pipeline | process raw fastq data and produce meaningful genomic data | Genomics library

 by   hartwigmedical Perl Version: v4.8 License: MIT

kandi X-RAY | pipeline Summary

kandi X-RAY | pipeline Summary

pipeline is a Perl library typically used in Artificial Intelligence, Genomics applications. pipeline has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. You can download it from GitHub.

Has been replaced by Pipeline5.
Support
    Quality
      Security
        License
          Reuse

            kandi-support Support

              pipeline has a low active ecosystem.
              It has 9 star(s) with 3 fork(s). There are 6 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 0 open issues and 5 have been closed. On average issues are closed in 136 days. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of pipeline is v4.8

            kandi-Quality Quality

              pipeline has 0 bugs and 0 code smells.

            kandi-Security Security

              pipeline has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
              pipeline code analysis shows 0 unresolved vulnerabilities.
              There are 0 security hotspots that need review.

            kandi-License License

              pipeline is licensed under the MIT License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              pipeline releases are available to install and integrate.

            Top functions reviewed by kandi - BETA

            kandi's functional review helps you automatically verify the functionalities of the libraries and avoid rework.
            Currently covering the most popular Java, JavaScript and Python libraries. See a Sample of pipeline
            Get all kandi verified functions for this library.

            pipeline Key Features

            No Key Features are available at this moment for pipeline.

            pipeline Examples and Code Snippets

            No Code Snippets are available at this moment for pipeline.

            Community Discussions

            QUESTION

            How to override a nested npm sub-dependency with a different package altogether (not just different package version number)?
            Asked 2022-Apr-04 at 01:19
            Overview

            I am having trouble resolving a ReDoS vulnerability identified by npm audit. My application has a nested sub-dependency ansi-html that is vulnerable to attack, but unfortunately, it seems that the maintainers have gone AWOL. As you can see in the comments section of that Github issue, to get around this problem, the community has made a fork of the repo called ansi-html-community located here, which addresses this vulnerability.

            Thus, I would like to replace all nested references of ansi-html with ansi-html-community.

            Problem

            My normal strategy of using npm-force-resolutions does not seem to be able to override nested sub-dependencies with a different package altogether but rather only the same packages that are a different version number. I have researched this for several hours, but unfortunately, the only way I have found to fix this would appear to be with yarn, which I am now seriously considering using instead of npm. However, this is not ideal as our entire CI/CD pipeline is configured to use npm.

            Does anyone know of any other way to accomplish nested sub-dependency package substitution/resolution without having to switch over to using yarn?

            Related Questions

            These are questions of interest that I was able to find, but unfortunately, they tend to only discuss methods to override package version number, not the package itself.

            Discusses how to override version number:

            How do I override nested NPM dependency versions?

            Has a comment discussion about npm shrinkwrap (not ideal):

            npm - how to override a dependent package's dependencies?

            Other related StackOverflow questions:

            CSE Index of related questions

            ...

            ANSWER

            Answered 2021-Oct-29 at 21:01

            I figured it out. As of October 2021, the solution using npm-force-resolutions is actually very similar to how you would specify it using yarn. You just need to provide a link to the tarball where you would normally specify the overriding version number. Your resolutions section of package.json should look like this:

            Source https://stackoverflow.com/questions/69548370

            QUESTION

            How to fix? "kex_exchange_identification: read: Connection reset by peer"
            Asked 2022-Mar-30 at 10:07

            I want to copy data with scp in GitLab pipeline using PRIVATE_KEY error is :

            ...

            ANSWER

            Answered 2021-Sep-30 at 19:40
            kex_exchange_identification: read: Connection reset by peer
            

            Source https://stackoverflow.com/questions/69394001

            QUESTION

            AzurePipeline failing due to: The reference assemblies for .NETFramework,Version=v4.6.1 were not found
            Asked 2022-Mar-25 at 09:30

            I have an Azure pipeline setup for my builds. I have been running into this issue recently and cannot figure out a way to fix this:

            ...

            ANSWER

            Answered 2022-Mar-16 at 06:02

            From Agent pool - Change Agent Specification from Window-Latest to Window-2019 ,It seems MS has done some changes in default agent

            Image

            Source https://stackoverflow.com/questions/71486310

            QUESTION

            Where are the using statements/directives in .NET 6
            Asked 2022-Mar-15 at 17:03

            I got up and running with Visual Studio 2022 Preview for a couple of days now.

            Got the first shock, there is no Startup.cs. Thats ok, a bit of reading, I know Startup is removed.

            Today got another slap. I see no using statements. Here it is.

            I just created a brand new .NET 6 web app and as I hover over the WebApplication class, I realized it stays in Microsoft.AspNetCore.Builder namespace. And the generated Program.cs class looks like this.

            So where is the using Microsoft.AspNetCore.Builder; statement?

            Whats the magic? Why is .net becoming mystical by the day?

            The full Program.cs file is as follows.

            ...

            ANSWER

            Answered 2022-Mar-15 at 17:03

            C# 10.0 introduces a new feature called global using directive (global using ;) which allows to specify namespaces to be implicitly imported in all files in the compilation. .NET 6 RC1 has this feature enabled by default in new project templates (see enable property in your .csproj).

            For Microsoft.NET.Sdk.Web next namespaces should be implicitly imported (plus the ones from Microsoft.NET.Sdk):

            • System.Net.Http.Json
            • Microsoft.AspNetCore.Builder
            • Microsoft.AspNetCore.Hosting
            • Microsoft.AspNetCore.Http
            • Microsoft.AspNetCore.Routing
            • Microsoft.Extensions.Configuration
            • Microsoft.Extensions.DependencyInjection
            • Microsoft.Extensions.Hosting
            • Microsoft.Extensions.Logging

            UPD

            To address your questions in comment:

            At the moment of writing the generated file containing default imports will be inside the obj folder named something like ProjectName.GlobalUsings.g.cs.

            To modify default imports you can add Using element to your .csproj file. Based on exposed attributes it allows several actions including addition and removal:

            Source https://stackoverflow.com/questions/69738921

            QUESTION

            NPM install task failing in Azure Devops, same code worked previously
            Asked 2022-Mar-12 at 12:38

            I have yaml pipeline running a build in Azure Devops. The Npm@1 task has started failing this morning. npm install works locally with npm version 6.14.5 and it's all green lights on npm Status.

            ...

            ANSWER

            Answered 2021-Dec-02 at 13:14

            I still don't know why this started failing all of a sudden but I have resolved the problem by updating node-sass to version 6.0.1.

            Source https://stackoverflow.com/questions/70199030

            QUESTION

            ASP.NET Core 6 how to access Configuration during startup
            Asked 2022-Mar-08 at 11:45

            In earlier versions, we had Startup.cs class and we get configuration object as follows in the Startup file.

            ...

            ANSWER

            Answered 2021-Oct-26 at 12:26

            WebApplicationBuilder returned by WebApplication.CreateBuilder(args) exposes Configuration and Environment properties:

            Source https://stackoverflow.com/questions/69722872

            QUESTION

            Microsoft.Extensions.Hosting.HostFactoryResolver+HostingListener+StopTheHostException
            Asked 2022-Mar-03 at 15:46

            I'm using Asp.Net Core Web Api 6

            I'm facing an error when migrating my DbContext and when updating the database

            The Error

            ...

            ANSWER

            Answered 2022-Mar-03 at 15:46

            Add try/catch similar to the above around IHostBulder.Build() in any .NET/EF Core 6.0 RC2 project, and attempt to add a migration can reproduce the issue.

            We can fix the issue with the following :

            Source https://stackoverflow.com/questions/70247187

            QUESTION

            How to use appsettings.json in Asp.net core 6 Program.cs file
            Asked 2022-Feb-25 at 21:39

            I'm trying to access appsettings.json in my Asp.net core v6 application Program.cs file, but in this version of .Net the Startup class and Program class are merged together and the using and another statements are simplified and removed from Program.cs. In this situation, How to access IConfiguration or how to use dependency injection for example ?

            Edited : Here is my default Program.cs that Asp.net 6 created for me

            ...

            ANSWER

            Answered 2021-Sep-30 at 11:13

            Assuming an appsettings.json

            Source https://stackoverflow.com/questions/69390676

            QUESTION

            Error NETSDK1045: The current .NET SDK does not support targeting .NET 6.0
            Asked 2022-Feb-19 at 07:38

            I spent 2 hours trying to figure out what's wrong with my pipeline for Azure Functions .NET6 (on Windows).

            ...

            ANSWER

            Answered 2021-Oct-27 at 08:50

            I found the solution here https://jaliyaudagedara.blogspot.com/2021/07/azure-devops-building-projects.html
            It works if I specify the .NET Core SDK version & set preview version to true

            Source https://stackoverflow.com/questions/69730032

            QUESTION

            "Configuring the trigger failed, edit and save the pipeline again" with no noticeable error and no further details
            Asked 2022-Feb-16 at 10:33

            I have run in to an odd problem after converting a bunch of my YAML pipelines to use templates for holding job logic as well as for defining my pipeline variables. The pipelines run perfectly fine, however I get a "Some recent issues detected related to pipeline trigger." warning at the top of the pipeline summary page and viewing details only states: "Configuring the trigger failed, edit and save the pipeline again."

            The odd part here is that the pipeline works completely fine, including triggers. Nothing is broken and no further details are given about the supposed issue. I currently have YAML triggers overridden for the pipeline, but I did also define the same trigger in the YAML to see if that would help (it did not).

            I'm looking for any ideas on what might be causing this or how I might be able to further troubleshoot it given the complete lack of detail that the error/warning provides. It's causing a lot of confusion among developers who think there might be a problem with their builds as a result of the warning.

            Here is the main pipeline. the build repository is a shared repository for holding code that is used across multiple repos in the build system. dev.yaml contains dev environment specific variable values. Shared holds conditionally set variables based on the branch the pipeline is running on.

            ...

            ANSWER

            Answered 2021-Aug-17 at 14:58

            I think I may have figured out the problem. It appears that this is related to the use of conditionals in the variable setup. While the variables will be set in any valid trigger configuration, it appears that the proper values are not used during validation and that may have been causing the problem. Switching my conditional variables to first set a default value and then replace the value conditionally seems to have fixed the problem.

            It would be nice if Microsoft would give a more useful error message here, something to the extent of the values not being found for a given variable, but adding defaults does seem to have fixed the problem.

            Source https://stackoverflow.com/questions/68819306

            Community Discussions, Code Snippets contain sources that include Stack Exchange Network

            Vulnerabilities

            No vulnerabilities reported

            Install pipeline

            You can download it from GitHub.

            Support

            For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .
            Find more information at:

            Find, review, and download reusable Libraries, Code Snippets, Cloud APIs from over 650 million Knowledge Items

            Find more libraries

            Stay Updated

            Subscribe to our newsletter for trending solutions and developer bootcamps

            Agree to Sign up and Terms & Conditions

            Share this Page

            share link

            Explore Related Topics

            Consider Popular Genomics Libraries

            Try Top Libraries by hartwigmedical

            hmftools

            by hartwigmedicalJava

            scripts

            by hartwigmedicalShell

            gridss-purple-linx

            by hartwigmedicalShell

            pipeline5

            by hartwigmedicalJava

            platinum

            by hartwigmedicalJava