Managing Data Libraries

Querying data libraries

list_libraries displays information about the data libraries and their contents in a Galaxy instance:

nebulizer list_libraries GALAXY [ LIBRARY[/PATH...] ]

By default all the libraries in the instance are listed; if the name of a data library (LIBRARY) is included then the datasets and folders in that library are listed. If a PATH (names of subfolders separated by /) is supplied then the contents of the matching folder are displayed.

For example: listing the data libraries in Galaxy main:

nebulizer list_libraries https://usegalaxy.org

List the contents of the “Tutorials” data library:

nebulizer list_libraries https://usegalaxy.org Tutorials

List the contents of the “ChIP_seq (Reb1)” folder in the “Tutorials” data library:

nebulizer list_libraries https://usegalaxy.org "Tutorial/ChIP_seq (Reb1)"
  • -l: list extended information about libraries, folders and datasets

Creating and populating data libraries

create_library creates a new data library:

nebulizer create_library GALAXY LIBRARY_NAME [--description DESCRIPTION] [--synopsis SYNOPSIS]

create_library_folder creates a new folder in an existing data library or folder:

nebulizer create_library_folder GALAXY LIBRARY_NAME/[PATH]

For example: create a data library called NGS data and a folder Run 21 within it:

nebulizer create_library GALAXY "NGS data 2020" \
  --description="Sequencing data analysed in 2020"
nebulizer create_library_folder GALAXY "NGS data 2020/Run 21"

add_library_datasets uploads datasets to a data library:

nebulizer add_library_datasets GALAXY LIBRARY_NAME/PATH FILE [FILE...]
  • --file-type: specify the Galaxy data type to assign to datasets
  • --dbkey: specify the dbkey for the datasets
  • --server: upload files from the filesystem of the server that Galaxy is running on (default is to upload from the local filesystem)
  • --link: create symlinks to the files on the server (if --server is also specified)

For example, add Fastq files to a data library folder:

nebulizer add_library_datasets galaxy "NGS data/Run 21" ~/Sample1_R*.fq \
  --file-type=fastqsanger --dbkey=hg38