Any automatic downloadable gatk3?
Dear GATK Team,
I have written a pipeline for variants identification in cancer exomes. It uses docker technology and both gatk3 and gatk4 that are automatically downloaded by docker hub to build the container. Unfortunately, now gatk3 is not more downloadable from your site.
Is there any way to download it automatically because it cannot be downloaded from google cloud platform? Or do gatk4 have an alternative to the CombineVariants command that I use in gatk3?
And for RealignerTargetCreator and IndelRealigner commands?
Thanks in advance
-
I have the same issue. I see that archived versions are available here, which is great, however public users do not seem to have storage.objects.get permissions.
Is there any way to grant this permission?
-
Heather Ward you now can access this bucket to download gatk3.
ale you can access gatk3 here: https://console.cloud.google.com/storage/browser/gatk-software/package-archive/gatk Here is the gatk3 official docker if this helps!
-
Hi Tiffany,
I also have a similar problem as ale, as I need to use UnifiedGenotyper (HaplotypeCaller is not usable for my type of data).
When I go to https://console.cloud.google.com/storage/browser/gatk-software/package-archive/gatk I also get the error:
Access requiredAdditional permissions required to retrieve this object. Ask a project owner to grant you the following permission: storage.objects.get -
Thank you Tiffany , but still get an error. If I go to https://console.cloud.google.com/storage/browser/gatk-software/package-archive/gatk it tells me to sign in with my google account. And if a sign in still cannot download GATK3. Same problems as James:
Access requiredAdditional permissions required to retrieve this object. Ask a project owner to grant you the following permission: storage.objects.get -
Sorry, everyone! We found our mistake and fixed it. Give it a try now and let us know if you have any issues.
-
Thank you! Now it works but only if I'am logged in with my google account. Otherwise I'm redirected to a login page and it asks me to sign in with my google credentials.
-
Tiffany Miller works now, thank you very much!
-
I still seem to face an issue using the https link to download jar with `wget https://storage.cloud.google.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef.tar.bz2`
Seems like somehow the package downlaoded is faulty.
Can anybody help?
-
Binal Modi try to wget from the googleapis link rather than the cloud link:
-
Is the documentation for GATK3 tools still available online? For example, I'm trying to find the documentation for DepthOfCoverage, and I can't seem to find it anymore. Thank you.
-
Josianne Lachapelle I found them here: https://github.com/broadinstitute/gatk-docs
-
Tiffany Miller I think we need a page on the website that has links to archived gatk3 versions. It could a super simple static page. We're getting people asking on the gatk4 github and as far as I can tell there isn't a discoverable way to find them in google cloud.
-
Thanks for the feedback Louis Bergelson. I'll pass this on.
Post is closed for comments.
13 comments