Update Docker Hub #11

joshmoore · 2019-05-17T13:50:32Z

see:

Preparations for a push of new images to docker hub. cF:

I'll likely re-tag the existing images with something in case something has broken in the meantime.

cc: @olatarkowska @ctrueden @chigozienri

joshmoore · 2019-05-17T13:59:14Z

[jamoore@idr1-slot2 fiji-dockerfiles]$ for x in openjdk- oracle-jdk; do for y in 6 7; do docker pull fiji/fiji:fiji-$x$y; done; done
...
[jamoore@idr1-slot2 fiji-dockerfiles]$ for x in openjdk- oracle-jdk; do for y in 6 7; do docker tag fiji/fiji:fiji-$x$y fiji/fiji:fiji-$x$y-legacy; done; done
fiji/fiji                                                                    fiji-oracle-jdk7                        4f3616fe21bd        4 years ago         870MB
fiji/fiji                                                                    fiji-oracle-jdk7-legacy                 4f3616fe21bd        4 years ago         870MB
fiji/fiji                                                                    fiji-oracle-jdk6                        0e90cf008100        4 years ago         786MB
fiji/fiji                                                                    fiji-oracle-jdk6-legacy                 0e90cf008100        4 years ago         786MB
fiji/fiji                                                                    fiji-openjdk-6                          d960bb9254be        4 years ago         727MB
fiji/fiji                                                                    fiji-openjdk-6-legacy                   d960bb9254be        4 years ago         727MB
fiji/fiji                                                                    fiji-openjdk-7                          d9016df6262c        4 years ago         876MB
fiji/fiji                                                                    fiji-openjdk-7-legacy                   d9016df6262c        4 years ago         876MB
fiji/fiji                                                                    latest                                  d9016df6262c        4 years ago         876MB
[jamoore@idr1-slot2 fiji-dockerfiles]$ docker push fiji/fiji:fiji-openjdk-7-legacy
The push refers to repository [docker.io/fiji/fiji]
5f70bf18a086: Layer already exists
a584354f99fa: Layer already exists
e7ae6c2513a1: Layer already exists
e75d841cf7bb: Layer already exists
2e71f96ed7ae: Layer already exists
2998cc39c7a6: Layer already exists
d3feddf6984f: Layer already exists
f39162388155: Layer already exists
0ae9a0356259: Layer already exists
230b028ff243: Layer already exists
fiji-openjdk-7-legacy: digest: sha256:99bbb5cdbca29ad5b07fba5245fc0d13eec8884fa8b6be731222f77c5e6d5238 size: 4678

Note: Only pushed fiji-openjdk-7-legacy for the moment, since it is the only tag that will be overwritten by the update.

joshmoore · 2019-05-17T14:21:07Z

Last commit produces tags of the form:

docker tag fiji/fiji:fiji-openjdk-8 fiji/fiji:fiji-openjdk-8.20190517
docker tag fiji/fiji:fiji-openjdk-7 fiji/fiji:fiji-openjdk-7.20190517
docker push fiji/fiji:fiji-openjdk-8.20190517
docker push fiji/fiji:fiji-openjdk-7.20190517
docker push fiji/fiji:fiji-openjdk-8
docker push fiji/fiji:fiji-openjdk-7
docker tag fiji/fiji:fiji-openjdk-8 fiji/fiji:latest
docker tag fiji/fiji:fiji-openjdk-8 fiji/fiji:20190517
docker push fiji/fiji:latest
docker push fiji/fiji:20190517

joshmoore · 2019-05-17T16:00:48Z

Updated to use @ctrueden's suggestion of downloading: https://gitter.im/fiji/fiji?at=5cded2ed75d9a575a6fa4a95

- use fiji user (id=1000) rather than root - add an entrypoint for sensible defaults - pre-create Java preferences directory - revert to binary rather than ImageJ.sh

joshmoore · 2019-05-17T20:37:03Z

Latest state is usable via:

[jamoore@idr1-slot2 fiji-dockerfiles]$ docker run --rm fiji/fiji:fiji-openjdk-8 --ij2 --headless --console --run demo.py 'name="foo"'
Hello foo

@olatarkowska: I'm thinking for the updates, one should build their own docker image, since otherwise runs won't be reproducible. I can add a build-arg though that will add update sites.

We're getting to the stage that I'd suggest deploying the openjdk-8 image as latest.

ctrueden · 2019-05-17T20:39:39Z

Thanks so much for working on this!

I'm no Docker expert, so am not qualified to review much of this. I support merging whenever you are confident things are working well.

One thing about openjdk8: it does not come bundled with JavaFX; the openjfx needs to be installed separately. So that will be an issue for all the Fiji plugins requiring JavaFX (there are several now). This concern might seem silly since JavaFX is a UI thing, and Docker is typically used headless, but A) there might be class loading issues, and B) I believe Fiji can run from Docker graphically over X11.

joshmoore · 2019-05-18T10:14:08Z

I support merging whenever you are confident things are working well.

I'll do a little more testing and get confirmation from @olatarkowska, then merge and push to Docker Hub. (Open to tag naming schemes beyond .${today} though)

openjfx needs to be installed separately

Makes sense. I'll likely try to tackle that in a follow-up.

Fiji can run from Docker graphically over X11.

I was thinking about adding in Xvfb by default, but perhaps that's an extra image. Likely another next step.

NB: I also think the image names can use some shortening.

(If anyone out there is following along, feel free to add opinions)

atarkowska

Thanks for updating, comments inline

fiji-openjdk-8/Dockerfile

atarkowska · 2019-05-20T08:27:24Z

fiji-openjdk-8/Dockerfile

@@ -8,16 +8,25 @@ FROM openjdk:8
 # Define maintainer.
 MAINTAINER Mark Hiner <hinerm@gmail.com>

+# Create a user.
+RUN useradd -u 1000 -ms /bin/bash fiji


you can run container as --user 1000:1000

Definitely, but then you can't use --update add-update-site, etc. can you? Certainly you get a warning from ImageJ warning that the installation is read-only.

Details:

$ docker build -t fiji:latest fiji_base Sending build context to Docker daemon 3.584kB Step 1/7 : FROM openjdk:8 8: Pulling from library/openjdk c5e155d5a1d1: Pull complete 221d80d00ae9: Pull complete 4250b3117dca: Pull complete 3b7ca19181b2: Pull complete 1eadaf4c0dff: Pull complete 4c1388ac89fe: Pull complete 73713755b9cb: Pull complete 5784ff1c0372: Pull complete Digest: sha256:db664aeefa56cb74b1c967089a064c9a1f9d3db33def7eb08c26c2afe8f137f0 Status: Downloaded newer image for openjdk:8 ---> bec43387959a Step 2/7 : MAINTAINER Mark Hiner <hinerm@gmail.com> ---> Running in 524515e9ffeb Removing intermediate container 524515e9ffeb ---> 01d838ff7d04 Step 3/7 : WORKDIR /opt/fiji ---> Running in 39b17bdc5757 Removing intermediate container 39b17bdc5757 ---> 17635fbcbc06 Step 4/7 : RUN wget -q https://downloads.imagej.net/fiji/latest/fiji-nojre.zip && unzip fiji-nojre.zip && rm fiji-nojre.zip ---> Running in 01db403bf91c Archive: fiji-nojre.zip inflating: Fiji.app/db.xml.gz inflating: Fiji.app/Contents/Info.plist inflating: Fiji.app/Contents/MacOS/ImageJ-macosx inflating: Fiji.app/Contents/MacOS/ImageJ-tiger ... inflating: Fiji.app/retro/retrotranslator-transformer-1.2.9.jar Removing intermediate container 01db403bf91c ---> 3891fdcac799 Step 5/7 : ENV PATH $PATH:/opt/fiji/Fiji.app ---> Running in 07ddf06b0f97 Removing intermediate container 07ddf06b0f97 ---> fde411c2f437 Step 6/7 : COPY entrypoint.sh /opt/fiji ---> ae4684674287 Step 7/7 : ENTRYPOINT ["./entrypoint.sh"] ---> Running in d5f1f226adee Removing intermediate container d5f1f226adee ---> 1b8de562c55e Successfully built 1b8de562c55e Successfully tagged fiji:latest

$ docker build -t fiji_biop:latest fiji Sending build context to Docker daemon 13.31kB Step 1/5 : FROM fiji:latest ---> 1b8de562c55e Step 2/5 : RUN ./entrypoint.sh --update add-update-site PTBIOP http://biop.epfl.ch/Fiji-Update ---> Running in 363adaca211d Updating the index of available files (Updating from ImageJ site: http://up... Updating from ImageJ site: http://update.imagej.net/ done Updating the index of available files (Updating from Fiji site: http://upda... Updating from Fiji site: http://update.fiji.sc/ done Updating the index of available files (Updating from Java-8 site: http://si... Updating from Java-8 site: http://sites.imagej.net/Java-8/ done ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ........................................ Done: Checksummer Removing intermediate container 363adaca211d ---> a623796983c8 Step 3/5 : RUN ./entrypoint.sh --update update ---> Running in 9c8d726de1f6 Updating the index of available files (Updating from ImageJ site: http://up... Updating from ImageJ site: http://update.imagej.net/ done Updating the index of available files (Updating from Fiji site: http://upda... Updating from Fiji site: http://update.fiji.sc/ done Updating the index of available files (Updating from Java-8 site: http://si... Updating from Java-8 site: http://sites.imagej.net/Java-8/ done Updating the index of available files (Updating from PTBIOP site: http://bi... Updating from PTBIOP site: http://biop.epfl.ch/Fiji-Update/ done ................................................................................ Done: Checksummer Step 5/5 : CMD ["--headless"] ---> Running in c538eac03832 Removing intermediate container c538eac03832 ---> 293c584578c2 Successfully built 293c584578c2 Successfully tagged fiji_biop:latest

2$ docker run --rm -v /data:/data fiji_biop:latest -macro /data/macro.ijm /data/test#/data/out May 20, 2019 11:52:32 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. [INFO] Overriding BIOP Run Macro...; identifier: command:ch.epfl.biop.macrorunner.B_Run_Macro; jar: file:/opt/fiji/Fiji.app/plugins/BIOP/B_Run_Macro-1.0.0-SNAPSHOT.jar [INFO] Overriding Get Spine From Circle Rois; identifier: command:Cirlces_Based_Spine; jar: file:/opt/fiji/Fiji.app/plugins/Max_Inscribed_Circles-1.1.0.jar Parsing XML File... please wait

I dont see any readonly

I don't know what dockerfiles you are building from, but I'm going to guess that in your fiji_base you are using USER root. That's one thing I got rid of. I very much prefer to not run root-based dockers on my systems.

ctrueden · 2019-05-20T18:52:51Z

Should we also change the MAINTAINER, since Mark isn't actually the one maintaining this? I looked up that metadata field the other day, and it's deprecated in favor of LABEL, with rather ad hoc semantics, so I didn't say anything till now, but seeing all these logs where it's blasting the wrong MAINTAINER in all capital letters is kinda bothering me now. 😆

joshmoore · 2019-05-20T20:25:03Z

👍 #15 😉

joshmoore · 2019-05-21T14:37:26Z

I've pushed to Docker Hub. If everyone is on board, I'll merge this and update fiji/fiji:latest:

fiji-openjdk-8: digest: sha256:0be12c68f5a42b3f319ffce6111be0b097d9c36b1c6237e7b8eb1685b9488572 size: 3251

joshmoore · 2019-05-21T14:47:10Z

General 👍 from https://gitter.im/fiji/fiji?at=5ce40eef13e9854e33411e9f

Updating the fiji/fiji:latest tag. Enjoy all!

joshmoore added 2 commits May 17, 2019 14:45

Add Makefile for building & releasing

193e3d4

Temporarily remove oracle-jdk8

9eda489

Add more tags

558a016

joshmoore added 2 commits May 17, 2019 16:33

Move to bootstrapJ8

9114c92

Use download strategy

171d631

Various improvements for openjdk-8

b6011dc

- use fiji user (id=1000) rather than root - add an entrypoint for sensible defaults - pre-create Java preferences directory - revert to binary rather than ImageJ.sh

This was referenced May 18, 2019

Propose new image names #12

Open

install JavaFX #13

Open

add xvfb and/or x11 support #14

Open

atarkowska suggested changes May 20, 2019

View reviewed changes

joshmoore added 2 commits May 21, 2019 14:45

Use gitter channel as maintainer (gh-15)

d8410ea

Docs and backwards compatibility for entrypoint.sh

56c8277

joshmoore force-pushed the dh-update branch from bed5101 to 56c8277 Compare May 21, 2019 14:11

atarkowska and others added 2 commits May 21, 2019 15:13

add travis

6c95d8d

Move to /opt/fiji

0e1a5e1

joshmoore mentioned this pull request May 21, 2019

Dh update #18

Closed

joshmoore closed this May 21, 2019

joshmoore reopened this May 21, 2019

joshmoore merged commit 876bf53 into master May 21, 2019

joshmoore deleted the dh-update branch May 21, 2019 14:47

joshmoore restored the dh-update branch May 21, 2019 16:56

joshmoore deleted the dh-update branch May 22, 2019 18:42

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Update Docker Hub #11

Update Docker Hub #11

joshmoore commented May 17, 2019 •

edited

Loading

joshmoore commented May 17, 2019

joshmoore commented May 17, 2019

joshmoore commented May 17, 2019

joshmoore commented May 17, 2019 •

edited

Loading

ctrueden commented May 17, 2019

joshmoore commented May 18, 2019

atarkowska left a comment

atarkowska May 20, 2019

joshmoore May 20, 2019

atarkowska May 20, 2019 •

edited by joshmoore

Loading

joshmoore May 21, 2019 •

edited

Loading

ctrueden commented May 20, 2019 •

edited

Loading

joshmoore commented May 20, 2019

joshmoore commented May 21, 2019

joshmoore commented May 21, 2019

Update Docker Hub #11

Update Docker Hub #11

Conversation

joshmoore commented May 17, 2019 • edited Loading

joshmoore commented May 17, 2019

joshmoore commented May 17, 2019

joshmoore commented May 17, 2019

joshmoore commented May 17, 2019 • edited Loading

ctrueden commented May 17, 2019

joshmoore commented May 18, 2019

atarkowska left a comment

Choose a reason for hiding this comment

atarkowska May 20, 2019

Choose a reason for hiding this comment

joshmoore May 20, 2019

Choose a reason for hiding this comment

atarkowska May 20, 2019 • edited by joshmoore Loading

Choose a reason for hiding this comment

joshmoore May 21, 2019 • edited Loading

Choose a reason for hiding this comment

ctrueden commented May 20, 2019 • edited Loading

joshmoore commented May 20, 2019

joshmoore commented May 21, 2019

joshmoore commented May 21, 2019

joshmoore commented May 17, 2019 •

edited

Loading

joshmoore commented May 17, 2019 •

edited

Loading

atarkowska May 20, 2019 •

edited by joshmoore

Loading

joshmoore May 21, 2019 •

edited

Loading

ctrueden commented May 20, 2019 •

edited

Loading