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Illumina / witty.er

What is true, thank you, ernestly. A large variant benchmarking tool analogous to hap.py for small variants.
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Problems with witty.er docker #5

Closed misago162 closed 4 years ago

misago162 commented 4 years ago

Hi

I'm trying to create the docker image and fails. I have tried to do it in differents way with the same result:

1.- Directly downloading the image from the docker repository:

$ singularity build wittyer.img docker://docker-general.dockerhub.illumina.com/wittyer:v0.3.1 INFO: Starting build... FATAL: While performing build: conveyor failed to get: pinging docker registry returned: Get https://docker-general.dockerhub.illumina.com/v2/: dial tcp: lookup docker-general.dockerhub.illumina.com on 10.1.12.3:53: no such host $

2.- Using the docker-build.sh script:

misanchez@computer:~/Documents/Software/witty.er$ ./docker-build.sh Sending build context to Docker daemon 36.69MB Step 1/11 : FROM microsoft/dotnet:2.0-sdk as builder ---> 9e06837225a4 Step 2/11 : WORKDIR /src ---> Using cache ---> b7ec75ca4f45 Step 3/11 : COPY . /src ---> Using cache ---> 54d169c6605b Step 4/11 : RUN dotnet publish -f netcoreapp2.0 -r linux-x64 -c Release -o /output && chmod +x /output/Wittyer ---> Running in 52a69375fc84 Microsoft (R) Build Engine version 15.7.179.6572 for .NET Core Copyright (C) Microsoft Corporation. All rights reserved.

Restoring packages for /src/Ilmn.Das.App.Wittyer.Test/Ilmn.Das.App.Wittyer.Test.csproj... Restoring packages for /src/Ilmn.Das.App.Wittyer/Ilmn.Das.App.Wittyer.csproj... Restoring packages for /src/Ilmn.Das.App.Wittyer.Test/Ilmn.Das.App.Wittyer.Test.csproj... Restoring packages for /src/Wittyer/Wittyer.csproj... Installing System.IO.UnmanagedMemoryStream 4.3.0. Installing System.IO.MemoryMappedFiles 4.3.0. Installing JetBrains.Annotations 11.1.0. Installing SourceLink.Embed.AllSourceFiles 2.8.1. Installing Newtonsoft.Json 12.0.1. Installing System.Collections.Immutable 1.5.0. Installing System.Composition.AttributedModel 1.1.0. Installing System.ComponentModel.Primitives 4.1.0. Installing System.Collections.Specialized 4.0.1. Installing System.ComponentModel 4.0.1. Installing System.ComponentModel.TypeConverter 4.1.0. Installing System.Diagnostics.TextWriterTraceListener 4.0.0. Installing System.ComponentModel.EventBasedAsync 4.0.11. Installing Microsoft.DotNet.PlatformAbstractions 1.0.3. Installing xunit.abstractions 2.0.2. Installing Microsoft.TestPlatform.ObjectModel 15.8.0. Installing Microsoft.Extensions.DependencyModel 1.0.3. Installing xunit.extensibility.core 2.4.0. Installing xunit.extensibility.execution 2.4.0. Installing System.Diagnostics.TraceSource 4.3.0. Installing xunit.runner.visualstudio 2.4.0. Installing Microsoft.TestPlatform.TestHost 15.8.0. Installing Microsoft.CodeCoverage 15.8.0. Installing Moq 4.9.0. Installing xunit.core 2.4.0. Installing xunit 2.4.0. Installing Microsoft.NET.Test.Sdk 15.8.0. Installing System.Linq.Queryable 4.3.0. Installing xunit.analyzers 0.10.0. Installing Castle.Core 4.3.1. Installing xunit.assert 2.4.0. Installing System.Xml.XPath.XDocument 4.0.1. Installing System.Diagnostics.StackTrace 4.0.1. Installing Microsoft.NETCore.DotNetHost 1.0.1. Installing Microsoft.CodeAnalysis.Common 1.3.0. Installing System.Security.Principal.Windows 4.0.0. Installing System.Security.Claims 4.0.1. Installing runtime.native.System.Net.Security 4.0.1. Installing Microsoft.NETCore.Jit 1.0.2. Installing Microsoft.NETCore.Windows.ApiSets 1.0.1. Installing Microsoft.NETCore.DotNetHostResolver 1.0.1. Installing dotnet-xunit 2.4.0-beta.1.build3958. Installing Microsoft.CodeAnalysis.CSharp 1.3.0. Installing Microsoft.CodeAnalysis.VisualBasic 1.3.0. Installing System.Net.NameResolution 4.0.0. Installing Microsoft.NETCore.App 1.0.0. Installing System.IO.MemoryMappedFiles 4.0.0. Installing System.Net.Security 4.0.0. Installing System.IO.UnmanagedMemoryStream 4.0.1. Installing Microsoft.NETCore.Runtime.CoreCLR 1.0.2. Installing System.Reflection.DispatchProxy 4.0.1. Installing System.Numerics.Vectors 4.1.1. Installing System.Net.WebHeaderCollection 4.0.1. Installing Libuv 1.9.0. Installing System.ComponentModel.Annotations 4.1.0. Installing Microsoft.VisualBasic 10.0.1. Installing System.Net.Requests 4.0.11. Installing System.Threading.Tasks.Parallel 4.0.1. Installing Microsoft.NETCore.DotNetHostPolicy 1.0.1. Installing System.IO.FileSystem.Watcher 4.0.0. Restore completed in 3.74 sec for /src/Ilmn.Das.App.Wittyer.Test/Ilmn.Das.App.Wittyer.Test.csproj. Installing runtime.linux-x64.Microsoft.NETCore.DotNetAppHost 2.0.0. Installing runtime.any.System.Text.Encoding.Extensions 4.3.0. Installing runtime.any.System.Collections 4.3.0. Installing runtime.any.System.Diagnostics.Tracing 4.3.0. Installing runtime.unix.System.Private.Uri 4.3.0. Installing runtime.linux-x64.Microsoft.NETCore.DotNetHostResolver 2.0.0. Installing runtime.any.System.Reflection.Primitives 4.3.0. Installing runtime.unix.System.Diagnostics.Debug 4.3.0. Installing runtime.linux-x64.Microsoft.NETCore.App 2.0.0. Installing runtime.any.System.Text.Encoding 4.3.0. Installing runtime.any.System.Reflection 4.3.0. Installing runtime.any.System.Globalization 4.3.0. Installing System.Private.Uri 4.3.0. Installing runtime.linux-x64.Microsoft.NETCore.DotNetHostPolicy 2.0.0. Installing runtime.unix.System.IO.FileSystem 4.3.0. Installing runtime.any.System.Runtime 4.3.0. Installing runtime.unix.System.Runtime.Extensions 4.3.0. Installing runtime.any.System.Runtime.InteropServices 4.3.0. Installing runtime.any.System.Resources.ResourceManager 4.3.0. Installing runtime.any.System.IO 4.3.0. Installing runtime.any.System.Threading.Tasks 4.3.0. Installing runtime.any.System.Runtime.Handles 4.3.0. Installing runtime.unix.System.Net.Primitives 4.3.0. Installing runtime.any.System.Threading.Timer 4.3.0. Installing runtime.unix.System.Console 4.3.0. Installing runtime.any.System.Diagnostics.Tools 4.3.0. Installing runtime.unix.System.Net.Sockets 4.3.0. Installing runtime.unix.Microsoft.Win32.Primitives 4.3.0. Installing runtime.any.System.Globalization.Calendars 4.3.0. Installing runtime.any.System.Reflection.Extensions 4.3.0. /src/Ilmn.Das.App.Wittyer.Test/Ilmn.Das.App.Wittyer.Test.csproj : error NU1101: Unable to find package Ilmn.Das.Std.XunitUtils. No packages exist with this id in source(s): nuget.org [/src/Ilmn.Das.App.Wittyer.sln] Generating MSBuild file /src/Ilmn.Das.App.Wittyer/obj/Ilmn.Das.App.Wittyer.csproj.nuget.g.props. Generating MSBuild file /src/Wittyer/obj/Wittyer.csproj.nuget.g.props. Generating MSBuild file /src/Ilmn.Das.App.Wittyer/obj/Ilmn.Das.App.Wittyer.csproj.nuget.g.targets. Generating MSBuild file /src/Wittyer/obj/Wittyer.csproj.nuget.g.targets. Restore completed in 4.58 sec for /src/Ilmn.Das.App.Wittyer/Ilmn.Das.App.Wittyer.csproj. Restore completed in 4.58 sec for /src/Wittyer/Wittyer.csproj. Generating MSBuild file /src/Ilmn.Das.App.Wittyer.Test/obj/Ilmn.Das.App.Wittyer.Test.csproj.nuget.g.props. Generating MSBuild file /src/Ilmn.Das.App.Wittyer.Test/obj/Ilmn.Das.App.Wittyer.Test.csproj.nuget.g.targets. Restore failed in 4.64 sec for /src/Ilmn.Das.App.Wittyer.Test/Ilmn.Das.App.Wittyer.Test.csproj. The command '/bin/sh -c dotnet publish -f netcoreapp2.0 -r linux-x64 -c Release -o /output && chmod +x /output/Wittyer' returned a non-zero code: 1 misanchez@bigsuport:~/Documents/Software/witty.er$

3.- And the same problem if I try to build the container from the Dockerfile:

misanchez@bigsuport:~/Documents/Software/witty.er$ docker build --tag witty.er:1.0 . Sending build context to Docker daemon 36.69MB Step 1/10 : FROM microsoft/dotnet:2.0-sdk as builder ---> 9e06837225a4 Step 2/10 : WORKDIR /src ---> Using cache ---> b7ec75ca4f45 Step 3/10 : COPY . /src ---> Using cache ---> 54d169c6605b Step 4/10 : RUN dotnet publish -f netcoreapp2.0 -r linux-x64 -c Release -o /output && chmod +x /output/Wittyer ---> Running in f47fc4a63c2c Microsoft (R) Build Engine version 15.7.179.6572 for .NET Core Copyright (C) Microsoft Corporation. All rights reserved.

Restoring packages for /src/Ilmn.Das.App.Wittyer.Test/Ilmn.Das.App.Wittyer.Test.csproj... Restoring packages for /src/Ilmn.Das.App.Wittyer/Ilmn.Das.App.Wittyer.csproj... Restoring packages for /src/Ilmn.Das.App.Wittyer.Test/Ilmn.Das.App.Wittyer.Test.csproj... Restoring packages for /src/Wittyer/Wittyer.csproj... Installing System.IO.UnmanagedMemoryStream 4.3.0. Installing System.IO.MemoryMappedFiles 4.3.0. Installing Newtonsoft.Json 12.0.1. Installing System.Collections.Immutable 1.5.0. Installing System.Composition.AttributedModel 1.1.0. Installing JetBrains.Annotations 11.1.0. Installing SourceLink.Embed.AllSourceFiles 2.8.1. Installing System.Xml.XPath.XDocument 4.0.1. Installing System.Diagnostics.StackTrace 4.0.1. Installing Microsoft.NETCore.DotNetHost 1.0.1. Installing Microsoft.CodeAnalysis.Common 1.3.0. Installing System.Security.Principal.Windows 4.0.0. Installing System.Security.Claims 4.0.1. Installing runtime.native.System.Net.Security 4.0.1. Installing Microsoft.NETCore.Windows.ApiSets 1.0.1. Installing Microsoft.NETCore.Jit 1.0.2. Installing Microsoft.NETCore.DotNetHostResolver 1.0.1. Installing dotnet-xunit 2.4.0-beta.1.build3958. Installing runtime.any.System.Collections 4.3.0. Installing Microsoft.CodeAnalysis.VisualBasic 1.3.0. Installing runtime.any.System.Text.Encoding.Extensions 4.3.0. Installing Microsoft.CodeAnalysis.CSharp 1.3.0. Installing runtime.any.System.Diagnostics.Tracing 4.3.0. Installing Microsoft.NETCore.App 1.0.0. Installing System.Net.NameResolution 4.0.0. Installing runtime.unix.System.Private.Uri 4.3.0. Installing System.Net.Security 4.0.0. Installing runtime.linux-x64.Microsoft.NETCore.DotNetAppHost 2.0.0. Installing Microsoft.NETCore.Runtime.CoreCLR 1.0.2. Installing runtime.any.System.Reflection.Primitives 4.3.0. Installing Microsoft.NETCore.DotNetHostPolicy 1.0.1. Installing runtime.any.System.Text.Encoding 4.3.0. Installing Libuv 1.9.0. Installing System.IO.UnmanagedMemoryStream 4.0.1. Installing runtime.unix.System.Diagnostics.Debug 4.3.0. Installing runtime.any.System.Reflection 4.3.0. Installing runtime.any.System.Globalization 4.3.0. Installing System.IO.MemoryMappedFiles 4.0.0. Installing System.Threading.Tasks.Parallel 4.0.1. Installing System.Private.Uri 4.3.0. Installing runtime.linux-x64.Microsoft.NETCore.DotNetHostResolver 2.0.0. Installing runtime.any.System.IO 4.3.0. Installing runtime.any.System.Runtime.InteropServices 4.3.0. Installing runtime.unix.System.IO.FileSystem 4.3.0. Installing System.Numerics.Vectors 4.1.1. Installing runtime.any.System.Threading.Tasks 4.3.0. Installing System.ComponentModel.Annotations 4.1.0. Installing runtime.linux-x64.Microsoft.NETCore.App 2.0.0. Installing System.Net.Requests 4.0.11. Installing System.ComponentModel 4.0.1. Installing System.Net.WebHeaderCollection 4.0.1. Installing System.IO.FileSystem.Watcher 4.0.0. Installing System.Reflection.DispatchProxy 4.0.1. Installing runtime.linux-x64.Microsoft.NETCore.DotNetHostPolicy 2.0.0. Installing Microsoft.VisualBasic 10.0.1. Installing runtime.unix.System.Runtime.Extensions 4.3.0. Installing runtime.any.System.Runtime.Handles 4.3.0. Installing runtime.any.System.Runtime 4.3.0. Installing runtime.any.System.Resources.ResourceManager 4.3.0. Restore completed in 3.69 sec for /src/Ilmn.Das.App.Wittyer.Test/Ilmn.Das.App.Wittyer.Test.csproj. Generating MSBuild file /src/Wittyer/obj/Wittyer.csproj.nuget.g.props. Generating MSBuild file /src/Ilmn.Das.App.Wittyer/obj/Ilmn.Das.App.Wittyer.csproj.nuget.g.props. Generating MSBuild file /src/Wittyer/obj/Wittyer.csproj.nuget.g.targets. Generating MSBuild file /src/Ilmn.Das.App.Wittyer/obj/Ilmn.Das.App.Wittyer.csproj.nuget.g.targets. Restore completed in 4.1 sec for /src/Wittyer/Wittyer.csproj. Restore completed in 4.1 sec for /src/Ilmn.Das.App.Wittyer/Ilmn.Das.App.Wittyer.csproj. Installing System.Collections.Specialized 4.0.1. Installing System.ComponentModel.Primitives 4.1.0. Installing System.ComponentModel.TypeConverter 4.1.0. Installing System.ComponentModel.EventBasedAsync 4.0.11. Installing System.Diagnostics.TextWriterTraceListener 4.0.0. Installing Microsoft.DotNet.PlatformAbstractions 1.0.3. Installing xunit.abstractions 2.0.2. Installing Microsoft.TestPlatform.ObjectModel 15.8.0. Installing Microsoft.Extensions.DependencyModel 1.0.3. Installing xunit.extensibility.core 2.4.0. Installing xunit.extensibility.execution 2.4.0. Installing System.Diagnostics.TraceSource 4.3.0. Installing Microsoft.TestPlatform.TestHost 15.8.0. Installing Microsoft.CodeCoverage 15.8.0. Installing xunit.core 2.4.0. Installing xunit.analyzers 0.10.0. Installing xunit.runner.visualstudio 2.4.0. Installing Moq 4.9.0. Installing xunit 2.4.0. Installing xunit.assert 2.4.0. Installing Microsoft.NET.Test.Sdk 15.8.0. Installing System.Linq.Queryable 4.3.0. Installing Castle.Core 4.3.1. Installing runtime.unix.System.Net.Sockets 4.3.0. Installing runtime.unix.System.Console 4.3.0. Installing runtime.unix.System.Net.Primitives 4.3.0. Installing runtime.any.System.Threading.Timer 4.3.0. Installing runtime.any.System.Diagnostics.Tools 4.3.0. Installing runtime.any.System.Globalization.Calendars 4.3.0. Installing runtime.unix.Microsoft.Win32.Primitives 4.3.0. Installing runtime.any.System.Reflection.Extensions 4.3.0. /src/Ilmn.Das.App.Wittyer.Test/Ilmn.Das.App.Wittyer.Test.csproj : error NU1101: Unable to find package Ilmn.Das.Std.XunitUtils. No packages exist with this id in source(s): nuget.org [/src/Ilmn.Das.App.Wittyer.sln] Generating MSBuild file /src/Ilmn.Das.App.Wittyer.Test/obj/Ilmn.Das.App.Wittyer.Test.csproj.nuget.g.props. Generating MSBuild file /src/Ilmn.Das.App.Wittyer.Test/obj/Ilmn.Das.App.Wittyer.Test.csproj.nuget.g.targets. Restore failed in 5.38 sec for /src/Ilmn.Das.App.Wittyer.Test/Ilmn.Das.App.Wittyer.Test.csproj. The command '/bin/sh -c dotnet publish -f netcoreapp2.0 -r linux-x64 -c Release -o /output && chmod +x /output/Wittyer' returned a non-zero code: 1 misanchez@bigsuport:~/Documents/Software/witty.er$

Can you help me, please?

Kentalot commented 4 years ago

Ok, I'll look at this today. Thanks for the bug report.

Kentalot commented 4 years ago

Fixed, please reclone and try again!

misago162 commented 4 years ago

Now it works, thanks a lot.

Miguel A. Sánchez Gómez

System Administrator CRG -Centre for Genomic Regulation C/ Dr. Aiguader, 88 Edif. PRBB 08003 Barcelona, Spain Phone Ext: #1171

From: Kentalot notifications@github.com Sent: Thursday, June 25, 2020 7:58 AM To: Illumina/witty.er Cc: Miguel Angel Sanchez Gomez; Author Subject: Re: [Illumina/witty.er] Problems with witty.er docker (#5)

Fixed, please reclone and try again!

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Illumina/witty.er/issues/5#issuecomment-649237164, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AOURTLIQCMLTOBZDURJZK5DRYLRRTANCNFSM4OBNZJUA.