https://github.com/heuermh/ensembl-mart-runner

Ensembl Mart runner.
https://github.com/heuermh/ensembl-mart-runner

bioinformatics

Last synced: 9 days ago
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Ensembl Mart runner.

• Host: GitHub
• URL: https://github.com/heuermh/ensembl-mart-runner
• Owner: heuermh
• License: lgpl-3.0
• Created: 2021-02-11T21:26:24.000Z (over 3 years ago)
• Default Branch: main
• Last Pushed: 2021-02-13T05:58:37.000Z (over 3 years ago)
• Last Synced: 2024-05-02T00:30:05.315Z (6 months ago)
• Topics: bioinformatics
• Language: Java
• Homepage:
• Size: 36.1 KB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: COPYING

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README

        
# ensembl-mart-runner

Ensembl Mart runner.

[![Maven Central](https://img.shields.io/maven-central/v/com.github.heuermh.ensemblmartrunner/ensembl-mart-runner.svg?maxAge=600)](http://search.maven.org/#search%7Cga%7C1%7Ccom.github.heuermh.ensemblmartrunner)

### Hacking ensembl-mart-runner

Install

 * JDK 1.8 or later, https://openjdk.java.net

 * Apache Maven 3.6.3 or later, https://maven.apache.org

To build

    $ mvn install

### Running ensembl-mart-runner

```

$ ensembl-mart-runner  --help

usage:

ensembl-mart-runner -i input.mart.xml.gz -o output.txt.gz

arguments:

   -a, --about  display about message [optional]

   -h, --help  display help message [optional]

   -i, --input-mart-xml-file [class java.io.File]  input Ensembl Mart XML file, default stdin [optional]

   -o, --output-text-file [class java.io.File]  output text file, default stdout [optional]

```

#### Compression

With `ensembl-mart-runner`, stdin and stdout should behave as expected, and files and streams

compressed with Zstandard (zstd), GZIP, BZip2, and block-compressed GZIP (BGZF) are handled

transparently. Use file extensions `.zst`, `.gz`, `.bz2`, and `.bgz` respectively to force the

issue, if necessary.