Command line API

Updated for basepair version 3.x

Command-line (CLI) bindings for Basepair's API. The CLI is a thin wrapper around the Python bindings, which are more fully-featured. If you can't accomplish something with the CLI, check the Python API instead.

All commands follow the pattern:

basepair <resource> <action> [options] -c /path/to/basepair.config.json

An outline of the contents on this page:

Creating a project
Creating a sample
Running an analysis
Downloading results
Managing pipelines and modules
Other commands

1. Creating a project

List your existing projects:

basepair project list -c /path/to/basepair.config.json

id     name          owner               last updated
------ ------------- ------------------- --------------------------
   784 Example Data  user@example.com    2022-03-11T14:01:19
  8611 Project 1     user@example.com    2022-05-15T19:20:06

Create a new project (requires a team ID, visible in your account settings):

basepair project create --name my_project --team 1234 -c /path/to/basepair.config.json

created: project with id 8658

Share a project with a collaborator:

basepair project update -u 8658 --team 1234 \
  --emails collaborator@example.com --perm view \
  -c /path/to/basepair.config.json

Permission levels: view, edit, admin.

2. Creating a sample

Create a sample within your project, specifying the sample name, data type, genome, and file locations:

basepair sample create --project 8658 \
  --name Untreat1 \
  --type atac-seq \
  --genome hg19 \
  --file1 /path/to/read_1.fastq.gz \
  --file2 /path/to/read_2.fastq.gz \
  -c /path/to/basepair.config.json

created: sample with id 75042
Sample id: 75042
Creating upload read_1.fastq.gz
  created: upload with id 138264
Creating upload read_2.fastq.gz
  created: upload with id 138265
Sample created successfully.

To see all available data types:

basepair sample create -h

Supported types: atac-seq, chip-seq, crispr, cutnrun, cutntag, dna-seq, other, panel, rna-seq, scaleBio_scRNA, scrna-seq, small-rna-seq, snap-chip, wes, wgs.

To list available genomes:

basepair genome list -c /path/to/basepair.config.json

List all samples in a project:

basepair sample list --project 8658 -c /path/to/basepair.config.json

Get details for a specific sample:

basepair sample get -u 75042 -c /path/to/basepair.config.json

Update a sample (e.g. change genome or data type):

basepair sample update -u 75042 --genome hg38 -c /path/to/basepair.config.json

3. Running an analysis

Run an analysis by specifying the project, sample, and pipeline:

basepair analysis create --project 8658 \
  --sample 75042 \
  --pipeline 19 \
  -c /path/to/basepair.config.json

created: analysis 91182 with sample id(s) 75042

To list all available pipelines:

basepair pipeline list -c /path/to/basepair.config.json

Run a differential-expression analysis with multiple samples and controls:

basepair analysis create \
  --sample 75042 75043 75044 \
  --control 75050 75051 \
  --pipeline 8 \
  -c /path/to/basepair.config.json

Override per-node parameters (format: node_id:argument:value):

basepair analysis create \
  --sample 75042 \
  --pipeline 8 \
  --params deseq2:padj:0.01 deseq2:lfc:1.5 \
  -c /path/to/basepair.config.json

List analyses in a project:

basepair analysis list --project 8658 -c /path/to/basepair.config.json

Restart a completed or failed analysis:

basepair analysis reanalyze -u 91182 -c /path/to/basepair.config.json

Stop a running analysis:

basepair analysis terminate -u 91182 -c /path/to/basepair.config.json

4. Downloading results

Download all files for a given analysis:

basepair analysis download -u 91182 -c /path/to/basepair.config.json

Download only the deduplicated alignment BAM files (tagged dedup):

basepair analysis download -u 91182 \
  --tags dedup \
  --tagkind subset \
  -c /path/to/basepair.config.json

Download only BAM files, saving to a specific directory:

basepair analysis download -u 91182 \
  --tags bam \
  --tagkind exact \
  -o ./bams \
  -c /path/to/basepair.config.json

Download everything except log files:

basepair analysis download -u 91182 \
  --tags log \
  --tagkind diff \
  -c /path/to/basepair.config.json

Tag filter modes:

Mode	Behaviour
`exact`	Only files whose tag set exactly matches the provided tags
`subset`	Any file that has at least one of the provided tags
`diff`	Exclude files that have the provided tag

To list all files of an analysis with their tags:

basepair analysis get -u 91182 -c /path/to/basepair.config.json

Download the execution log:

basepair analysis download-log -u 91182 -o ./logs -c /path/to/basepair.config.json

5. Managing pipelines and modules

Create a pipeline from a YAML definition file:

basepair pipeline create --file /path/to/pipeline.yaml -c /path/to/basepair.config.json

Update an existing pipeline:

basepair pipeline update -u 380 --file /path/to/pipeline.yaml -c /path/to/basepair.config.json

Create a module:

basepair module create --file /path/to/module.yaml -c /path/to/basepair.config.json

List modules for a pipeline:

basepair module list --pipeline 19 -c /path/to/basepair.config.json

6. Other commands

Get JSON output — add --json to any get or list command:

basepair analysis list --project 8658 --json -c /path/to/basepair.config.json
basepair sample get -u 75042 --json -c /path/to/basepair.config.json

Download a file by ID:

basepair file download -u 456789 -o ./downloads -c /path/to/basepair.config.json

Delete resources:

basepair analysis delete -u 91182 -c /path/to/basepair.config.json
basepair sample delete -u 75042 -c /path/to/basepair.config.json

1. Creating a project​

2. Creating a sample​

3. Running an analysis​

4. Downloading results​

5. Managing pipelines and modules​

6. Other commands​

On this page