Kive | Archival and automation of bioinformatic pipelines and data | BPM library

by cfe-lab Python Version: v0.16.2 License: BSD-3-Clause

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

kandi X-RAY | Kive Summary

Kive is a Python library typically used in Healthcare, Pharma, Life Sciences, Automation, BPM applications. Kive has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can download it from GitHub.

We developed our new framework ("Kive") as a Django application. Django is a Python framework for developing web applications. Kive is built on a PostgreSQL relational database. The database records the digital "fingerprint" (md5 checksum) of every version of pipeline components and data sets, their locations in the filesystem, and their relations to each other. Executing a pipeline version on a data set is completely automated by Kive, which distributes jobs across computing resources (such as a computing cluster) and records every intermediate step in the database. Any intermediate step that can be re-used in subsequent pipeline versions will be loaded to minimize computing time. Read/write privileges to pipelines and data sets in Kive are specific to users and groups. Kive also features a web-based graphical user interface, including a point-and-click toolkit for assembling and running pipelines that is implemented in HTML5 Canvas and JavaScript. We used Kive to track versions of pipelines being developed in-house for processing and interpreting raw data sets from an Illumina MiSeq. This pipeline comprises 8 scripts written in Python, Ruby, and R. For more information, read about how we fixed a problem with [bad cycles in our example application][example]. You can see the active tasks in our [milestones].

Support

Quality

Security

License

Reuse

Support

Kive has a low active ecosystem.

It has 7 star(s) with 1 fork(s). There are 7 watchers for this library.

It had no major release in the last 12 months.

There are 81 open issues and 747 have been closed. On average issues are closed in 660 days. There are 3 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of Kive is v0.16.2

Quality

Kive has no bugs reported.

Security

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

License

Kive is licensed under the BSD-3-Clause License. This license is Permissive.

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

Reuse

Kive releases are available to install and integrate.

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

Installation instructions are not available. Examples and code snippets are available.

Top functions reviewed by kandi - BETA

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

Remap two fastq files
Update a dataset
Count the number of lines in a file
Count the number of files in the given file
Map two fastq files
Build a SMALL index
Check if the logger is set
Run a pipeline
Build dataset name
Bulk add new datasets
Convert alignments to counts
Parse alignment results
Clean the dataset_file
Create a new dataset
Parse command line arguments
Merge two reads
Build the root view
Checks the status of a slurm job
Reads the slurm file
Create a new archive
Plot size of jobs and memory
View of a dataset
Translate a sequence
Create a dataset
Compute pairwise pairwise alignment
Generate a coverage plot

Get all kandi verified functions for this library.

Kive Key Features

No Key Features are available at this moment for Kive.

Kive Examples and Code Snippets

No Code Snippets are available at this moment for Kive.

Community Discussions

Trending Discussions on Kive

Getting DOM node text with Puppeteer and headless Chrome

generate java classes from xsd importing other xsd from jar provided via catalog

QUESTION

Getting DOM node text with Puppeteer and headless Chrome

Asked 2019-Dec-31 at 18:58

I'm trying to use headless Chrome and Puppeteer to run our Javascript tests, but I can't extract the results from the page. Based on this answer, it looks like I should use page.evaluate(). That section even has an example that looks like what I need.

...

ANSWER

Answered 2017-Sep-13 at 16:50

I found three solutions to this problem, depending on how complicated your extraction is. The simplest option is a related function that I hadn't noticed: page.$eval(). It basically does what I was trying to do: combines page.$() and page.evaluate(). Here's an example that works:

Source https://stackoverflow.com/questions/46202985

QUESTION

generate java classes from xsd importing other xsd from jar provided via catalog

Asked 2019-Sep-24 at 08:15

I have some XSD where some share common definitions. I separated this common definitions into a separate XSD. So far I imported this common.xsd via relative paths across the projects. Thsi worked because all projects kived in the dame SCM repository.

Now I separate the projects into separate SCM repositories and I need to change the access to the common.xsd whch already lives in its own project (common-xml.jar).

I read tis: http://www.sagehill.net/docbookxsl/WriteCatalog.html and https://github.com/highsource/maven-jaxb2-plugin/wiki/Using-Catalogs but it does not work or me. The catalog is not used and xjc looks up the common.xsd in the path configuret in maven-jaxb2-plugin/configuration/schemaDirectory.

Even if I add maven-jaxb2-plugin/configuration/arg>-Dxml.catalog.verbosity=999 (or run mvn -X -Dxml.catalog.verbosity=999 ... it does not even tell to read the catalog file.

I only get output for the catalog file when I use the XML form and keep the element, but this leads to a timeout since the proxy does only allow browsers to connect to the internet (corporate policy).

I also read this answer Maven - Have an XSD as a dependency but it results in the same problem: xjc looks in the schema directory for the file to include but I want to avoid to extract it to a place where it might by checked in into the SCM accidentally...

How do I force xjc to lookup the location for the XSD to import somewere else?

this is my maven project configuration:

...

ANSWER

Answered 2019-Sep-24 at 08:15

sometimes reading carefully solves problems...

https://github.com/highsource/maven-jaxb2-plugin/wiki/Using-Catalogs:

Due to the bug in the XJC this only works if schemaLocation is not specified. So, unfortunately the following combination does not work at the moment.

PUBLIC "http://www.w3.org/1999/xlink" "w3c/1999/xlink.xsd"

Removing the schemaLocation attribute from the import solved the problem.

Source https://stackoverflow.com/questions/57977802

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

Vulnerabilities

No vulnerabilities reported

Install Kive

You can download it from GitHub.
You can use Kive like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.

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: