Docker issue

[weiss480]

I am trying to run CRISPResso on my new MacBook Air, but I am getting this warning that prevents the program from running. I am not sure why. Any advice on how to fix this?

WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested

[kclem]

We use docker automated builds for dockerhub, but automated ARM builds aren't available. This issue seems to track it: docker/roadmap#109

I've built a one-off build for you for version 2.1.1 that you can pull here:

docker pull pinellolab/crispresso2:v2.1.1_arm

Let me know if it works.

[weiss480]

Hi Kendell, It didn't seem to work. This is what I entered into the terminal. Did I miss something? Thanks

@.*** ~ % docker pull pinellolab/crispresso2:v2.1.1_arm

v2.1.1_arm: Pulling from pinellolab/crispresso2

b8f262c62ec6: Already exists

fa9712f20293: Already exists

6ec1e76960c6: Already exists

a1eedd497dca: Pull complete

ec962e6d33b1: Pull complete

a4d59ff12389: Pull complete

4f4fb700ef54: Pull complete

7aa507130790: Pull complete

Digest: sha256:06cee95c99a4987a0491ec4101577a6a2495e138a77d98f730fc115239d8528b

Status: Downloaded newer image for pinellolab/crispresso2:v2.1.1_arm

docker.io/pinellolab/crispresso2:v2.1.1_arm

(base) @.*** ~ % docker run -v ${PWD}:/DATA -w /DATA -i pinellolab/crispresso2 CRISPResso -h

WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested

On Mon, Jun 21, 2021 at 10:46 AM Kendell Clement @.***> wrote:

We use docker automated builds for dockerhub, but automated ARM builds aren't available. This issue seems to track it: docker/roadmap#109 https://github.com/docker/roadmap/issues/109

I've built a one-off build for you for version 2.1.1 that you can pull here:

docker pull pinellolab/crispresso2:v2.1.1_arm

Let me know if it works.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/pinellolab/CRISPResso2/issues/105#issuecomment-865143591, or unsubscribe https://github.com/notifications/unsubscribe-auth/AURCY5BYADP2K5LRBL4M6CTTT5NGXANCNFSM47AL76UQ .

--

Trevor Weiss

PhD Candidate

Department of Plant and Microbial Biology

Zhang Laboratory http://zhanglabumn.net

Centers for Genome Engineering https://cge.umn.edu and Precision Plant Genomics https://cppg.umn.edu

Phone: (515) 509 0193

[kclem]

Hm. Try this one: docker pull pinellolab/crispresso2:v2.1.1_armv6

[kclem]

Or actually, try this one: docker pull pinellolab/crispresso2:v2.1.1_armv8

I'm not sure how lenient the platform is (v6 vs v8)

I built this package from source using: docker build --platform linux/arm64/v8 -t pinellolab/crispresso2:v2.1.1_armv8 . in case anyone in the future (me) needs to rebuild for new macs.

[weiss480]

That worked. Thanks!

On Mon, Jun 21, 2021 at 1:27 PM Kendell Clement @.***> wrote:

Or actually, try this one: docker pull pinellolab/crispresso2:v2.1.1_armv8

I'm not sure how lenient the platform is (v6 vs v8)

I built this package from source using: docker build --platform linux/arm64/v8 -t pinellolab/crispresso2:v2.1.1_armv8 . in case anyone in the future (me) needs to rebuild for new macs.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/pinellolab/CRISPResso2/issues/105#issuecomment-865251599, or unsubscribe https://github.com/notifications/unsubscribe-auth/AURCY5HAH4OMSLZUHQ4FWETTT577PANCNFSM47AL76UQ .

--

Trevor Weiss

PhD Candidate

Department of Plant and Microbial Biology

Zhang Laboratory http://zhanglabumn.net

Centers for Genome Engineering https://cge.umn.edu and Precision Plant Genomics https://cppg.umn.edu

Phone: (515) 509 0193

[kclem]

FYI, in our move to python3, I tried to build the arm version, but bowtie2 doesn't have support for arm via apt or conda. You'll have to stick with the python2 version for the time being.

> docker run --platform linux/arm64/v8 -it continuumio/miniconda3
$ apt-get update && apt-get install bowtie2
Reading package lists... Done
Building dependency tree
Reading state information... Done
Package bowtie2 is not available, but is referred to by another package.
This may mean that the package is missing, has been obsoleted, or
is only available from another source

E: Package 'bowtie2' has no installation candidate

$ conda install -c bioconda bowtie2
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

  - bowtie2

Current channels:

  - https://conda.anaconda.org/bioconda/linux-aarch64
  - https://conda.anaconda.org/bioconda/noarch
  - https://repo.anaconda.com/pkgs/main/linux-aarch64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/linux-aarch64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.