the software from theDTU site(you must agree to the license agreement). On linux and maxos systems we typically use tcsh.In order to use MSFragger within inSPIRE-Interactive you should download fromMSFragger(you must agree to the license agreements). You will also need java which can be installed using:conda install -c conda-forge openjdkIn order to use Skyline within inSPIRE-Interactive you will need to download docker and insure can be run within inSPIRE. See instructions fromdocker documentation. (Skyline itself is open source).Writing the Config File.The following configurations should be set for inSPIRE-interactive:KeyDescriptionmaxInspireCpusThe number of CPUs from your computer that you wish to dedicate to inSPIRE execution.fraggerPathThe file path to the .jar file of MSFragger (e.g. for version 3.7 the end of this path should be: MSFragger-3.7/MSFragger-3.7.jar)fraggerMemoryThe ammount of memory (GB) that is available for MSFragger execution.netMHCpanThe command that can be used to run NetMHCpan (e.g. on Linux we usetcshto execute NetMHCpan and so our config key istcsh /data/inSPIRE-Server/netMHCpan-4.1/netMHCpan).Example of Windows Config---
fraggerPath:  C:/Program Files/MSFragger-3.7/MSFragger-3.7.jar
fraggerMemory: 240
maxInspireCpus: 20
skylineRunner: C:/Program Files/Skyline/SkylineRunner.exe
rescoreCommand: C:/Program Files/percolator-v3-05/bin/percolator.exe