# Latest **URL:** https://help.anvilproject.org/latest.md?page=1 [Latest](https://help.anvilproject.org/latest.md) · [Categories](https://help.anvilproject.org/categories.md) · [Tags](https://help.anvilproject.org/tags.md) **Page:** 2 --- ## [Gaining access to and processing dbGaP datasets which are unavailable on Anvil Data Explorer](https://help.anvilproject.org/t/gaining-access-to-and-processing-dbgap-datasets-which-are-unavailable-on-anvil-data-explorer/366)
**Author:** [@nuwan](https://help.anvilproject.org/u/nuwan)\ **Replies:** 1\ **Last updated:** [January 7, 2026, 4:27pm UTC](https://help.anvilproject.org/t/gaining-access-to-and-processing-dbgap-datasets-which-are-unavailable-on-anvil-data-explorer/366 "2026-01-07T16:27:34Z")
Is there a recommended process for accessing datasets that are not available on AnVIL? For example, let’s say I want to process eMerge PGx data on the AnVIL and I have approval for the dataset. Currently, that data is no… --- ## [AnVIL Demos: AnVIL Data Explorer: Building and Exporting Dataset Cohorts on December 17, 2025](https://help.anvilproject.org/t/anvil-demos-anvil-data-explorer-building-and-exporting-dataset-cohorts-on-december-17-2025/363)
**Author:** [@nakucher](https://help.anvilproject.org/u/nakucher)\ **Replies:** 4\ **Last updated:** [December 17, 2025, 4:00pm UTC](https://help.anvilproject.org/t/anvil-demos-anvil-data-explorer-building-and-exporting-dataset-cohorts-on-december-17-2025/363 "2025-12-17T16:00:23Z")
Topic: AnVIL Data Explorer: Building and Exporting Dataset Cohorts December 17, 2025 at 10:00 AM ET on Zoom 10:00 AM - 10:30 AM ET – Demo on AnVIL Join us for a demo of the AnVIL Data Explorer, a cohort bu… --- ## [Phs003067 data access](https://help.anvilproject.org/t/phs003067-data-access/364)
**Author:** [@ddvo](https://help.anvilproject.org/u/ddvo)\ **Replies:** 1\ **Last updated:** [December 12, 2025, 6:38pm UTC](https://help.anvilproject.org/t/phs003067-data-access/364 "2025-12-12T18:38:24Z")
Hi, our lab has been granted access to the phs003067.v2.p2 accession but we are unable to access the data through Terra and AnVIL. From other posts in the forum, it appears that this might be an issue with the data also … --- ## [Workflow "out of memory" issue](https://help.anvilproject.org/t/workflow-out-of-memory-issue/350)
**Author:** [@yxhan](https://help.anvilproject.org/u/yxhan)\ **Replies:** 5\ **Last updated:** [December 2, 2025, 5:46pm UTC](https://help.anvilproject.org/t/workflow-out-of-memory-issue/350 "2025-12-02T17:46:12Z")
Dear AnVIL Community, I’d like to learn your experience with WholeGenomeGermlineSingleSample v3.3.4 workflow. I consistently encounter “out of memory” errors at the MarkDuplicates stage. From my understanding, the memo… --- ## [AnVIL Demos: AnVIL meets the new security requirements under the Genomic Data Sharing Policy on November 19, 2025](https://help.anvilproject.org/t/anvil-demos-anvil-meets-the-new-security-requirements-under-the-genomic-data-sharing-policy-on-november-19-2025/358)
**Author:** [@nakucher](https://help.anvilproject.org/u/nakucher)\ **Replies:** 1\ **Last updated:** [November 19, 2025, 3:51pm UTC](https://help.anvilproject.org/t/anvil-demos-anvil-meets-the-new-security-requirements-under-the-genomic-data-sharing-policy-on-november-19-2025/358 "2025-11-19T15:51:06Z")
Topic: AnVIL meets the new security requirements under the Genomic Data Sharing Policy November 19, 2025 at 10:00 AM ET on Zoom 10:00 AM - 10:30 AM ET – Demo on AnVIL On October 4, 2024, NIH updated its Ge… --- ## [How to download data to institutional cluster](https://help.anvilproject.org/t/how-to-download-data-to-institutional-cluster/359)
**Author:** [@Wesley\_Au](https://help.anvilproject.org/u/Wesley_Au)\ **Replies:** 1\ **Last updated:** [November 17, 2025, 3:20pm UTC](https://help.anvilproject.org/t/how-to-download-data-to-institutional-cluster/359 "2025-11-17T15:20:26Z")
I’m wondering if there is functionality to download data that I have access to to my institutional cluster using the metadata file. --- ## [AnVIL Demos: Introducing the All of Us + AnVIL Imputation Service on October 15, 2025](https://help.anvilproject.org/t/anvil-demos-introducing-the-all-of-us-anvil-imputation-service-on-october-15-2025/354)
**Author:** [@nakucher](https://help.anvilproject.org/u/nakucher)\ **Replies:** 1\ **Last updated:** [October 15, 2025, 4:10pm UTC](https://help.anvilproject.org/t/anvil-demos-introducing-the-all-of-us-anvil-imputation-service-on-october-15-2025/354 "2025-10-15T16:10:22Z")
Topic: Introducing the All of Us and AnVIL Imputation Service October 15, 2025 at 10:00 AM ET on Zoom 10:00 AM - 10:30 AM ET – Demo on AnVIL Learn how to use the All of Us + AnVIL Imputation Service, a too… --- ## [How can I find single cell datasets to analyze in AnVIL?](https://help.anvilproject.org/t/how-can-i-find-single-cell-datasets-to-analyze-in-anvil/349)
**Author:** [@SMO](https://help.anvilproject.org/u/SMO)\ **Replies:** 1\ **Last updated:** [September 17, 2025, 8:12pm UTC](https://help.anvilproject.org/t/how-can-i-find-single-cell-datasets-to-analyze-in-anvil/349 "2025-09-17T20:12:35Z")
A user wrote in recently asking how to find single cell sequencing datasets to analyze in AnVIL. One thought might be to search for file extensions such as .h5, .h5ad or .mtx in AnVIL’s Data Explorer. --- ## [AnVIL Demo: Galaxy Learning and Modeling (GLEAM): Machine Learning accessible and best practices on September 17, 2025](https://help.anvilproject.org/t/anvil-demo-galaxy-learning-and-modeling-gleam-machine-learning-accessible-and-best-practices-on-september-17-2025/348)
**Author:** [@nakucher](https://help.anvilproject.org/u/nakucher)\ **Replies:** 1\ **Last updated:** [September 17, 2025, 2:49pm UTC](https://help.anvilproject.org/t/anvil-demo-galaxy-learning-and-modeling-gleam-machine-learning-accessible-and-best-practices-on-september-17-2025/348 "2025-09-17T14:49:10Z")
Join our next AnVIL Demo! Topic: Galaxy Learning and Modeling (GLEAM): Machine Learning accessible and best practices September 17, 2025 at 10:00 AM ET on Zoom 11:00 AM - 11:30 AM ET – Demo on AnVIL Learn… --- ## [“Retry with More Memory” feature for Terra workflow](https://help.anvilproject.org/t/retry-with-more-memory-feature-for-terra-workflow/347)
**Author:** [@yxhan](https://help.anvilproject.org/u/yxhan)\ **Replies:** 3\ **Last updated:** [September 17, 2025, 1:18pm UTC](https://help.anvilproject.org/t/retry-with-more-memory-feature-for-terra-workflow/347 "2025-09-17T13:18:27Z")
\*\*Wondering why the “Retry with More Memory” feature is “Disabled“ for the Terra workfow “1-WholeGenomeGermlineSingleSample”. So should we pre-set the memory by setting the “memory\_multiplier“ values?\*\* \*\*Thanks in adv… --- ## [Help on Rstudio](https://help.anvilproject.org/t/help-on-rstudio/346)
**Author:** [@Jacob\_Ayembilla](https://help.anvilproject.org/u/Jacob_Ayembilla)\ **Replies:** 1\ **Last updated:** [September 15, 2025, 1:33pm UTC](https://help.anvilproject.org/t/help-on-rstudio/346 "2025-09-15T13:33:35Z")
My RStudio in Terra is giving me this: approaching session memory limit. session memory used 56, 498MiB, limit: 59648. system memory used 54566 out of 60278 (9% free). I am a newcomer and l am on Google Cloud $300 credit… --- ## [gTEX data download for Azure user](https://help.anvilproject.org/t/gtex-data-download-for-azure-user/345)
**Author:** [@Minsu\_Cho](https://help.anvilproject.org/u/Minsu_Cho)\ **Replies:** 1\ **Last updated:** [September 8, 2025, 5:34pm UTC](https://help.anvilproject.org/t/gtex-data-download-for-azure-user/345 "2025-09-08T17:34:53Z")
Hello all. I am aware the default terra gtex download is from google cloud. My institution though provides Microsoft Azure, not Google Cloud, so I am unable to create a Google billing project to download data. I would … --- ## [Set up access permission to subfolders of a google storage (gs)? Is it possible?](https://help.anvilproject.org/t/set-up-access-permission-to-subfolders-of-a-google-storage-gs-is-it-possible/344)
**Author:** [@truckload](https://help.anvilproject.org/u/truckload)\ **Replies:** 1\ **Last updated:** [September 8, 2025, 4:37pm UTC](https://help.anvilproject.org/t/set-up-access-permission-to-subfolders-of-a-google-storage-gs-is-it-possible/344 "2025-09-08T16:37:22Z")
Our lab has data resulted from several research projects on AnVIL. While the top analysts would need access to all of them, some individuals only work on one of the project. I am wondering how to organized the data so t… --- ## [AnVIL Demo: Open Discussion Forum on July 16, 2025](https://help.anvilproject.org/t/anvil-demo-open-discussion-forum-on-july-16-2025/314)
**Author:** [@SMO](https://help.anvilproject.org/u/SMO)\ **Replies:** 4\ **Last updated:** [August 25, 2025, 4:02pm UTC](https://help.anvilproject.org/t/anvil-demo-open-discussion-forum-on-july-16-2025/314 "2025-08-25T16:02:15Z")
Join our next AnVIL Demo! Topic: Open Discussion Forum July 16, 2025 at 10:00 AM EST (your time zone) on Zoom 10:00 AM - 11:00 AM EST – Open Forum Discussion In this meeting, we’ll have an open forum to chat about AnVI… --- ## [dbGaP access - sequencing data](https://help.anvilproject.org/t/dbgap-access-sequencing-data/289)
**Author:** [@AKKB](https://help.anvilproject.org/u/AKKB)\ **Replies:** 10\ **Last updated:** [August 25, 2025, 3:33pm UTC](https://help.anvilproject.org/t/dbgap-access-sequencing-data/289 "2025-08-25T15:33:39Z")
Hello We are seeking access to sequencing data from a set of iPSCs provided by the California’s Stem Cell Agency (CIRM), which are available through your database. Recently, we had our request for data access approved … --- ## [Using NIH Controlled-access Data on AnVIL Under the Updated NIH GDS Policy](https://help.anvilproject.org/t/using-nih-controlled-access-data-on-anvil-under-the-updated-nih-gds-policy/329)
**Author:** [@SMO](https://help.anvilproject.org/u/SMO)\ **Replies:** 0\ **Last updated:** [August 19, 2025, 2:04pm UTC](https://help.anvilproject.org/t/using-nih-controlled-access-data-on-anvil-under-the-updated-nih-gds-policy/329 "2025-08-19T14:04:20Z")
This post is based on common questions we receive through the help@lists.anvilproject.org email. It is shared here so the wider community can benefit. We’ll update this post as new guidance or resources become available. … --- ## [AnVIL Demo: Open Discussion Forum on August 20, 2025](https://help.anvilproject.org/t/anvil-demo-open-discussion-forum-on-august-20-2025/331)
**Author:** [@nakucher](https://help.anvilproject.org/u/nakucher)\ **Replies:** 1\ **Last updated:** [August 20, 2025, 3:38pm UTC](https://help.anvilproject.org/t/anvil-demo-open-discussion-forum-on-august-20-2025/331 "2025-08-20T15:38:16Z")
​Join our next AnVIL Demo! Topic: Open Discussion Forum August 20, 2025 at 10:00 AM EST on Zoom 11:00 AM - 12:00 PM ET – Open Q&A We’ll open up the floor to questions about the demo presented, and will have AnVIL and Te… --- ## [Permissions and accounts for getting started / first project](https://help.anvilproject.org/t/permissions-and-accounts-for-getting-started-first-project/328)
**Author:** [@sbplaisier](https://help.anvilproject.org/u/sbplaisier)\ **Replies:** 1\ **Last updated:** [August 18, 2025, 4:09pm UTC](https://help.anvilproject.org/t/permissions-and-accounts-for-getting-started-first-project/328 "2025-08-18T16:09:48Z")
Hello, I am new to AnVIL and had some basic questions. I am a staff scientist and a billing account was set up for our lab tied to my PI. I was able to log in and see that our billing account exists on STRIDES and get… --- ## [Terra warp-pipelines out of memory issue](https://help.anvilproject.org/t/terra-warp-pipelines-out-of-memory-issue/321)
**Author:** [@yxhan](https://help.anvilproject.org/u/yxhan)\ **Replies:** 5\ **Last updated:** [July 25, 2025, 1:40pm UTC](https://help.anvilproject.org/t/terra-warp-pipelines-out-of-memory-issue/321 "2025-07-25T13:40:25Z")
Hello~ I am using the Terra workflow \[warp-pipelines/1-WholeGenomeGermlineSingleSample\] to try the variants calling. The input files are the uBAMs, which size ranges from 4GB - 40GB for each. As we did high depth WGS, t… --- ## [Username Change Request](https://help.anvilproject.org/t/username-change-request/320)
**Author:** [@yxhan](https://help.anvilproject.org/u/yxhan)\ **Replies:** 6\ **Last updated:** [July 23, 2025, 7:19pm UTC](https://help.anvilproject.org/t/username-change-request/320 "2025-07-23T19:19:06Z")
Hello, I’d like to request a username change or get in touch with a site moderator. Could someone assist me? Thanks! --- ## [AnVIL Demo: Getting Started on AnVIL on June 18, 2025](https://help.anvilproject.org/t/anvil-demo-getting-started-on-anvil-on-june-18-2025/310)
**Author:** [@nakucher](https://help.anvilproject.org/u/nakucher)\ **Replies:** 0\ **Last updated:** [June 12, 2025, 3:06pm UTC](https://help.anvilproject.org/t/anvil-demo-getting-started-on-anvil-on-june-18-2025/310 "2025-06-12T15:06:31Z")
​​Join our next AnVIL Demo! Topic: Getting Started on AnVIL June 18, 2025 at 10:00 AM EST (your time zone) on Zoom 11:00 AM - 11:30 AM ET – Demo on AnVIL In this demo, Natalie Kucher from the Johns Hopkins University wi… --- ## [Bioconductor 3.20, learnr, and ggplot in rendered .Rmd document](https://help.anvilproject.org/t/bioconductor-3-20-learnr-and-ggplot-in-rendered-rmd-document/308)
**Author:** [@Sayumi](https://help.anvilproject.org/u/Sayumi)\ **Replies:** 0\ **Last updated:** [June 10, 2025, 5:05pm UTC](https://help.anvilproject.org/t/bioconductor-3-20-learnr-and-ggplot-in-rendered-rmd-document/308 "2025-06-10T17:05:03Z")
Hello, I have been running into an issue where code that generates a plot using ggplot2 in a rendered learnr .Rmd document times out and cannot be run no matter how simple or complex the plot is. This issue doesn’t occ… --- ## [Gcloud with start up script on jupyter](https://help.anvilproject.org/t/gcloud-with-start-up-script-on-jupyter/304)
**Author:** [@camancuso](https://help.anvilproject.org/u/camancuso)\ **Replies:** 7\ **Last updated:** [June 2, 2025, 2:21pm UTC](https://help.anvilproject.org/t/gcloud-with-start-up-script-on-jupyter/304 "2025-06-02T14:21:57Z")
I’m trying to copy some files from one terra gcp bucket to a computational environment that I spin up. I’m trying to use the command (made up bucket id) gcloud storage cp --recursive "gs://fc-1111-111-1111-111111/module… --- ## [Which R package to use, AnVIL or AnVILGCP?](https://help.anvilproject.org/t/which-r-package-to-use-anvil-or-anvilgcp/306)
**Author:** [@truckload](https://help.anvilproject.org/u/truckload)\ **Replies:** 1\ **Last updated:** [May 22, 2025, 10:03pm UTC](https://help.anvilproject.org/t/which-r-package-to-use-anvil-or-anvilgcp/306 "2025-05-22T22:03:14Z")
Hi. I recently used some functions in the R package “AnVIL”. But my code received many warning about the function related to methods being deprecated (copied at the end of the message). So I changed to the suggested fun… --- ## [Allow easy file management via command line, for Rstudio and Jupyter environment](https://help.anvilproject.org/t/allow-easy-file-management-via-command-line-for-rstudio-and-jupyter-environment/305)
**Author:** [@truckload](https://help.anvilproject.org/u/truckload)\ **Replies:** 1\ **Last updated:** [May 21, 2025, 7:09pm UTC](https://help.anvilproject.org/t/allow-easy-file-management-via-command-line-for-rstudio-and-jupyter-environment/305 "2025-05-21T19:09:40Z")
Terra allows us to run Rstudio and Jupyter notebooks. It seems to me that the two GUI interfaces are mutually exclusive. If I starts a VM with Rstudio, I don’t have the terminal tab on the menu on the right side. The … --- ## [Join us at the AnVIL Community Conference 2025 in Nashville, TN!](https://help.anvilproject.org/t/join-us-at-the-anvil-community-conference-2025-in-nashville-tn/299)
**Author:** [@nakucher](https://help.anvilproject.org/u/nakucher)\ **Replies:** 0\ **Last updated:** [May 1, 2025, 1:32pm UTC](https://help.anvilproject.org/t/join-us-at-the-anvil-community-conference-2025-in-nashville-tn/299 "2025-05-01T13:32:37Z")
We are thrilled to announce the AnVIL Community Conference on September 4-5, 2025 in Nashville, TN with an opening networking event on the evening of September 3, 2025. This event is a key event for researchers in the ge… --- ## [Push docker containers on google container registry or artifact registry](https://help.anvilproject.org/t/push-docker-containers-on-google-container-registry-or-artifact-registry/238)
**Author:** [@truckload](https://help.anvilproject.org/u/truckload)\ **Replies:** 11\ **Last updated:** [May 14, 2025, 2:44am UTC](https://help.anvilproject.org/t/push-docker-containers-on-google-container-registry-or-artifact-registry/238 "2025-05-14T02:44:32Z")
Hi. I am trying to use google container registry to store an image of software needed for my analysis. I will use the image to configure the application environment using the option “Container image”. I had followed th… --- ## [Are files from other google storage bucket copied over when running WDL?](https://help.anvilproject.org/t/are-files-from-other-google-storage-bucket-copied-over-when-running-wdl/301)
**Author:** [@truckload](https://help.anvilproject.org/u/truckload)\ **Replies:** 2\ **Last updated:** [May 8, 2025, 7:16pm UTC](https://help.anvilproject.org/t/are-files-from-other-google-storage-bucket-copied-over-when-running-wdl/301 "2025-05-08T19:16:59Z")
Hi, I have a bioinformatic scenario where I have several questions regarding accessing the data files on cloud storage. For example, I would like to use the sequence dataset in the Terra workspace, Terra. It seem gvcf… --- ## [What is the best way to manage WDL and json files?](https://help.anvilproject.org/t/what-is-the-best-way-to-manage-wdl-and-json-files/300)
**Author:** [@truckload](https://help.anvilproject.org/u/truckload)\ **Replies:** 2\ **Last updated:** [May 8, 2025, 6:50pm UTC](https://help.anvilproject.org/t/what-is-the-best-way-to-manage-wdl-and-json-files/300 "2025-05-08T18:50:07Z")
Hi, I went through the tutorial video on working with a WDL. I wonder if people use command line in the terminal to move files, editing them using vi in the terminal, and validating WDL and uploading the final version o… --- ## [Mounting a Google Cloud Storage bucket in WDL workflow](https://help.anvilproject.org/t/mounting-a-google-cloud-storage-bucket-in-wdl-workflow/303)
**Author:** [@truckload](https://help.anvilproject.org/u/truckload)\ **Replies:** 2\ **Last updated:** [May 8, 2025, 6:21pm UTC](https://help.anvilproject.org/t/mounting-a-google-cloud-storage-bucket-in-wdl-workflow/303 "2025-05-08T18:21:15Z")
Hi. I have used dsub to submit and run batch scripts in the cloud. (GitHub - DataBiosphere/dsub: Open-source command-line tool to run batch computing tasks and workflows on backend services such as Google Cloud.) dsub … [Previous page](https://help.anvilproject.org/latest.md) [Next page](https://help.anvilproject.org/latest.md?page=2)