Cannot install SAPP
Hi, I am trying to get a working version of SAPP, but so far have no luck.
- [http://download.systemsbiology.nl] does not load for me to download the binaries
- I don't know where to get the docker image.
docker run -it -v "$(pwd)"/Data:/SAPP/Data wurssb/sappgalaxy /bin/bash
Unable to find image 'wurssb/sappgalaxy:latest' locally
docker: Error response from daemon: pull access denied for wurssb/sappgalaxy, repository does not exist or may require 'docker login': denied: requested access to the resource is denied.
See 'docker run --help'.
- [https://gitlab.com/sapp/sapp] does not contain an
install.py
file - [https://gitlab.com/sapp/sapp]
bash build.sh
fails with the following:
Already up to date.
Skipping tests, run './install.sh test' to perform tests
Starting a Gradle Daemon (subsequent builds will be faster)
FAILURE: Build failed with an exception.
* Where:
Build file '/data/users/branko/temp/SAPP/sapp/build.gradle' line: 87
* What went wrong:
A problem occurred evaluating root project 'SAPP'.
> Connection timed out (Connection timed out)
* Try:
> Run with --info or --debug option to get more log output.
> Run with --scan to get full insights.
* Exception is:
org.gradle.api.GradleScriptException: A problem occurred evaluating root project 'SAPP'.
at org.gradle.groovy.scripts.internal.DefaultScriptRunnerFactory$ScriptRunnerImpl.run(DefaultScriptRunnerFactory.java:93)
at org.gradle.configuration.DefaultScriptPluginFactory$ScriptPluginImpl.lambda$apply$0(DefaultScriptPluginFactory.java:133)
at org.gradle.configuration.ProjectScriptTarget.addConfiguration(ProjectScriptTarget.java:79)
at org.gradle.configuration.DefaultScriptPluginFactory$ScriptPluginImpl.apply(DefaultScriptPluginFactory.java:136)
at org.gradle.configuration.BuildOperationScriptPlugin$1.run(BuildOperationScriptPlugin.java:65)
at org.gradle.internal.operations.DefaultBuildOperationRunner$1.execute(DefaultBuildOperationRunner.java:29)
at org.gradle.internal.operations.DefaultBuildOperationRunner$1.execute(DefaultBuildOperationRunner.java:26)
at org.gradle.internal.operations.DefaultBuildOperationRunner$2.execute(DefaultBuildOperationRunner.java:66)
at org.gradle.internal.operations.DefaultBuildOperationRunner$2.execute(DefaultBuildOperationRunner.java:59)
at org.gradle.internal.operations.DefaultBuildOperationRunner.execute(DefaultBuildOperationRunner.java:157)
at org.gradle.internal.operations.DefaultBuildOperationRunner.execute(DefaultBuildOperationRunner.java:59)
at org.gradle.internal.operations.DefaultBuildOperationRunner.run(DefaultBuildOperationRunner.java:47)
at org.gradle.internal.operations.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:68)
at org.gradle.configuration.BuildOperationScriptPlugin.lambda$apply$0(BuildOperationScriptPlugin.java:62)
at org.gradle.configuration.internal.DefaultUserCodeApplicationContext.apply(DefaultUserCodeApplicationContext.java:44)
at org.gradle.configuration.BuildOperationScriptPlugin.apply(BuildOperationScriptPlugin.java:62)
at org.gradle.api.internal.project.DefaultProjectStateRegistry$ProjectStateImpl.lambda$applyToMutableState$0(DefaultProjectStateRegistry.java:360)
at org.gradle.api.internal.project.DefaultProjectStateRegistry$ProjectStateImpl.fromMutableState(DefaultProjectStateRegistry.java:378)
at org.gradle.api.internal.project.DefaultProjectStateRegistry$ProjectStateImpl.applyToMutableState(DefaultProjectStateRegistry.java:359)
at org.gradle.configuration.project.BuildScriptProcessor.execute(BuildScriptProcessor.java:42)
at org.gradle.configuration.project.BuildScriptProcessor.execute(BuildScriptProcessor.java:26)
at org.gradle.configuration.project.ConfigureActionsProjectEvaluator.evaluate(ConfigureActionsProjectEvaluator.java:35)
at org.gradle.configuration.project.LifecycleProjectEvaluator$EvaluateProject.lambda$run$0(LifecycleProjectEvaluator.java:109)
at org.gradle.api.internal.project.DefaultProjectStateRegistry$ProjectStateImpl.lambda$applyToMutableState$0(DefaultProjectStateRegistry.java:360)
at org.gradle.api.internal.project.DefaultProjectStateRegistry$ProjectStateImpl.lambda$withProjectLock$2(DefaultProjectStateRegistry.java:408)
at org.gradle.internal.work.DefaultWorkerLeaseService.withLocks(DefaultWorkerLeaseService.java:270)
at org.gradle.api.internal.project.DefaultProjectStateRegistry$ProjectStateImpl.withProjectLock(DefaultProjectStateRegistry.java:408)
at org.gradle.api.internal.project.DefaultProjectStateRegistry$ProjectStateImpl.fromMutableState(DefaultProjectStateRegistry.java:389)
at org.gradle.api.internal.project.DefaultProjectStateRegistry$ProjectStateImpl.applyToMutableState(DefaultProjectStateRegistry.java:359)
at org.gradle.configuration.project.LifecycleProjectEvaluator$EvaluateProject.run(LifecycleProjectEvaluator.java:100)
at org.gradle.internal.operations.DefaultBuildOperationRunner$1.execute(DefaultBuildOperationRunner.java:29)
at org.gradle.internal.operations.DefaultBuildOperationRunner$1.execute(DefaultBuildOperationRunner.java:26)
at org.gradle.internal.operations.DefaultBuildOperationRunner$2.execute(DefaultBuildOperationRunner.java:66)
at org.gradle.internal.operations.DefaultBuildOperationRunner$2.execute(DefaultBuildOperationRunner.java:59)
at org.gradle.internal.operations.DefaultBuildOperationRunner.execute(DefaultBuildOperationRunner.java:157)
at org.gradle.internal.operations.DefaultBuildOperationRunner.execute(DefaultBuildOperationRunner.java:59)
at org.gradle.internal.operations.DefaultBuildOperationRunner.run(DefaultBuildOperationRunner.java:47)
at org.gradle.internal.operations.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:68)
at org.gradle.configuration.project.LifecycleProjectEvaluator.evaluate(LifecycleProjectEvaluator.java:72)
at org.gradle.api.internal.project.DefaultProject.evaluate(DefaultProject.java:760)
at org.gradle.api.internal.project.DefaultProject.evaluate(DefaultProject.java:151)
at org.gradle.api.internal.project.DefaultProjectStateRegistry$ProjectStateImpl.ensureConfigured(DefaultProjectStateRegistry.java:328)
at org.gradle.execution.TaskPathProjectEvaluator.configure(TaskPathProjectEvaluator.java:33)
at org.gradle.execution.TaskPathProjectEvaluator.configureHierarchy(TaskPathProjectEvaluator.java:47)
at org.gradle.configuration.DefaultProjectsPreparer.prepareProjects(DefaultProjectsPreparer.java:50)
at org.gradle.configuration.BuildTreePreparingProjectsPreparer.prepareProjects(BuildTreePreparingProjectsPreparer.java:64)
at org.gradle.configuration.BuildOperationFiringProjectsPreparer$ConfigureBuild.run(BuildOperationFiringProjectsPreparer.java:52)
at org.gradle.internal.operations.DefaultBuildOperationRunner$1.execute(DefaultBuildOperationRunner.java:29)
at org.gradle.internal.operations.DefaultBuildOperationRunner$1.execute(DefaultBuildOperationRunner.java:26)
at org.gradle.internal.operations.DefaultBuildOperationRunner$2.execute(DefaultBuildOperationRunner.java:66)
at org.gradle.internal.operations.DefaultBuildOperationRunner$2.execute(DefaultBuildOperationRunner.java:59)
at org.gradle.internal.operations.DefaultBuildOperationRunner.execute(DefaultBuildOperationRunner.java:157)
at org.gradle.internal.operations.DefaultBuildOperationRunner.execute(DefaultBuildOperationRunner.java:59)
at org.gradle.internal.operations.DefaultBuildOperationRunner.run(DefaultBuildOperationRunner.java:47)
at org.gradle.internal.operations.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:68)
at org.gradle.configuration.BuildOperationFiringProjectsPreparer.prepareProjects(BuildOperationFiringProjectsPreparer.java:40)
at org.gradle.initialization.VintageBuildModelController.lambda$prepareProjects$3(VintageBuildModelController.java:89)
at org.gradle.internal.model.StateTransitionController.lambda$doTransition$12(StateTransitionController.java:227)
at org.gradle.internal.model.StateTransitionController.doTransition(StateTransitionController.java:238)
at org.gradle.internal.model.StateTransitionController.doTransition(StateTransitionController.java:226)
at org.gradle.internal.model.StateTransitionController.lambda$transitionIfNotPreviously$10(StateTransitionController.java:201)
at org.gradle.internal.work.DefaultSynchronizer.withLock(DefaultSynchronizer.java:34)
at org.gradle.internal.model.StateTransitionController.transitionIfNotPreviously(StateTransitionController.java:197)
at org.gradle.initialization.VintageBuildModelController.prepareProjects(VintageBuildModelController.java:89)
at org.gradle.initialization.VintageBuildModelController.prepareToScheduleTasks(VintageBuildModelController.java:71)
at org.gradle.internal.build.DefaultBuildLifecycleController.lambda$prepareToScheduleTasks$2(DefaultBuildLifecycleController.java:134)
at org.gradle.internal.model.StateTransitionController.lambda$doTransition$12(StateTransitionController.java:227)
at org.gradle.internal.model.StateTransitionController.doTransition(StateTransitionController.java:238)
at org.gradle.internal.model.StateTransitionController.doTransition(StateTransitionController.java:226)
at org.gradle.internal.model.StateTransitionController.lambda$maybeTransition$9(StateTransitionController.java:187)
at org.gradle.internal.work.DefaultSynchronizer.withLock(DefaultSynchronizer.java:34)
at org.gradle.internal.model.StateTransitionController.maybeTransition(StateTransitionController.java:183)
at org.gradle.internal.build.DefaultBuildLifecycleController.prepareToScheduleTasks(DefaultBuildLifecycleController.java:132)
at org.gradle.internal.buildtree.DefaultBuildTreeWorkPreparer.scheduleRequestedTasks(DefaultBuildTreeWorkPreparer.java:33)
at org.gradle.internal.buildtree.DefaultBuildTreeLifecycleController.lambda$doScheduleAndRunTasks$2(DefaultBuildTreeLifecycleController.java:89)
at org.gradle.composite.internal.DefaultIncludedBuildTaskGraph.withNewWorkGraph(DefaultIncludedBuildTaskGraph.java:75)
at org.gradle.internal.buildtree.DefaultBuildTreeLifecycleController.doScheduleAndRunTasks(DefaultBuildTreeLifecycleController.java:88)
at org.gradle.internal.buildtree.DefaultBuildTreeLifecycleController.lambda$runBuild$4(DefaultBuildTreeLifecycleController.java:106)
at org.gradle.internal.model.StateTransitionController.lambda$transition$6(StateTransitionController.java:166)
at org.gradle.internal.model.StateTransitionController.doTransition(StateTransitionController.java:238)
at org.gradle.internal.model.StateTransitionController.lambda$transition$7(StateTransitionController.java:166)
at org.gradle.internal.work.DefaultSynchronizer.withLock(DefaultSynchronizer.java:44)
at org.gradle.internal.model.StateTransitionController.transition(StateTransitionController.java:166)
at org.gradle.internal.buildtree.DefaultBuildTreeLifecycleController.runBuild(DefaultBuildTreeLifecycleController.java:103)
at org.gradle.internal.buildtree.DefaultBuildTreeLifecycleController.scheduleAndRunTasks(DefaultBuildTreeLifecycleController.java:69)
at org.gradle.tooling.internal.provider.ExecuteBuildActionRunner.run(ExecuteBuildActionRunner.java:31)
at org.gradle.launcher.exec.ChainingBuildActionRunner.run(ChainingBuildActionRunner.java:35)
at org.gradle.internal.buildtree.ProblemReportingBuildActionRunner.run(ProblemReportingBuildActionRunner.java:49)
at org.gradle.launcher.exec.BuildOutcomeReportingBuildActionRunner.run(BuildOutcomeReportingBuildActionRunner.java:69)
at org.gradle.tooling.internal.provider.FileSystemWatchingBuildActionRunner.run(FileSystemWatchingBuildActionRunner.java:119)
at org.gradle.launcher.exec.BuildCompletionNotifyingBuildActionRunner.run(BuildCompletionNotifyingBuildActionRunner.java:41)
at org.gradle.launcher.exec.RootBuildLifecycleBuildActionExecutor.lambda$execute$0(RootBuildLifecycleBuildActionExecutor.java:40)
at org.gradle.composite.internal.DefaultRootBuildState.run(DefaultRootBuildState.java:128)
at org.gradle.launcher.exec.RootBuildLifecycleBuildActionExecutor.execute(RootBuildLifecycleBuildActionExecutor.java:40)
at org.gradle.internal.buildtree.DefaultBuildTreeContext.execute(DefaultBuildTreeContext.java:40)
at org.gradle.launcher.exec.BuildTreeLifecycleBuildActionExecutor.lambda$execute$0(BuildTreeLifecycleBuildActionExecutor.java:65)
at org.gradle.internal.buildtree.BuildTreeState.run(BuildTreeState.java:53)
at org.gradle.launcher.exec.BuildTreeLifecycleBuildActionExecutor.execute(BuildTreeLifecycleBuildActionExecutor.java:65)
at org.gradle.launcher.exec.RunAsBuildOperationBuildActionExecutor$3.call(RunAsBuildOperationBuildActionExecutor.java:61)
at org.gradle.launcher.exec.RunAsBuildOperationBuildActionExecutor$3.call(RunAsBuildOperationBuildActionExecutor.java:57)
at org.gradle.internal.operations.DefaultBuildOperationRunner$CallableBuildOperationWorker.execute(DefaultBuildOperationRunner.java:204)
at org.gradle.internal.operations.DefaultBuildOperationRunner$CallableBuildOperationWorker.execute(DefaultBuildOperationRunner.java:199)
at org.gradle.internal.operations.DefaultBuildOperationRunner$2.execute(DefaultBuildOperationRunner.java:66)
at org.gradle.internal.operations.DefaultBuildOperationRunner$2.execute(DefaultBuildOperationRunner.java:59)
at org.gradle.internal.operations.DefaultBuildOperationRunner.execute(DefaultBuildOperationRunner.java:157)
at org.gradle.internal.operations.DefaultBuildOperationRunner.execute(DefaultBuildOperationRunner.java:59)
at org.gradle.internal.operations.DefaultBuildOperationRunner.call(DefaultBuildOperationRunner.java:53)
at org.gradle.internal.operations.DefaultBuildOperationExecutor.call(DefaultBuildOperationExecutor.java:73)
at org.gradle.launcher.exec.RunAsBuildOperationBuildActionExecutor.execute(RunAsBuildOperationBuildActionExecutor.java:57)
at org.gradle.launcher.exec.RunAsWorkerThreadBuildActionExecutor.lambda$execute$0(RunAsWorkerThreadBuildActionExecutor.java:36)
at org.gradle.internal.work.DefaultWorkerLeaseService.withLocks(DefaultWorkerLeaseService.java:270)
at org.gradle.internal.work.DefaultWorkerLeaseService.runAsWorkerThread(DefaultWorkerLeaseService.java:119)
at org.gradle.launcher.exec.RunAsWorkerThreadBuildActionExecutor.execute(RunAsWorkerThreadBuildActionExecutor.java:36)
at org.gradle.tooling.internal.provider.ContinuousBuildActionExecutor.execute(ContinuousBuildActionExecutor.java:103)
at org.gradle.tooling.internal.provider.SubscribableBuildActionExecutor.execute(SubscribableBuildActionExecutor.java:64)
at org.gradle.internal.session.DefaultBuildSessionContext.execute(DefaultBuildSessionContext.java:46)
at org.gradle.tooling.internal.provider.BuildSessionLifecycleBuildActionExecuter$ActionImpl.apply(BuildSessionLifecycleBuildActionExecuter.java:100)
at org.gradle.tooling.internal.provider.BuildSessionLifecycleBuildActionExecuter$ActionImpl.apply(BuildSessionLifecycleBuildActionExecuter.java:88)
at org.gradle.internal.session.BuildSessionState.run(BuildSessionState.java:69)
at org.gradle.tooling.internal.provider.BuildSessionLifecycleBuildActionExecuter.execute(BuildSessionLifecycleBuildActionExecuter.java:62)
at org.gradle.tooling.internal.provider.BuildSessionLifecycleBuildActionExecuter.execute(BuildSessionLifecycleBuildActionExecuter.java:41)
at org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:63)
at org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:31)
at org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:58)
at org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:42)
at org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:47)
at org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:31)
at org.gradle.launcher.daemon.server.exec.ExecuteBuild.doBuild(ExecuteBuild.java:65)
at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:37)
at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:104)
at org.gradle.launcher.daemon.server.exec.WatchForDisconnection.execute(WatchForDisconnection.java:39)
at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:104)
at org.gradle.launcher.daemon.server.exec.ResetDeprecationLogger.execute(ResetDeprecationLogger.java:29)
at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:104)
at org.gradle.launcher.daemon.server.exec.RequestStopIfSingleUsedDaemon.execute(RequestStopIfSingleUsedDaemon.java:35)
at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:104)
at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.create(ForwardClientInput.java:78)
at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.create(ForwardClientInput.java:75)
at org.gradle.util.internal.Swapper.swap(Swapper.java:38)
at org.gradle.launcher.daemon.server.exec.ForwardClientInput.execute(ForwardClientInput.java:75)
at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:104)
at org.gradle.launcher.daemon.server.exec.LogAndCheckHealth.execute(LogAndCheckHealth.java:55)
at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:104)
at org.gradle.launcher.daemon.server.exec.LogToClient.doBuild(LogToClient.java:63)
at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:37)
at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:104)
at org.gradle.launcher.daemon.server.exec.EstablishBuildEnvironment.doBuild(EstablishBuildEnvironment.java:84)
at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:37)
at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:104)
at org.gradle.launcher.daemon.server.exec.StartBuildOrRespondWithBusy$1.run(StartBuildOrRespondWithBusy.java:52)
at org.gradle.launcher.daemon.server.DaemonStateCoordinator$1.run(DaemonStateCoordinator.java:297)
at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:64)
at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:48)
Caused by: java.net.ConnectException: Connection timed out (Connection timed out)
at build_3tc2foo38yu1uz6fnsvbnqk0b$_run_closure7.doCall(/data/users/branko/temp/SAPP/sapp/build.gradle:87)
at build_3tc2foo38yu1uz6fnsvbnqk0b$_run_closure8.doCall(/data/users/branko/temp/SAPP/sapp/build.gradle:97)
at org.gradle.util.internal.ClosureBackedAction.execute(ClosureBackedAction.java:72)
at org.gradle.util.internal.ConfigureUtil.configureTarget(ConfigureUtil.java:155)
at org.gradle.util.internal.ConfigureUtil.configure(ConfigureUtil.java:106)
at org.gradle.api.internal.project.DefaultProject.dependencies(DefaultProject.java:1241)
at org.gradle.internal.metaobject.BeanDynamicObject$MetaClassAdapter.invokeMethod(BeanDynamicObject.java:484)
at org.gradle.internal.metaobject.BeanDynamicObject.tryInvokeMethod(BeanDynamicObject.java:196)
at org.gradle.internal.metaobject.CompositeDynamicObject.tryInvokeMethod(CompositeDynamicObject.java:98)
at org.gradle.internal.extensibility.MixInClosurePropertiesAsMethodsDynamicObject.tryInvokeMethod(MixInClosurePropertiesAsMethodsDynamicObject.java:34)
at org.gradle.groovy.scripts.BasicScript$ScriptDynamicObject.tryInvokeMethod(BasicScript.java:135)
at org.gradle.internal.metaobject.AbstractDynamicObject.invokeMethod(AbstractDynamicObject.java:163)
at org.gradle.groovy.scripts.BasicScript.invokeMethod(BasicScript.java:84)
at build_3tc2foo38yu1uz6fnsvbnqk0b.run(/data/users/branko/temp/SAPP/sapp/build.gradle:96)
at org.gradle.groovy.scripts.internal.DefaultScriptRunnerFactory$ScriptRunnerImpl.run(DefaultScriptRunnerFactory.java:91)
... 152 more
* Get more help at https://help.gradle.org
BUILD FAILED in 2m 17s
ls: cannot access '/data/users/branko/temp/SAPP/sapp/build/libs/': No such file or directory
File selected
Error: Unable to access jarfile /data/users/branko/temp/SAPP/sapp/build/libs/
cp: cannot stat '/data/users/branko/temp/SAPP/sapp/build/libs/': No such file or directory
- submodules like [https://gitlab.com/sapp/Conversion] are not available
Is there a docker, conda or binary version that is readily usable and available?