tools | Python package with helper tools for the nf-core community | Genomics library

by nf-core Python Version: 2.8 License: MIT

X-Ray Key Features Code Snippets(2)Community Discussions(10)Vulnerabilities Install Support

kandi X-RAY | tools Summary

tools is a Python library typically used in Artificial Intelligence, Genomics applications. tools has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can install using 'pip install tools' or download it from GitHub, PyPI.

A python package with helper tools for the nf-core community. Read this documentation on the nf-core website:

Support

Quality

Security

License

Reuse

Support

tools has a low active ecosystem.

It has 188 star(s) with 140 fork(s). There are 110 watchers for this library.

It had no major release in the last 12 months.

There are 177 open issues and 601 have been closed. On average issues are closed in 114 days. There are 22 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of tools is 2.8

Quality

tools has 0 bugs and 0 code smells.

Security

tools has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

tools code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

tools is licensed under the MIT License. This license is Permissive.

Permissive licenses have the least restrictions, and you can use them in most projects.

Reuse

tools releases are available to install and integrate.

Deployable package is available in PyPI.

Build file is available. You can build the component from source.

Installation instructions, examples and code snippets are available.

It has 9547 lines of code, 532 functions and 92 files.

It has high code complexity. Code complexity directly impacts maintainability of the code.

Top functions reviewed by kandi - BETA

kandi has reviewed tools and discovered the below as its top functions. This is intended to give you an instant insight into tools implemented functionality, and help decide if they suit your requirements.

Create the pipeline
Get the module info
Generate the help text for the module
Print module info
Render the template
Fix linting
Download a logo from the website
Download logo logo
Lint a module
Return a list of validation parameters that describe the schema
Run module_todo
Validates the schema params for the pipeline
Parse arguments
Generate a list of version numbers
Determine the git version of a module
Get the rendered renderables
Setup requests cache
Checks if a module has changed
Check the README file
Validate the schema
Parse the multiqc config file
Validate the module s meta yaml
Verify that the sample sheet contains the required columns
Update the configuration of the refgenie
Download a singularity image
Create a parameter dictionary

Get all kandi verified functions for this library.

tools Key Features

No Key Features are available at this moment for tools.

tools Examples and Code Snippets

Step 2. Load the Tools that you want to make available

maven

Lines of Code : 1

License : No License

Copy

Map the web tools .

java

Lines of Code : 4

License : Permissive (MIT License)

Copy

@GetMapping("/utils")
    public String webUtils(Model model) {
        return "utils";
    }

Community Discussions

Trending Discussions on tools

Build was configured to prefer settings repositories over project repositories but repository 'maven' was added by build file 'build.gradle'

AngularFireModule and AngularFireDatabaseModule not being found in @angular/fire

Error: MainActivity must extend android.app.Activity [Instantiatable]

Android Studio Bumblebee Wifi pairing Issue

Could not GET 'play-services-location/maven-metadata.xml'. Received status code 502 from server: Bad Gateway

Java, Intellij IDEA problem Unrecognized option: --add-opens=jdk.compiler/com.sun.tools.javac.code=ALL-UNNAMED

Android app won't build -- The minCompileSdk (31) specified in a dependency's androidx.work:work-runtime:2.7.0-beta01

Error when trying to run my React Native app on Android

Flutter iOS Error Class AMSupportURLConnectionDelegate is implemented in both /usr/lib/libamsupport.dylib (0x203913130)

android:exported needs to be explicitly specified for . Apps targeting Android 12 and higher are required to specify

QUESTION

Build was configured to prefer settings repositories over project repositories but repository 'maven' was added by build file 'build.gradle'

Asked 2022-Apr-04 at 13:12

I want to add jitpack.io as a repository in my gradle file. This is my gradle root file:

...

ANSWER

Answered 2021-Sep-16 at 11:02

Android introduced a new way to define repositories.

Remove the dependencyResolutionManagement block from the setting.gradle file to have your project work the old way.

Source https://stackoverflow.com/questions/69163511

QUESTION

AngularFireModule and AngularFireDatabaseModule not being found in @angular/fire

Asked 2022-Apr-01 at 12:56

I am trying to implement Firebase Realtime Database into a angular project and Im getting stuck at one of the very first steps. Importing AngularFireModule and AngularFireDatabaseModule. It gives me the following error:

...

ANSWER

Answered 2021-Aug-26 at 13:20

AngularFire 7.0.0 was launched yesterday with a new API that has a lot of bundle size reduction benefits.

Instead of top level classes like AngularFireDatabase, you can now import smaller independent functions.

Source https://stackoverflow.com/questions/68939014

QUESTION

Error: MainActivity must extend android.app.Activity [Instantiatable]

Asked 2022-Mar-31 at 02:13

I tried upgrading Android Gradle Plugin from 4.2.2 to 7.0.1 using the upgrade assistant which is available in Android Studio at Tools > AGP Upgrade Assistant. The only change it made was to my project-level build.gradle file:

...

ANSWER

Answered 2021-Aug-24 at 16:35

the Android Gradle Plugin documentation still says classpath 'com.android.tools.build:gradle:4.2.0' instead of 7.0.1.

You need to read further down the page, to this and this. That table is only relevant for pre-7.0.0 versions.

Is this a bug in Android Gradle Plugin 7.0.1?

Quite possibly. Or, perhaps beyond, as the Instantiatable Lint check has a history of problems.

If your scenario does not match one of those three August 2021 bugs, and you are in position to provide a reproducible test case, file a fresh issue! Beyond that, if a clean-and-rebuild is not clearing up your problem, you might need to simply disable the Instantiatable Lint check for the time being by adding the following to all of your build.gradle files at the application or library level (i.e. all except your project-level build.gradle):

Source https://stackoverflow.com/questions/68899665

QUESTION

Android Studio Bumblebee Wifi pairing Issue

Asked 2022-Mar-29 at 15:31

I have used Android Studio Bumblebee's latest function (Wifi pairing) for 2 - 3 days before it stopped working.
I am now receiving the error "This system does not meet the requirements to support Wi-Fi pairing. Please update to the latest version of "platform-tools" using the SDK manager"

I have updated everything to the latest version.

...

ANSWER

Answered 2022-Feb-02 at 03:53

My guess is that you have an old version of platform-tools/adb installed somewhere (you can verify this by running which adb in your command prompt).

Find the right platform-tools

You can find the pathway to the platform-tools/adb you want to use in Android Studios under Settings -> Appearance & Behavior -> System Settings -> Android SDK.

Inside of this folder should be another folder called "platform-tools".

Update your PATH You'll want to add this folder to your PATH and remove the old one.

Restart Android Studio For the changes to take effect, you'll need to restart the IDE.

File -> Invalidate Caches -> Invalidate and Restart

Another Solution If the above doesn't work, you can also uninstall and reinstall platform-tools using the sdkmanager command.

Source https://stackoverflow.com/questions/70944858

QUESTION

Could not GET 'play-services-location/maven-metadata.xml'. Received status code 502 from server: Bad Gateway

Asked 2022-Mar-28 at 07:02

I have a project which was running well yesterday, but today I find this problem:

Could not resolve all files for configuration ':app:debugRuntimeClasspath'. Could not resolve com.google.android.gms:play-services-location:16.+. Required by: project :app > project :location > Failed to list versions for com.google.android.gms:play-services-location. > Unable to load Maven meta-data from https://google.bintray.com/exoplayer/com/google/android/gms/play-services-location/maven-metadata.xml. > Could not get resource 'https://google.bintray.com/exoplayer/com/google/android/gms/play-services-location/maven-metadata.xml'. > Could not GET 'https://google.bintray.com/exoplayer/com/google/android/gms/play-services-location/maven-metadata.xml'. Received status code 502 from server: Bad Gateway

acutely I'm using classpath 'com.android.tools.build:gradle:4.1.0'with distributionUrl=https://services.gradle.org/distributions/gradle-6.5-bin.zip I have followed this question and I upgraded 'com.android.tools.build:gradle:4.1.0' to classpath 'com.android.tools.build:gradle:4.2.0' then I changed distributionUrl=https://services.gradle.org/distributions/gradle-6.5-bin.zip to distributionUrl=https\://services.gradle.org/distributions/gradle-6.7.1-all.zip but I still got the error.

my android/build.gradle:

...

ANSWER

Answered 2021-Dec-01 at 09:09

It looks like a temporary issue, the server with these libraries is down. I have the same problem now with Room:

Source https://stackoverflow.com/questions/70166663

QUESTION

Java, Intellij IDEA problem Unrecognized option: --add-opens=jdk.compiler/com.sun.tools.javac.code=ALL-UNNAMED

Asked 2022-Mar-26 at 15:23

I have newly installed

...

ANSWER

Answered 2021-Jul-28 at 07:22

You are running the project via Java 1.8 and add the --add-opens option to the runner. However Java 1.8 does not support it.

So, the first option is to use Java 11 to run the project, as Java 11 can recognize this VM option.

Another solution is to find a place where --add-opens is added and remove it. Check Run configuration in IntelliJ IDEA (VM options field) and Maven/Gradle configuration files for argLine (Maven) and jvmArgs (Gradle)

Source https://stackoverflow.com/questions/68554693

QUESTION

Android app won't build -- The minCompileSdk (31) specified in a dependency's androidx.work:work-runtime:2.7.0-beta01

Asked 2022-Mar-11 at 16:01

I'm trying to build a project in my M1,

but I got this error when I run npx react-native run-android

...

ANSWER

Answered 2021-Sep-02 at 23:03

The error is being caused because one of your dependencies is internally using WorkManager 2.7.0-beta01 that was released today (which needs API 31). In my case it was CheckAarMetadata.kt.

You can fix it by forcing Gradle to use an older version of Work Manager for the transitive dependency that works with API 30. In your build.gradle file add:

Source https://stackoverflow.com/questions/69037481

QUESTION

Error when trying to run my React Native app on Android

Asked 2022-Mar-06 at 07:58

I've built my React Native app and tested and troubleshooted with my iOS devices for months. Now I'm trying to built and test the app on Android for the first time. The thing is, that I keep getting errors trying to run the Android-version of my app. After hours of debugging and troubleshooting, I tried to create a new RN project and see if that could run on my emulator and device. I got that part working and then I wanted to copy/paste the files of my existing app project into the new project.

I pasted my existing assets, styles, the source JS-files and the package.json file into the new project, ran npm install and then I ended up with the exact same error message as I had in the original project when I run react-native run-android.

The full error message is here:

...

ANSWER

Answered 2021-Aug-21 at 13:43

I've hit this same issue and have temporarily resolved it by uninstalling react-native-video (npm uninstall --save react-native-video). That's not a great answer as I need that component, but I don't have a full solution yet. I think somehow com.yqritc:android-scalablevideoview:1.0.4. is required by react-native-video but has gotten lost or removed. Other thoughts are welcome.

UPDATE: Resolved! In your build.gradle in your Android folder you need to add the repository "jcenter()" in allprojects (not in build dependencies) like this...

Source https://stackoverflow.com/questions/68835157

QUESTION

Flutter iOS Error Class AMSupportURLConnectionDelegate is implemented in both /usr/lib/libamsupport.dylib (0x203913130)

Asked 2022-Mar-01 at 05:29

Hi am facing an issue while running flutter project in MacBook Air M1 chip Lap. Tried all possibilities couldn't find where is the exact problem.

All basic solutions like flutter clean, flutter pub get, pod deintegrate & install, flutter build ios, flutter run but still same issue. only on iOS simulator not deploying.

Any solution for this. Thanks in advance.

Error

...

ANSWER

Answered 2022-Feb-02 at 04:43

I have been facing this same issue for some time now. the same setup is working nicely in a mac with intel chip. But i have even done a resetup of my system, m1 mac still throws the same error.

Source https://stackoverflow.com/questions/70936334

QUESTION

android:exported needs to be explicitly specified for . Apps targeting Android 12 and higher are required to specify

Asked 2022-Feb-23 at 14:13

After upgrading to android 12, the application is not compiling. It shows

"Manifest merger failed with multiple errors, see logs"

Error showing in Merged manifest:

Merging Errors: Error: android:exported needs to be explicitly specified for . Apps targeting Android 12 and higher are required to specify an explicit value for android:exported when the corresponding component has an intent filter defined. See https://developer.android.com/guide/topics/manifest/activity-element#exported for details. main manifest (this file)

I have set all the activity with android:exported="false". But it is still showing this issue.

My manifest file:

...

ANSWER

Answered 2021-Aug-04 at 09:18

I'm not sure what you're using to code, but in order to set it in Android Studio, open the manifest of your project and under the "activity" section, put android:exported="true"(or false if that is what you prefer). I have attached an example.

Source https://stackoverflow.com/questions/68554294

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

Vulnerabilities

No vulnerabilities reported

Install tools

Manually building JSONSchema documents is not trivial and can be very error prone. Instead, the nf-core schema build command collects your pipeline parameters and gives interactive prompts about any missing or unexpected params. If no existing schema is found it will create one for you. Once built, the tool can send the schema to the nf-core website so that you can use a graphical interface to organise and fill in the schema. The tool checks the status of your schema on the website and once complete, saves your changes locally.
--dir <pipeline_dir>: Specify a pipeline directory other than the current working directory
--no-prompts: Make changes without prompting for confirmation each time. Does not launch web tool.
--web-only: Skips comparison of the schema against the pipeline parameters and only launches the web tool.
--url <web_address>: Supply a custom URL for the online tool. Useful when testing locally.
You can install modules from nf-core/modules in your pipeline using nf-core modules install. A module installed this way will be installed to the ./modules/nf-core/modules directory. You can pass the module name as an optional argument to nf-core modules install instead of using the cli prompt, eg: nf-core modules install fastqc. You can specify a pipeline directory other than the current working directory by using the --dir <pipeline dir>.
--force: Overwrite a previously installed version of the module.
--prompt: Select the module version using a cli prompt.
--sha <commit_sha>: Install the module at a specific commit from the nf-core/modules repository.

Support

Each test result name on the left is a terminal hyperlink. In most terminals you can ctrl + click ( cmd + click) these links to open documentation specific to this test in your browser. Alternatively visit https://nf-co.re/tools-docs/lint_tests/index.html and find your test to read more.

Find more information at: