Package: permedcoe
HPC/Exascale Centre of Excellence in Personalised MedicineBase Building BlockThis package provides the base for allBuilding Blocks (BBs)developed in theHPC/Exascale Centre of Excellence in Personalised Medicine(PerMedCoE) project.Table of ContentsHPC/Exascale Centre of Excellence in Personalised MedicineBase Building BlockTable of ContentsUser instructionsRequirementsInstallationCommand lineOption execute:Option template:Option deploy:Public APIUninstallDeveloper instructionsBuilding blockLicenseContactUser instructionsRequirementsPython >= 3.6SingularityInstallationThere are two ways to install this package (from Pypi and manually):From Pypi:This package is publicly available in Pypi:pipinstallpermedcoeor more specifically:python3-mpipinstallpermedcoeFrom source code:This package provides an automatic installation script:./install.shCommand lineThis package provides thepermedcoecommand:$permedcoe-h
usage:permedcoe[-h][-d][-l{debug,info,warning,error,critical}]{execute,x,template,t,deploy,d}...

positionalarguments:{execute,x,template,t,deploy,d}execute(x)Executeabuildingblock.template(t)Showsanexampleoftherequestedtemplate.deploy(d)Downloadanddeploytherequestedworkfloworbuildingblock.

options:-h,--helpshowthishelpmessageandexit-d,--debugEnabledebugmode.Overrideslog_level(default:False)-l{debug,info,warning,error,critical},--log_level{debug,info,warning,error,critical}Setlogginglevel.(default:error)Option execute:It enables to execute single building blocks or applications:$permedcoeexecute-h
usage:permedcoeexecute[-h]{building_block,bb,application,app}...

positionalarguments:{building_block,bb,application,app}building_block(bb)Executeabuildingblock.application(app)Executeanapplication.

optionalarguments:-h,--helpshowthishelpmessageandexitIn particular for building blocks:$permedcoeexecutebuilding_block-h
usage:permedcoeexecutebuilding_block[-h]name[parameters...]positionalarguments:nameBuildingBlocktoexecuteparametersBuildingBlockparameters(default:None)options:-h,--helpshowthishelpmessageandexitSpecifying the particular building block to execute (must be installed), provides more detailed information:$permedcoeexecutebuilding_blockMaBoSS_BB-h
usage:permedcoe[-h][-cCONFIG][-d][-l{debug,info,warning,error,critical}][--tmpdirTMPDIR][--processesPROCESSES][--gpusGPUS][--memoryMEMORY][--mount_pointsMOUNT_POINTS]{default,sensitivity}...ThisbuildingblockusesMaBoSStoscreenallthepossibleknockoutsofagivenBooleanmodel.Itproducesacandidategenelistformattedasatextfile(singlegeneperrow).MoreinformationonMaBoSScanbefoundin[StollG.etal.(2017)](https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btx123)andinthe[MaBoSSGitHubrepository](https://github.com/maboss-bkmc/MaBoSS-env-2.0).positionalarguments:{default,sensitivity}options:-h,--helpshowthishelpmessageandexit-cCONFIG,--configCONFIG(CONFIG)Configurationfilepath-d,--debugEnableBuildingBlockdebugmode.Overrideslog_level-l{debug,info,warning,error,critical},--log_level{debug,info,warning,error,critical}Setlogginglevel--tmpdirTMPDIRTempdirectorytobemountedinthecontainer--processesPROCESSESNumberofprocessesforMPIexecutions--gpusGPUSRequirementsforGPUjobs--memoryMEMORYMemoryrequirement--mount_pointsMOUNT_POINTSCommaseparatedalias:foldertobemountedinthecontainerIn particular for building blocks:$permedcoeexecuteapplication-h
usage:permedcoeexecuteapplication[-h][-w{none,pycompss,nextflow,snakemake}][-fFLAGS[FLAGS...]]name[parameters[parameters...]]positionalarguments:nameApplicationtoexecuteparametersApplicationparameters(default:None)optionalarguments:-h,--helpshowthishelpmessageandexit-w{none,pycompss,nextflow,snakemake},--workflow_manager{none,pycompss,nextflow,snakemake}Workflowmanagertouse(default:none)-fFLAGS[FLAGS...],--flagsFLAGS[FLAGS...]Workflowmanagerflags(default:None)Option template:It available to create a skeleton of a building block or an application:$permedcoetemplate-h
usage:permedcoetemplate[-h][-t{all,pycompss,nextflow,snakemake}]{bb,building_block,app,application}name

positionalarguments:{bb,building_block,app,application}CreatesaBuildingBlockorApplicationtemplate.nameBuildingBlockorApplicationname.

optionalarguments:-h,--helpshowthishelpmessageandexit-t{all,pycompss,nextflow,snakemake},--type{all,pycompss,nextflow,snakemake}Applicationtype.(default:all)Option deploy:It available to deploy an existing Building Block or Workflow in alocal machine (e.g. laptop):$permedcoedeploy-h
usage:permedcoedeploy[-h]{building_block,bb,workflow,wf}...

positionalarguments:{building_block,bb,workflow,wf}building_block(bb)Aspecificbuildingblock.workflow(wf)Aspecificworkflow.

options:-h,--helpshowthishelpmessageandexitFor the deployment in supercomputers, please contact PerMedCoE:https://permedcoe.eu/contact/.Public APIThepermedcoepackage provides a set of public decorators, parameter type definition and functions to be used in the Building Block implementation.Public decorators:frompermedcoeimportcontainerfrompermedcoeimportconstraintfrompermedcoeimportbinaryfrompermedcoeimportmpifrompermedcoeimporttaskParameter type definition:frompermedcoeimportTypefrompermedcoeimportFILE_INfrompermedcoeimportFILE_OUTfrompermedcoeimportFILE_INOUTfrompermedcoeimportDIRECTORY_INfrompermedcoeimportDIRECTORY_OUTfrompermedcoeimportDIRECTORY_INOUTfrompermedcoeimportStdIOStreamfrompermedcoeimportSTDINfrompermedcoeimportSTDOUTfrompermedcoeimportSTDERRFunctions:frompermedcoeimportget_environmentfrompermedcoeimportset_debugfrompermedcoeimportinvokerClasses:frompermedcoeimportArgumentsUninstallUninstall can be done as usualpippackages:There are two ways to uninstall this package, that depends on the way that it was installed (from Pypi or usinginstall.sh):From Pypi:pipuninstallpermedcoeor more specifically:python3-mpipuninstallpermedcoeFrom manual installation (usinginstall.sh):./uninstall.shAnd then the folder can be cleaned as well using theclean.shscript../clean.shDeveloper instructionsBuilding blockIf you are willing to implement your Building Block (BB), check the following repositories,
where you will find documentation, tutorials, and BB/application samples:DocumentationTutorialbasic_applicationLysozyme_in_waterLicenseApache 2.0Contacthttps://permedcoe.eu/contact/This software has been developed for thePerMedCoE project, funded by the European Commission (EU H2020951773).