ngb set_srv|srv [<NGB_API_URL>] [options]
//Options:
//-t (--table) Print result as a human-readable table
//-j (--json) Print result as a JSON string
Description
Sets NGB server API URL. By default CLI uses localhost to call API. If one need to use CLI on a remote machine - appropriate URL should be set.
URL should be specified using the following format: http://{NGB_SERVER_NAME_OR_IP}:{NGB_SERVER_PORT}/catgenome
When URL is set - it would be stored and used next time CLI is launched
Example
//Sets remote server for CLI
ngb set_srv http://10.248.33.51:8080/catgenome
ngb version|v
Description
Prints CLI version to the console standard output.
ngb search|s [<QUERY>] [options]
//Options:
//-l (--like) If specified - search will be done using a substring. Be default strong equality comparison will be used
//-t (--table) Print result as a human-readable table
//-j (--json) Print result as a JSON string
Description
Searches for a specified string in reference and file names. By default, command will search for exactly equal name, if -l option is specified - a search query will used as a substring.
Example
//Search for all objects, that contain "vcf" substring in their names and ouput result as a human-readable table
ngb search -l vcf -t
//Search file, named exactly "sample_1.bam" and ouput result as a json string
ngb search sample_1.bam
ngb reg_ref|rr [<PATH_TO_GENOME_FASTA>] [options]
//Options:
//-n (--name) [value] Use specified value for reference sequence name. If not specified - fasta file name will be used. Should be unique and mustn't be a number (it will be recognized as ID).
//-t (--table) Print result as a human-readable table
//-j (--json) Print result as a JSON string
//-g (--genes) [value] Add a gene (gtf or gff) file to the reference. If file is already registered, it can be addressed by name or an identifier. Otherwise a path to the file should be provided.
//-ngc (--nogccontent) Disables calculation of GC-content for large scale reference view
//-pt (--pretty) Add pretty name to the reference genome
Description
Registers a specified reference sequence file. FASTA, FA, FNA files are accepted. GZip-compressed files are not supported. Path to local file and remote URL are accepted as a path to the reference. For local files, NGB will try to find a matching “fai” index in the folder with the reference, if index isn’t found it will be created. For remote references, “fai” index must be present on the remote source. NGB assumes that reference index will have the same name as reference with “fai” extension added. If reference path is “/opt/genomes/hg38.fa”, NGB will look for index file at path “/opt/genomes/hg38.fa.fai”.
Example
//Register reference, use "grch.38.fa" as name
ngb reg_ref /opt/genomes/grch.38.fa
//Register reference, use "grch38" as name
ngb rr /opt/genomes/grch.38.fa -n grch38
ngb list_ref|lr [options]
//Options:
//-t (--table) Print result as a human-readable table
//-j (--json) Print result as a JSON string
Description
Lists all reference sequences registered on the NGB server. The command output format is specified by -t and -j options, default format is Json.
Example
//List all reference files from the server
ngb list_ref -t
ngb del_ref|dr [<REFERENCE_NAME|REFERENCE_ID>] [options]
//Options:
//-t (--table) Print result as a human-readable table
//-j (--json) Print result as a JSON string
Description
Deletes a specified reference sequence file from NGB server. Reference file can be addressed by name or an identifier (retrieved from reg_ref command, at registration time or search command)
Example
//Delete reference with name "grch38"
ngb del_ref grch38
//Delete reference with id 1
ngb dr 1
ngb add_genes|ag [<REFERENCE_NAME|REFERENCE_ID>] [<FILE_NAME|FILE_ID|FILE_PATH>] [options]
//Options:
//-t (--table) Print result as a human-readable table
//-j (--json) Print result as a JSON string
Description
Adds a gene (GFF or GTF) file to the reference on NGB server. Reference file can be addressed by name or an identifier (retrieved from reg_ref command, at registration time or search command). If gene file is already registered on NGb server, it can be addressed by name or by an identifier. Otherwise a path to the gene file should be provided.
Example
//Add a regitered gene file to the reference with name "grch38"
ngb add_genes grch38 genes.gtf
//Add a new gene file to the reference with name ID "1"
ngb ag 1 /opt/tracks/genes.gtf
ngb remove_genes|rg [<REFERENCE_NAME|REFERENCE_ID>] [options]
//Options:
//-t (--table) Print result as a human-readable table
//-j (--json) Print result as a JSON string
Description
Removes any gene file from the reference on NGB server. Reference file can be addressed by name or an identifier (retrieved from reg_ref command, at registration time or search command)
Example
//Remove gene file from the reference with name "grch38"
ngb remove_genes grch38
//Remove gene file from the reference with ID "1"
ngb rg 1
ngb add_ann|an [<REFERENCE_NAME|REFERENCE_ID>] [<FILE_NAMES|FILE_IDS|FILE_PATHS>] [options]
//Options:
//-t (--table) Print result as a human-readable table
//-j (--json) Print result as a JSON string
Description
Adds an annotation (GFF, GTF, BED) file to the reference on NGB server. Reference file can be addressed by name or an identifier (retrieved from reg_ref command, at registration time or search command). If annotation file is already registered on NGb server, it can be addressed by name or by an identifier. Otherwise a path to the annotation file should be provided.
Example
//Add a regitered gene file to the reference with name "grch38"
ngb add_ann grch38 annotation.gtf
//Add a new annotation file to the reference with name ID "1"
ngb an 1 /opt/tracks/annotation.gtf
ngb remove_ann|ran [<REFERENCE_NAME|REFERENCE_ID>] [<FILE_NAMES|FILE_IDS|FILE_PATHS>] [options]
//Options:
//-t (--table) Print result as a human-readable table
//-j (--json) Print result as a JSON string
Description
Removes an annotation (GFF, GTF, BED) file from the reference on NGB server. Reference file can be addressed by name or an identifier (retrieved from reg_ref command, at registration time or search command). Annotation file can be addressed by name or by an identifier.
Example
//Remove an annotation file from the reference with name "grch38"
ngb remove_ann grch38 annotation.gtf
ngb reg_file|rf [<REFERENCE_NAME>|<REFERENCE_ID>] [<PATH_TO_NGS_FILE>] [options]
//Options:
//-n (--name) [value] Use specified value for file name. If not specified - filesystem name will be used. Should be unique and mustn't be a number (it will be recognized as ID).
//-ni (--no_index) Defines if a feature index should not be built during file registration (could be used to speed up registration process)
//-t (--table) Print result as a human-readable table
//-j (--json) Print result as a JSON string
//-pt (--pretty) Add pretty name to the file
Description
Registers a specified file. At least two arguments have to be specified:
Previously registered reference sequence file from NGB server. Reference file can be addressed by name or an identifier
Flesystem path to the file to be registered. BAM, VCF, GFF, GTF, BED, SEG, WIG, BED GRAPH files are accepted. GZipped files are also accepted in a format
Example
//Register file, use "sample.vcf" as name for reference with id 18
ngb reg_file 18 /opt/tracks/sample.vcf
//Register file, use "sample" as name for reference with name grch38
ngb reg_file grch38 /opt/tracks/sample.vcf -n sample
//Register indexed file, use "sample.bam" as name
ngb reg_file grch38 /opt/tracks/sample.bam?/opt/tracks/sample.bam.bai
//Register indexed file, use "sample.bam" as name, index for the BAM file is contained in the same directory as the BAM file
ngb reg_file grch38 /opt/tracks/sample.bam
//Register file with relative path
ngb reg_file hg19 ../tracks/sample.vcf
ngb del_file|df [<FILE_NAME>|<FILE_ID>] [options]
//Options:
//-t (--table) Print result as a human-readable table
//-j (--json) Print result as a JSON string
Description
Deletes a specified file from NGB server. File can be addressed by name or an identifier (retrieved from reg_file command, at registration time or search command)
Example
//Delete file with name "my_sample"
ngb del_file my_sample
//Delete file with id 18
ngb df 18
ngb index_file|if [<PATH_TO_NGS_FILE>] [options]
//Options:
//-t (--table) Print result as a human-readable table
//-j (--json) Print result as a JSON string
Description
Command builds a feature index for a specified file.
This can be useful to reindex a file or to create one if a file was registered with --no_index option.
Feature index is used for search and filtering capabilities for BED/VCF/GFF/GTF files.
File could be address by name or an identifier.
Note: this command is used for internal NGB indexing - it could not be used to index BAM/CRAM files
Example
//Build index for "sample.vcf" file
ngb index_file sample.vcf
//Build index for a file with identifier "18"
ngb if 18
ngb reg_dataset|rd [<REFERENCE_NAME>|<REFERENCE_ID>] [<DATASET_NAME>] [<files_names>|<files_ids>|<files_paths>] [options]
//Options:
//-p (--parent) [value] Specifies dataset parent for registration. Parent could addressed using a name or an indentifier
//-t (--table) Print result as a human-readable table
//-j (--json) Print result as a JSON string
//-pt (--pretty) Add pretty name to the dataset
Description
Registers a dataset. At least two arguments have to be specified:
Optionally a list of files to be added to a newly created dataset can be specified. Also a parent dataset could be specified to build a dtaset hierarchy
Files can be addressed:
Note: both options can be used in one command
Example
//Create new dataset with name "new_dataset" and use reference, named "grch38", do not add any files at the moment
ngb reg_dataset grch38 new_dataset
//Create new dataset with name "new_dataset" and use reference with id "1"
ngb rd 1 new_dataset
//Create new dataset with name "new_dataset" and reference "grch38", add two files
//(previously registered: "my_sample", "sample.vcf") to "new_dataset"
ngb rd grch38 new_dataset my_sample sample.vcf
//Create new dataset with name "new_dataset" and reference "grch38", register
//two files and add them to new_dataset
ngb rd grch38 new_dataset /opt/tracks/sample.vcf /opt/tracks/sample.bam /opt/tracks/sample.bam.bai
ngb add_dataset|add [<DATASET_NAME>|<DATASET_ID>] [<FILES_NAMES>|<FILES_IDS>|<FILES_PATHS>] [options]
//Options:
//-t (--table) Print result as a human-readable table
//-j (--json) Print result as a JSON string
Description
Adds file (-s) to a specified dataset. Dataset can be addressed by name or by an identifier (retrieved from reg_dataset command, at registration time, or search command)
Files can be addressed:
Note: both options can be used in one command
Example
//Add one file (named "my_sample") to dataset named "new_dataset"
ngb add_dataset new_dataset my_sample
//Add two files (named "my_sample" and "sample.vcf") to dataset named "new_dataset"
ngb add new_dataset my_sample sample.vcf
//Add three files (with identifiers: "1","2" and "3") to dataset with id "1"
ngb add 1 1 2 3
ngb remove_dataset|rmd [<DATASET_NAME>|<DATASET_ID>] [<FILE_NAME>|<FILE_ID>] [options]
//Options:
//-t (--table) Print result as a human-readable table
//-j (--json) Print result as a JSON string
Description
Removes a file from a specified dataset. Dataset can be addressed by name or by an identifier (retrieved from reg_dataset command, at registration time, or search command)
Only previously registered files (see reg_file command) can be addressed. A file name or an identifier can be used.
Example
//Remove one file (named "my_sample") from dataset named "new_dataset"
ngb remove_dataset new_dataset my_sample
//Remove two files (named "my_sample" and "sample.vcf") from dataset named "new_dataset"
ngb rmd new_dataset my_sample sample.vcf
//Remove three files (with identifiers: "1","2" and "3") from dataset with id "1"
ngb rmd 1 1 2 3
ngb move_dataset|md [<DATASET_NAME>|<DATASET_ID>] [options]
//Options:
//-p (--parent) Change the dataset's parent to this value
Description
Changes the dataset’s hierarchy. Without options the command will move the specified dataset to the top level od datasets’ hierarchy (dataset’s parent will be removed). If option -p (–parent) is specified the dataset’s parent will be changed to this option value.
Example
//Make dataset with ID 21 a top level dataset without a parent
ngb move_dataset 21
//Make dataset with name "data_parent" the parent dataset for a dataset with name "data_1"
ngb md data_1 -p data_parent
ngb list_dataset|ld [options]
//Options:
//-t (--table) Print result as a human-readable table
//-j (--json) Print result as a JSON string
//-p (--parent) List dataset's hierarchy structure for a specified by this option root dataset
Description
Lists datasets registered on NGB server. By default the command will output only top-level datasets without nested datasets. Dataset’s hierarchy may be loaded with an option ‘parent’: if a parent dataset is set, the command will output the parent itself and all nested datasets. Parent dataset may be addressed by name or ID.
Example
//List all top-level datasets from the server
ngb list_dataset
//List hierarchy tree for a dataset with the name "data_1"
ngb ld -p data_1
ngb del_dataset|dd [<DATASET_NAME>|<DATASET_ID>] [options]
//Options:
//-t (--table) Print result as a human-readable table
//-j (--json) Print result as a JSON string
//-f (--force) Allow to delete project with nested projects
Description
Deletes a specified dataset from NGB server. Dataset could be addressed by name or by an identifier (retrieved from reg_dataset command, at registration time, or search command)
Files that were added to a dataset are not deleted by this command, as soon they might be used (now or later) in other datasets.
Example
//Delete dataset, named "new_dataset"
ngb del_dataset new_dataset
//Delete dataset with id "1"
ngb dd 1
ngb url [<DATASET_NAME>|<DATASET_ID>] [<FILE_IDS>|<FILE_NAMES>] [options]
//Options:
//-loc (--location) chr:startIndex-endIndex Browse selected files on a specific location
//-loc (--location) chr Browse selected files on a specific chromosome
Description
Create an URL, that will open NGB browser with selected tracks, opened on a optionally specified position
Example
//Create URL for dataset with name 'data' and files with IDs 42, 45 and a file with name 'sample.vcf'
ngb url data 42 45 sample.vcf
//Create URL for dataset with ID '5' and a file with name 'sample.vcf' on a chromosome 1 on positions from 13476 to 23476
ngb url 5 sample.vcf -loc 1:13476-23476
//Create URL for dataset with name 'data' and a file with name 'sample.vcf' on a chromosome 1
ngb url data sample.vcf -loc 1
ngb sort [<ORIGINAL_FILE_PATH>] [<SORTED_FILE_PATH>] [options]
//Options:
//-m (--max_memory) [value] Specifies amount of memory in megabytes to use for sorting (default: 500). Since memory usage estimation is approximate, real memory usage may vary to some extend.
Description
Sorts given feature file. At least one argument should be specified:
Optional argument is:
.sorted. suffix in the name.
Sorted file will be automatically BGZip-compressed, if a target file name contains .gz postfix. If target file is not specified, file compression is inherited from the original file.Example ``` //Will sort given VCF file and place it in the same folder with original file (‘/samples/sample.vcf.gz’) with name: sample.sorted.vcf.gz ngb sort /samples/sample.vcf.gz
//Will sort given GFF file and place sorted file to the specified path ‘/samples/sample-sorted.gff’ ngb sort /samples/sample.gff /samples/sample-sorted.gff
//Will sort given BED file, compress result and place sorted file to the specified path ‘/samples/sorted_sample.bed.gz’ ngb sort /samples/unsorted.bed /samples/sorted_sample.bed.gz