# Help **URL:** https://help.anvilproject.org/c/help/12.md [Latest](https://help.anvilproject.org/latest.md) · [Categories](https://help.anvilproject.org/categories.md) · [Tags](https://help.anvilproject.org/tags.md) --- ## [About the Help category](https://help.anvilproject.org/t/about-the-help-category/281)
**Author:** [@Javier-CP](https://help.anvilproject.org/u/Javier-CP)\ **Replies:** 0\ **Last updated:** [March 11, 2025, 7:02pm UTC](https://help.anvilproject.org/t/about-the-help-category/281 "2025-03-11T19:02:04Z")
This category is your go-to place for general questions and support related to the AnVIL platform. If you have questions about finding or accessing data, check out the Data Access category. For all other questions, wh… --- ## [Release schedule for base images on AnVIL/Terra](https://help.anvilproject.org/t/release-schedule-for-base-images-on-anvil-terra/390)
**Author:** [@camancuso](https://help.anvilproject.org/u/camancuso)\ **Replies:** 1\ **Last updated:** [September 16, 2026, 3:47pm UTC](https://help.anvilproject.org/t/release-schedule-for-base-images-on-anvil-terra/390 "2026-09-16T15:47:20Z")
I might have missed this somewhere, but is there a release schedule for when the base images on Terra/AnVIL are updated? Or how long in advance they tell people? Or if old versions of the images are still useable after a… --- ## [ID.me identity verification requirement for non-US researcher accessing GTEx controlled data](https://help.anvilproject.org/t/id-me-identity-verification-requirement-for-non-us-researcher-accessing-gtex-controlled-data/421)
**Author:** [@stephanie.binder](https://help.anvilproject.org/u/stephanie.binder)\ **Replies:** 1\ **Last updated:** [September 16, 2026, 2:09pm UTC](https://help.anvilproject.org/t/id-me-identity-verification-requirement-for-non-us-researcher-accessing-gtex-controlled-data/421 "2026-09-16T14:09:37Z")
Hello, I am a researcher based in Germany with an existing eRA Commons account and approved dbGaP access to GTEx (phs000424). I have successfully created a Terra account using my institutional email address. Following … --- ## [Docker and samtools availability on RStudio VM environment](https://help.anvilproject.org/t/docker-and-samtools-availability-on-rstudio-vm-environment/419)
**Author:** [@truckload](https://help.anvilproject.org/u/truckload)\ **Replies:** 5\ **Last updated:** [September 15, 2026, 4:38pm UTC](https://help.anvilproject.org/t/docker-and-samtools-availability-on-rstudio-vm-environment/419 "2026-09-15T16:38:52Z")
In the VM Environment setting for RStudio, I don’t see docker, or samtools installed on the Application configuration. Does it mean I have to install those packages myself? That would mean I have to use the startup scrip… --- ## [Moving data from Anvil to Google cloud bucket in Asia](https://help.anvilproject.org/t/moving-data-from-anvil-to-google-cloud-bucket-in-asia/406)
**Author:** [@Younes](https://help.anvilproject.org/u/Younes)\ **Replies:** 1\ **Last updated:** [July 7, 2026, 2:25pm UTC](https://help.anvilproject.org/t/moving-data-from-anvil-to-google-cloud-bucket-in-asia/406 "2026-07-07T14:25:55Z")
Dear AnVIL support team. We have gained access though dbGAP to a dataset that is avaialble through AnVIL. In AnVIL data explorer, it says that the dataset can only be exported to Terra. I want to know whether it is possi… --- ## [GTEx access via samtools](https://help.anvilproject.org/t/gtex-access-via-samtools/402)
**Author:** [@MARGAUX\_HUJOEL](https://help.anvilproject.org/u/MARGAUX_HUJOEL)\ **Replies:** 1\ **Last updated:** [June 3, 2026, 12:32pm UTC](https://help.anvilproject.org/t/gtex-access-via-samtools/402 "2026-06-03T12:32:28Z")
I am trying to access GTEx crams (to which I have access) via samtools and the gsurl. I am having issues setting up billing. I linked terra to my GCP account and created a billing project. However I am having issues find… --- ## [Longer than normal start up times](https://help.anvilproject.org/t/longer-than-normal-start-up-times/389)
**Author:** [@camancuso](https://help.anvilproject.org/u/camancuso)\ **Replies:** 11\ **Last updated:** [May 12, 2026, 3:39pm UTC](https://help.anvilproject.org/t/longer-than-normal-start-up-times/389 "2026-05-12T15:39:47Z")
I have noticed that creating computational environments on Terra/AnVIL is taking much longer than usual. Using the same start up script which installs packages using BiocManager::install() , last year it would take about… --- ## [Follow-up Questions after Reviewing Anvil Resources](https://help.anvilproject.org/t/follow-up-questions-after-reviewing-anvil-resources/386)
**Author:** [@jkaralis](https://help.anvilproject.org/u/jkaralis)\ **Replies:** 1\ **Last updated:** [April 3, 2026, 4:17pm UTC](https://help.anvilproject.org/t/follow-up-questions-after-reviewing-anvil-resources/386 "2026-04-03T16:17:46Z")
Hello. Our research group is looking to use Anvil for our ABCD-related projects, and we have a few questions after reviewing the information present from the learn page and getting started with the Anvil web-book. Could … --- ## [Download large file from gs with time-out error](https://help.anvilproject.org/t/download-large-file-from-gs-with-time-out-error/370)
**Author:** [@truckload](https://help.anvilproject.org/u/truckload)\ **Replies:** 3\ **Last updated:** [February 9, 2026, 10:16pm UTC](https://help.anvilproject.org/t/download-large-file-from-gs-with-time-out-error/370 "2026-02-09T22:16:46Z")
I am trying to download a set of 132 data files from Terra workspace GS location. I will have no issue download each one of them from the google cloud console, gs listing site by point and click. But I have a hard time d… --- ## [GPU Availability on AnVIL](https://help.anvilproject.org/t/gpu-availability-on-anvil/367)
**Author:** [@avahoffman](https://help.anvilproject.org/u/avahoffman)\ **Replies:** 0\ **Last updated:** [January 8, 2026, 2:17pm UTC](https://help.anvilproject.org/t/gpu-availability-on-anvil/367 "2026-01-08T14:17:26Z")
Hi readers! Passing along a question about our GPU availability on AnVIL: Check out predefinedMachineType. You should be able to use any GPU available on GCP. See this Terra release note See relevant Cromwell documen… --- ## [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… --- ## [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. --- ## [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… --- ## [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. … --- ## [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! --- ## [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… --- ## [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 … --- ## [Question: GTEx v10 smallRNA expression read counts](https://help.anvilproject.org/t/question-gtex-v10-smallrna-expression-read-counts/263)
**Author:** [@farzamani](https://help.anvilproject.org/u/farzamani)\ **Replies:** 5\ **Last updated:** [May 8, 2025, 1:34pm UTC](https://help.anvilproject.org/t/question-gtex-v10-smallrna-expression-read-counts/263 "2025-05-08T13:34:06Z")
Hi, The improvement from GTEx v8 is really impressive and I believe a lot of people will benefit from it. I have a question regarding the data for small RNA-seq (this one: GTEx\_Analysis\_v10\_smallRNA\_gene\_reads.txt.gz). … --- ## [Galaxy error when billing account is interrupted](https://help.anvilproject.org/t/galaxy-error-when-billing-account-is-interrupted/29)
**Author:** [@edmundotogo](https://help.anvilproject.org/u/edmundotogo)\ **Replies:** 0\ **Last updated:** [February 23, 2021, 10:11pm UTC](https://help.anvilproject.org/t/galaxy-error-when-billing-account-is-interrupted/29 "2021-02-23T22:11:45Z")
My Galaxy instance was interrupted when the billing account stopped after the free trial and resulted in an error. The only option I have now is to delete it (which I did not do). I have reached out to the support team … --- ## [Software installation](https://help.anvilproject.org/t/software-installation/270)
**Author:** [@truckload](https://help.anvilproject.org/u/truckload)\ **Replies:** 2\ **Last updated:** [February 27, 2025, 4:38pm UTC](https://help.anvilproject.org/t/software-installation/270 "2025-02-27T16:38:09Z")
Where can I find a list of software that are readily available on the Terra workspace terminal. Can I install software by myself using sudo command? More specifically, is git installed on Terra workspace? Would you plea… --- ## [Cost of downloading GTEx files](https://help.anvilproject.org/t/cost-of-downloading-gtex-files/250)
**Author:** [@Daniela\_Puiu](https://help.anvilproject.org/u/Daniela_Puiu)\ **Replies:** 1\ **Last updated:** [December 20, 2024, 5:14pm UTC](https://help.anvilproject.org/t/cost-of-downloading-gtex-files/250 "2024-12-20T17:14:48Z")
I am reaching out to inquire about the cost of downloading the GTEx data files Google charges around $0.10 per GB transferred. However, I understand that GTEx is part of the STRIDES Initiative which provides free acces… [Next page](https://help.anvilproject.org/c/help/12.md?page=1)