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