jvarkit

ScanLabGuru

scan the files stored in labguru

Usage

Usage: java -jar dist/scanlabguru.jar  [options] Files
Usage: scanlabguru [options] Files
  Options:
  * --api-key, -A
      API key (can be a string or an existing file
      Default: <empty string>
    --base
      Labguru base URI.
      Default: https://cle.inserm.fr
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
    --version
      print version and exit

Keywords

• labguru
• lims
• vcf
• sam

Compilation

Requirements / Dependencies

• java compiler SDK 11. Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew scanlabguru

The java jar file will be installed in the dist directory.

Creation Date

20240325

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/labguru/ScanLabGuru.java

Contribute

• Issue Tracker: http://github.com/lindenb/jvarkit/issues
• Source Code: http://github.com/lindenb/jvarkit

License

The project is licensed under the MIT license.

Citing

Should you cite scanlabguru ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030

Motivation: scan the files stored in labguru

usage:

jvarkit -jar jvarkit.jar scanlabguru -A api.txt <projectid1> <projectid2> <projectid3>

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