Hi,
How to updated qiime2 in docker without losing my history.
What kind of history do you want to preserve? In your current Docker install, where is that history saved now?
3 Likes
My Old history that I done and generated by Galaxy Build by runnig q2 2022.11.
( Running QIIME 2 inside Galaxy (alpha release version)
1 Like
Thank you for telling me more!
I really like the idea of keeping your Galaxy history while upgrading to the newest version of Qiime2!
Let's see if there's a way to do that. Let's wait and see what the developers suggest.
1 Like
Hi,
I still need to install qiime2 2023.2 in docker and running it in Galaxy with localhost8080!!
Happy Mubarek Ramadan ( will start soon 23/03/2023)
Thanks.
1 Like
Hi @azithro13!
Happy Ramadan to you as well!
Preserving the history is going to depend on how the Galaxy container is being used. If you have a volume mounted (you should see this in Docker Desktop, or in the command which would involve a -v flag), then it shouldn't be an issue as you can still use that volume (which has the history) with a new container.
That said, I haven't updated the QIIME 2 galaxy container in some time, so there may not be much to do at all for the moment.
We do however have QIIME 2 on the toolshed now, so it may be possible to just use the admin panel and install the more recent version which won't impact the history at all. However that would require the container to use docker tools which I may not have configured correctly when I baked the very first image. My plan is to circle back on all of this and create a proper "Galaxy Flavor" for QIIME 2 which should be substantially simpler than it used to be.
2 Likes
Hi ebolyen
Thank you for the answer but also thanks for the quality of it. now I understand and because I'm not programmeur informatique I've been installing q2 2023.2 but I found many difficulties tha t I posted about PORT tcp and that wrote this imange (Quay.io) have not port!! could you Sir explain to me how I get the port for running the new version or how I update the the q2 2022.11 version by the simplest way .
thanks again from the bottom of my heart.
Hi,
I have this from the powershell:
Status: Downloaded newer image for Quay
Quay
PS C:\WINDOWS\system32> docker image inspect Quay
[
{
"Id": "sha256:367a3b3c47a88644f56ebbface2cf088ee7314ef969a5ef171bdbaaa021c01a0",
"RepoTags": [
"Quay"
],
"RepoDigests": [
"quay.io/qiime2/core@sha256:269010083c9d0f9f1e89ec5379f3763f0b9e5ccd2ece1d4961ea9094204a45f9"
],
"Parent": "",
"Comment": "buildkit.dockerfile.v0",
"Created": "2023-03-07T17:25:51.42643916Z",
"Container": "",
"ContainerConfig": {
"Hostname": "",
"Domainname": "",
"User": "",
"AttachStdin": false,
"AttachStdout": false,
"AttachStderr": false,
"Tty": false,
"OpenStdin": false,
"StdinOnce": false,
"Env": null,
"Cmd": null,
"Image": "",
"Volumes": null,
"WorkingDir": "",
"Entrypoint": null,
"OnBuild": null,
"Labels": null
},
"DockerVersion": "",
"Author": "",
"Config": {
"Hostname": "",
"Domainname": "",
"User": "",
"AttachStdin": false,
"AttachStdout": false,
"AttachStderr": false,
"Tty": false,
"OpenStdin": false,
"StdinOnce": false,
"Env": [
"PATH=/opt/conda/envs/qiime2-2023.2/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin",
"LANG=C.UTF-8",
"LC_ALL=C.UTF-8",
"MPLBACKEND=agg",
"HOME=/home/qiime2",
"XDG_CONFIG_HOME=/home/qiime2"
],
"Cmd": [
"/bin/bash"
],
"ArgsEscaped": true,
"Image": "",
"Volumes": {
"/data": {}
},
"WorkingDir": "/data",
"Entrypoint": null,
"OnBuild": null,
"Labels": {
"maintainer": "Anaconda, Inc",
"org.opencontainers.image.created": "2022-12-23T15:47:51.857Z",
"org.opencontainers.image.description": "Repository of Docker images created by Continuum Analytics",
"org.opencontainers.image.licenses": "",
"org.opencontainers.image.revision": "e50c6323cd703e0c2df7aa56eb18e05757df2402",
"org.opencontainers.image.source": "GitHub - ContinuumIO/docker-images: Repository of Docker images created by Anaconda",
"org.opencontainers.image.title": "docker-images",
"org.opencontainers.image.url": "GitHub - ContinuumIO/docker-images: Repository of Docker images created by Anaconda",
"org.opencontainers.image.version": "22.11.1"
}
},
"Architecture": "amd64",
"Os": "linux",
"Size": 5269901831,
"VirtualSize": 5269901831,
"GraphDriver": {
"Data": {
"LowerDir": "/var/lib/docker/overlay2/1ec3777a1897d3fd54ddedfb39c818a6fc14d19a97303f82818850e1182d17a0/diff:/var/lib/docker/overlay2/acb53198301103a19ff33c0895ea512f0ff26f4ad73c4b11c03123e3e2b4416c/diff:/var/lib/docker/overlay2/a53efa156774e0e9e5ab3422663388fa768bc8d4ba030fee93f3355218db5e1f/diff:/var/lib/docker/overlay2/f656131adf7e17d35e97036c73bcdfd6057da000fdb74cc8a1a143ca10c5e468/diff:/var/lib/docker/overlay2/60f4baea6d3f7f5428a1bb1b7145e3e5e91abc26dfc52bfe2de64f400f9c2332/diff:/var/lib/docker/overlay2/d115e7b09d920fdf9783f9c0707c253a52f1e023b84ffc850a25721e60ac9752/diff:/var/lib/docker/overlay2/9eef2d6eb8da475c5ad9b95f8b711f98f762198c9e35510911658a03604528ab/diff:/var/lib/docker/overlay2/63aaa0cee9515bcca2de5dcf3d5e08838a68e37392c5f70f40ff3d0403bb32e9/diff:/var/lib/docker/overlay2/e376230596278b94dac6e8877a672b1055a7e3b06540ebacbb24c0ea397f86bc/diff:/var/lib/docker/overlay2/8113a7acb8f360e3797946dcbacea10db08b959a81a57e11f26f05d18ddfd498/diff:/var/lib/docker/overlay2/5c985f11a696de5ad94b990da0959c7575bc7b9277503b2ffcef75da4f42566b/diff:/var/lib/docker/overlay2/d51a9344f453091f7825c2e866b298569206ffd58f3a7191dc6c4008063901fb/diff:/var/lib/docker/overlay2/06f861c94dacbdcaaf80628bba97a6091a39905f1745be286cc8f2279f03212d/diff:/var/lib/docker/overlay2/bd5073a0dc4f245f8a8b488de44280315b9746465c5f4dfa195a053d3d66e20d/diff:/var/lib/docker/overlay2/1c2b36d5e5dfc4d2617e6f053e075866fcdd951ef0a3e3bc33932ec4e76a3a6c/diff:/var/lib/docker/overlay2/2a9786ada67d2bffc7cbf946e65ccbecc8402e2deecc38cf23b9f1f493239e9e/diff",
"MergedDir": "/var/lib/docker/overlay2/5bf8c79a42dfd76fa5c96a07227f01d363fc7a966a8ed8f8ce6aa7cc2bd77235/merged",
"UpperDir": "/var/lib/docker/overlay2/5bf8c79a42dfd76fa5c96a07227f01d363fc7a966a8ed8f8ce6aa7cc2bd77235/diff",
"WorkDir": "/var/lib/docker/overlay2/5bf8c79a42dfd76fa5c96a07227f01d363fc7a966a8ed8f8ce6aa7cc2bd77235/work"
},
"Name": "overlay2"
},
"RootFS": {
"Type": "layers",
"Layers": [
"sha256:8a70d251b65364698f195f5a0b424e0d67de81307b79afbe662abd797068a069",
"sha256:32a72a3896c67c39ec1f1376dec404a3e60687338c73a2874df035586f38e54c",
"sha256:92d9617bd3c6523f732e174b1dd126481d58bfe6fcb3da1257258e842c747c54",
"sha256:4bd86db9ffdf09b7588524aec3795a98636ce10e24b6bf0468b2e3a9d5081316",
"sha256:5f70bf18a086007016e948b04aed3b82103a36bea41755b6cddfaf10ace3c6ef",
"sha256:ec197080d105942a79ab54f444fa148b0460b097dd436bd281c859a6aa0b7fb0",
"sha256:56deb8a7736e58f38054877b37ca94bbd689307022240d4be2f95c8232f29036",
"sha256:ff574b588bb834b90195dacb5284306cc3dea149832d8caf7a2d745dd753ccfc",
"sha256:c043f1aac19051efa1d950860daf8f8efd6b7b34138e6cfe90c732875b0f25bc",
"sha256:32825ee8fe29f577b3c34b92ac1d60b6607f12c70516261f31a9bb67799174ed",
"sha256:9a00cce3ae753cc57cee3c04040213e11ed4ce4ef60f34febbabb5aa6d2e276e",
"sha256:91e96e4d6541e9335c8c6deede61c80c36d52ec372903dbdf0cbfa7977c1ac68",
"sha256:94bc4bfff0cba12a4f646d14c334248a9987c45233ec12c301b57adaf024e972",
"sha256:6da70bf9155fa245acda3e26c93e896d02c56cf0f082ca68ad60d1a81ab70040",
"sha256:0f52f121b5106e8c404faf6786b70d80801c2fb4792d77fc77d5c8e8b00a3745",
"sha256:9d47796bc1e5eb62e1e061a97510522750770d627d08fac7762de5dc691dee69",
"sha256:f17767d1600d7f9154673d32067d6b52c83dd7ca7ced92c050e189ff176569bb"
]
},
"Metadata": {
"LastTagTime": "0001-01-01T00:00:00Z"
}
}
]
PS C:\WINDOWS\system32> docker run -p 8080:80 Quay
but the STATUT IS EXITED I couldn't run it I don't know why and how it wrok?!!
Hi @azithro13,
Sorry for the delay. Using http://quay.io/qiime2/core:2023.2 won't work since it doesn't have a Galaxy server pre-installed. Right now we don't have a dockerized galaxy image for 2023.2. Sorry!
1 Like
Thank you Evan,
Have a nice Ramadan
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