Command Line API

Modified on Tue, 24 May, 2022 at 10:53 AM

Updated for basepair version 2.0.0

Command Line (CLI) bindings for Basepair's API. The CLI bindings are just a wrapper around the Python bindings, which are more fully featured. So if there is something you cannot do via the command line, then check out the Python API. An outline of the contents on this page:

Creating a project
Creating a sample
Running an analysis
Downloading results

1. Creating a project

First, check your available projects. Your initial Basepair account starts with two existing projects, one containing example data and an empty "Project 1":

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

id  name          owner fullname    last updated                visibility
----  ------------  ----------------  --------------------------  ------------
 784  Example Data  Amit Sinha        2022-03-11T14:01:19.850152  public
8611  Project 1     Username     2022-05-15T19:20:06.378477  private

Now, create a new project:

basepair project create --name new_project -c /path/to/basepair.config.json

created: project with id 8658

2. Creating a sample

Create a sample within your new project, specifying the sample name, data type, genome of interest, and location of data files:

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 and other available metadata:

basepair sample create -h

To see all available genomes:

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

You can check the samples in a project with:

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

3. Running an analysis

To run an analysis, such as ATAC-seq alignment with bowtie2 in this case, specify 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 see all available pipelines:

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

4. Downloading results

Download the entire analysis directory tree and all associated files to the current directory by specifying the analysis ID:

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

To download only the alignment BAM and BAM index files from an analysis and the associated directory tree:

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

To see all files of an analysis and their associated tags:

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

To download only the heatmaps and bigwig track from an analysis:

basepair analysis download -u 90747 \
--tags png igv \
--tagkind subset \
-c /path/to/basepair.config.json