The AnVIL project is an analysis, visualization, and informatics cloud-based space for data access, sharing and computing across large genomic-related data sets.
For R users with the limited computing resources, we introduce the AnVILWorkflow package. This package allows users to run workflows implemented in Terra without installing software, writing any workflow, or managing cloud resources. Terra is a cloud-based genomics platform and its computing resources rely on Google Cloud Platform (GCP).
Use of this package requires AnVIL and Google cloud computing billing accounts. Consult AnVIL training guides for details on establishing these accounts.
If you use AnVILWorkflow within Terra’s RStudio, you don’t need extra authentication and gcloud SDK. If you use this package locally, it requires gcloud SDK and the billing account used in Terra. You can [install][] the gcloud sdk.
Check whether your system has the installation with
AnVIL::gcloud_exists(). It should return TRUE
to use AnVILWorkflow package.
If it returns FALSE, install the gcloud SDK following
this script:
You need Terra account setup. Once you have your own Terra account, you need two pieces of information to use AnVILWorkflow package:
You can setup your working environment using
setCloudEnv() function like below. Provide the
input values with YOUR account information!
accountEmail <- "[email protected]"
billingProjectName <- "YOUR_BILLING_ACCOUNT"
setCloudEnv(accountEmail = accountEmail,
billingProjectName = billingProjectName)The remainder of this vignette assumes that an Terra account has been established and successfully linked to a Google cloud computing billing account.
Here is the table of major functions for three workflow steps - prepare, run, and check result.
| Steps | Functions | Description |
|---|---|---|
| Prepare | cloneWorkspace |
Copy the template workspace |
updateInput |
Take user’s inputs | |
| Run | runWorkflow |
Launch the workflow in Terra |
stopWorkflow |
Abort the submission | |
monitorWorkflow |
Monitor the status of your workflow run | |
| Result | getOutput |
List or download your workflow outputs |
You can find all the available workspaces you have access to using
AnVIL::avworkspaces() function. Workspaces manually curated
by this package are separately checked using
availableAnalysis() function. The values under
analysis column can be used for the analysis argument,
simplifying the cloning process. For this vignette, we use
"salmon".
> availableAnalysis()
analysis workspaceNamespace workspaceName configuration_namespace configuration_name
1 bioBakery waldronlab-terra-rstudio mtx_workflow_biobakery_version3_template mtx_workflow_biobakery_version3 mtx_workflow_biobakery_version3
2 salmon bioconductor-rpci-anvil Bioconductor-Workflow-DESeq2 bioconductor-rpci-anvil AnVILBulkRNASeq
3 pathml waldronlab-terra-rstudio pathml_stain_normalization_template PathML Preprocessing
description
1 Microbiome analysis using bioBakery
2 Trascript quantification from RNAseq using Salmon | Differential gene expression analysis using DESeq2
3 Stain normalization step of PathML pipelineWe will refer the existing workspaces, that you have access to and
want to use for your analysis, as ‘template’ workspaces. The first step
of using this package is cloning the template workspace using
cloneWorkspace function. Note that you need to provide a
unique name for the cloned workspace through
workspaceName argument. Once you successfully clone the
workspace, the function will return the name of the cloned workspace.
For example, the successfully execution of the below script will return
{YOUR_BILLING_ACCOUNT}/salmon_test.
If you want to clone any other workspace that you have access to but
is not curated by this pacakge, you can directly enter the name of the
target workspace as a templateName. For example, to clone
the Tumor_Only_CNV
workspace:
You can review the current inputs using currentInput
function. Below shows all the required and optional inputs for the
workflow.
config <- getWorkflowConfig(workspaceName = salmonWorkspaceName)
current_input <- currentInput(salmonWorkspaceName, config = config)
current_inputYou can modify/update inputs of your workflow using
updateInput function. To minimize the formatting issues, we
recommend to make any change in the current input table returned from
the currentInput function. Under the default
(dry=TRUE), the updated input table will be returned
without actually updating Terra/AnVIL. Set dry=FALSE, to
make a change in Terra/AnVIL.
You can launch the workflow using runWorkflow()
function. You need to specify the inputName of your
workflow. If you don’t provide it, this function will return the list of
input names you can use for your workflow.
Example error outputs:
runWorkflow(slamonWorkspaceName, config = config)
# You should provide the inputName from the followings:
# [1] "AnVILBulkRNASeq_set"
#> Error in runWorkflow(salmonWorkspaceName):The last three columns (status, succeeded,
and failed) show the submission and the result status.
The workspace Bioconductor-Workflow-DESeq2 is the
template workspace you cloned at the beginning using the
analysis = "salmon" argument in
cloneWorkspace() function. This template workspace has
already a history of the previous submissions, so we will check the
output examples in this workspace.
You can check all the output files from the most recently succeeded
submission using getOutput function. If you specify the
submissionId argument, you can get the output files of that
specific submission.
sessionInfo()
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#> [22] shiny_1.9.1 rlang_1.1.4 futile.logger_1.4.3
#> [25] AnVIL_1.17.20 cachem_1.1.0 yaml_2.3.10
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#> [31] dplyr_1.1.4 httpuv_1.6.15 DT_0.33
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#> [49] tibble_3.2.1 tidyselect_1.2.1 sys_3.4.3
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