Run Terra pipelines via command line

You can run Terra pipelines via the command line by installing the altocumulus package.

Install altocumulus for Broad users

Request an UGER node:

reuse UGER
qrsh -q interactive -l h_vmem=4g -pe smp 8 -binding linear:8 -P regevlab

The above command requests an interactive shell using the regevlab project with 4G memory per thread, 8 threads. Feel free to change the memory, thread, and project parameters.

Add conda to your path:

reuse Anaconda3

Activate the alto virtual environment:

source activate /seq/regev_genome_portal/conda_env/cumulus

Install altocumulus for non-Broad users

  1. Make sure you have conda installed. If you haven’t installed conda, use the following commands to install it on Linux:

    wget .
    bash -p /home/foo/miniconda3
    mv /home/foo/miniconda3

    where /home/foo/miniconda3 should be replaced by your own folder holding Miniconda3.

Or use the following commdands for MacOS installation:

curl -O curl -O
bash -p /Users/foo/miniconda3
mv /Users/foo/miniconda3

where ``/Users/foo/miniconda3`` should be replaced by your own folder holding Miniconda3.
  1. Create a conda environment named “alto” and install altocumulus:

    conda create -n alto -y pip
    source activate alto
    git clone
    cd altocumulus
    pip install -e .

When the installation is done, type alto fc_run -h in terminal to see if you can see the help information.

Run Terra workflows via alto fc_run

alto fc_run runs a Terra method. Features:

  • Uploads local files/directories in your inputs to a Google Cloud bucket updates the file paths to point to the Google Cloud bucket.

    Your sample sheet can point to local file paths. In this case, alto run will take care of uploading directories (e.g. fastq directories) and modifying the sample sheet to point to a Google Cloud bucket.

  • Creates or uses an existing workspace.

  • Uses the latest version of a method unless the method version is specified.


Required options are in bold.

Name Description
--method <METHOD>
Specify a Terra workflow <METHOD> to use.
<METHOD> is of format Namespace/Name (e.g. cumulus/cellranger_workflow).
A snapshot version number can optionally be specified (e.g. cumulus/cellranger_workflow/4); otherwise the latest snapshot of the method is used.
--workspace <WORKSPACE>
Specify which Terra workspace <WORKSPACE> to use.
<WORKSPACE> is also of format Namespace/Name (e.g. foo/bar). The workspace will be created if it does not exist.
--inputs <WDL_INPUTS>
Specify the WDL input JSON file to use.
It can be a local file, a JSON string, or a Google bucket URL directing to a remote JSON file.
--bucket-folder <folder>
Store inputs to <folder> under workspace’s google bucket.
-o <updated_json>
--upload <updated_json>
Upload files/directories to Google bucket of the workspace, and generate an updated input JSON file (with local paths replaced by Google bucket URLs) to <updated_json> on local machine.
Disable Terra cache calling


This example shows how to use alto fc_run to run cellranger_workflow to extract gene-count matrices from sequencing output.

  1. Prepare your sample sheet example_sample_sheet.csv as the following:


    where /my-local-path is the top-level directory of your BCL files on your local machine.

    Note that sample_1, sample_2, sample_3, and sample_4 are sequenced on 2 flowcells.

  2. Prepare your JSON input file inputs.json for cellranger_workflow:

        "cellranger_workflow.input_csv_file" : "/my-local-path/sample_sheet.csv",
        "cellranger_workflow.output_directory" : "gs://url/outputs",
        "cellranger_workflow.delete_input_bcl_directory": true

    where gs://url/outputs is the folder on Google bucket of your workspace to hold output.

  3. Run the following command to kick off your Terra workflow:

    alto fc_run -m cumulus/cellranger_workflow -i inputs.json -w myworkspace_namespace/myworkspace_name -o inputs_updated.json

    where myworkspace_namespace/myworkspace_name should be replaced by your workspace namespace and name.

Upon success, alto fc_run returns a URL pointing to the submitted Terra job for you to monitor.

If for any reason, your job failed. You could rerun it without uploading files again via the following command:

alto fc_run -m cumulus/cellranger_workflow -i inputs_updated.json -w myworkspace_namespace/myworkspace_name

because inputs_updated.json is the updated version of inputs.json with all local paths being replaced by their corresponding Google bucket URLs after uploading.