phoenix | read pipeline

by CDCgov Python Version: v1.1.1 License: Apache-2.0

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

kandi X-RAY | phoenix Summary

phoenix is a Python library. phoenix has no bugs, it has a Permissive License and it has low support. However phoenix has 1 vulnerabilities and it build file is not available. You can download it from GitHub.

Describe the purpose of your project. Add additional sections as necessary to help collaborators and potential collaborators understand and use your project.

Support

Quality

Security

License

Reuse

Support

phoenix has a low active ecosystem.

It has 37 star(s) with 10 fork(s). There are 5 watchers for this library.

It had no major release in the last 12 months.

There are 4 open issues and 22 have been closed. On average issues are closed in 21 days. There are 2 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of phoenix is v1.1.1

Quality

phoenix has no bugs reported.

Security

phoenix has 1 vulnerability issues reported (0 critical, 1 high, 0 medium, 0 low).

License

phoenix is licensed under the Apache-2.0 License. This license is Permissive.

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

Reuse

phoenix releases are available to install and integrate.

phoenix has no build file. You will be need to create the build yourself to build the component from source.

Installation instructions, examples and code snippets are available.

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phoenix Key Features

No Key Features are available at this moment for phoenix.

phoenix Examples and Code Snippets

No Code Snippets are available at this moment for phoenix.

Community Discussions

No Community Discussions are available at this moment for phoenix.Refer to stack overflow page for discussions.

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

Vulnerabilities

No vulnerabilities reported

Install phoenix

There are several options for install if you do not already have it on your system:. Install Docker or Singularity >=3.8.0 for full pipeline reproducibility. Email HAISeq@cdc.gov, with the subject line "krakenDB invite request" to request access to the sharefile link and provide the email address to send invite to. Download the hash.k2d, opts.k2d, and taxo.k2d files needed for the kraken2 subworkflow of PHoeNIx from the CDC sharefile link. You CANNOT use a different krakenDB for this as it needs to match the ktax_map.k2 file that is included in the pipeline. At this time this is not downloadable via command line. Once downloaded the folder containing these files is passed to PHoeNIx via the --kraken2db. If you ran the v1.0.0-dev version of the pipeline and already downloaded the hash.k2d file there is no need to redownload it. The opts.k2d, and taxo.k2d are found in the phoenix/assets/databases folder. You can just copy these over into a new folder to pass to the PHoeNIx.
Install Nextflow (>=21.10.3). There are several options for install if you do not already have it on your system: Install into conda environment, which will require a version of Anaconda to be installed on your system. mamba create -n nextflow -c bioconda nextflow=21.10.6 If you prefer a to use curl or wget for install see the Nextflow Documentaiton
Install Docker or Singularity >=3.8.0 for full pipeline reproducibility.
Email HAISeq@cdc.gov, with the subject line "krakenDB invite request" to request access to the sharefile link and provide the email address to send invite to.
Download the hash.k2d, opts.k2d, and taxo.k2d files needed for the kraken2 subworkflow of PHoeNIx from the CDC sharefile link. You CANNOT use a different krakenDB for this as it needs to match the ktax_map.k2 file that is included in the pipeline. At this time this is not downloadable via command line. Once downloaded the folder containing these files is passed to PHoeNIx via the --kraken2db. If you ran the v1.0.0-dev version of the pipeline and already downloaded the hash.k2d file there is no need to redownload it. The opts.k2d, and taxo.k2d are found in the phoenix/assets/databases folder. You can just copy these over into a new folder to pass to the PHoeNIx.
(optional) If you installed nextflow via a conda environment activate the nextflow environment with:
Run PHoeNIx on a test sample loaded with the package with a single command: nextflow run cdcgov/phoenix -r v1.0.0 -profile <singularity/docker/custom>,test -entry PHOENIX --kraken2db $PATH_TO_DB
Start running your own analysis with a samplesheet! nextflow run cdcgov/phoenix -r v1.0.0 -profile <singularity/docker/custom> -entry PHOENIX --input <path_to_samplesheet.csv> --kraken2db $PATH_TO_DB

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 .

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