bigdataprocessor2 plugin on conda

[lldelisle]

Dear developers,
I would like to use bigdataprocessor2 on fiji on command line on a HPC. I would like you know if you would agree to put your plugin on conda? If yes, do you want to write the recipe or help me to do so?
Here is an example of a conda recipe for a fiji plugin: https://github.com/bioconda/bioconda-recipes/tree/master/recipes/fiji-morpholibj
Thanks

[tischi]

Dear @lldelisle,

Thank you very much for your interest!

Let me first point out that there is code inside BDP2 for submitting processing jobs from ImageJ to a Slurm cluster: https://github.com/bigdataprocessor/bigdataprocessor2/blob/master/src/main/java/de/embl/cba/bdp2/cluster/BDP2MacroClusterSubmitterCommand.java

The good thing about this is that it will process all the time points of a data set in parallel, thus potentially speeding up processing massively. We could discuss whether this also may be an option for you. Let me know. This solution relies on my image-cluster code, which comes with BDP2.

However, while this is convenient I am actually not sure whether submitting and managing jobs from ImageJ is the way to go. I think it could be better to use standard tools (e.g. nextflow) to orchestrate and submit BPP2 jobs to an HPC. Thus, I would be super interested to be able to run BDP2 via conda. It would be amazing if you could help there!

[lldelisle]

I am quite new to the imaging field so I may say things totally stupids.
For morpholibj, the plugin installation was super simple. I just needed to copy a jar file into the plugin folder. Is it the same for BDP2? In the documentation, you only propose to add BDP to the sites. This can only be done by GUI. Is there somewhere a jar I could use or do you have dependencies?
Thanks

[tischi]

I think we should not "manually" download the jars.

One can install update sites via command line.

This looks interesting (we only need one update site): https://forum.image.sc/t/add-more-than-one-update-site-via-commandline/6481

Could you try? We only need the BDP2 update site.

[imagejan]

For what it's worth, here's the full documentation of updater commands available from the command line:

https://imagej.net/plugins/updater#command-line-usage

[lldelisle]

Thanks, I will need to give a try and come back to you.

[tischi]

@lldelisle

I don't know whether this helps you but within a Dockerfile this seems to work:

WORKDIR /opt
RUN wget https://downloads.imagej.net/fiji/latest/fiji-linux64.zip && \
  unzip fiji-linux64.zip && \
  rm fiji-linux64.zip

RUN Fiji.app/ImageJ-linux64 --update add-update-site IJPB-plugins http://sites.imagej.net/IJPB-plugins/
RUN Fiji.app/ImageJ-linux64 --update add-update-site BigDataProcessor http://sites.imagej.net/BigDataProcessor/
RUN Fiji.app/ImageJ-linux64 --update add-update-site MoBIE-beta http://sites.imagej.net/MoBIE-beta/

RUN echo "alias fiji=/opt/Fiji.app/ImageJ-linux64" >> /etc/bashrc

[lldelisle]

Thanks. In fact --update add-update-site only add the website to the list of site but then you need to "Install" BDP2.
You can list what is in the site:

$ ImageJ  --update list-from-site BigDataProcessor
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option PermSize=128m; support was removed in 8.0
Picked up _JAVA_OPTIONS: -Dawt.useSystemAAFontSettings=on
Java HotSpot(TM) 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release
Done: Checksummer
plugins/bigDataProcessor1_-0.7.4.jar    (INSTALLED)     20200810161257
jars/bigDataProcessor2-1.4.7.jar        (NOT_INSTALLED) 20220208175049
jars/bigdataviewer-bioformats-0.2.22.jar        (NOT_INSTALLED) 20211105174438
jars/bigdataviewer-spimdata-extras-0.1.4.jar    (NOT_INSTALLED) 20211105174438
jars/imagej-cluster-1.0.0.jar   (NOT_INSTALLED) 20211213103451
jars/imagej-utils-0.6.4.jar     (NOT_INSTALLED) 20211213103451
jars/imaris-writer-0.2.3.jar    (INSTALLED)     20201120104900
jars/lazyRatioViewer-0.1.0.jar  (NOT_INSTALLED) 20200717171928

Then to install it:

ImageJ --update update plugins/bigDataProcessor1_-0.7.4.jar jars/bigDataProcessor2-1.4.7.jar jars/bigdataviewer-bioformats-0.2.22.jar jars/bigdataviewer-spimdata-extras-0.1.4.jar jars/imagej-cluster-1.0.0.jar jars/imagej-utils-0.6.4.jar jars/imaris-writer-0.2.3.jar jars/lazyRatioViewer-0.1.0.jar

[imagejan]

update [<files>]

The <files> parameter is optional. If you just run:

ImageJ --update update

... it should install all up-to-date files from all active update sites, if I understand correctly.

[tischi]

Yes, @lldelisle, after adding all the "websites" one has to do a final "update", see last line in below example:

  Fiji.app/ImageJ-linux64 --headless --update add-update-site BigDataProcessor https://sites.imagej.net/BigDataProcessor/ && \
  Fiji.app/ImageJ-linux64 --headless --update add-update-site MoBIE-beta https://sites.imagej.net/MoBIE-beta/ && \
  Fiji.app/ImageJ-linux64 --headless --update add-update-site CSBDeep https://sites.imagej.net/CSBDeep/ && \
  Fiji.app/ImageJ-linux64 --headless --update add-update-site StarDist https://sites.imagej.net/StarDist/ && \
  Fiji.app/ImageJ-linux64 --headless --update update  # <= this is needed

[lldelisle]

Definitely, for a personnal usage this is perfect.
The issue, is that I don't want a conda recipe to update everything. I want just to update the BigDataProcessor.
By the way, I noticed that on a fresh installation of Fiji I got:

plugins/bigDataProcessor1_-0.7.4.jar    (NEW)   20200810161257
jars/bigDataProcessor2-1.4.7.jar        (NEW)   20220208175049
jars/bigdataviewer-bioformats-0.2.22.jar        (NEW)   20211105174438
jars/bigdataviewer-core-8.0.2-platybrowser.jar  (OBSOLETE_MODIFIED)     0
jars/bigdataviewer-spimdata-extras-0.1.4.jar    (NEW)   20211105174438
jars/bigdataviewer-vistools-1.0.0-beta-18-platybrowser.jar      (OBSOLETE_MODIFIED)     0
jars/imagej-cluster-1.0.0.jar   (NEW)   20211213103451
jars/imagej-utils-0.6.4.jar     (NEW)   20211213103451
jars/imaris-writer-0.2.3.jar    (NEW)   20201120104900
jars/imglib2-5.8.0.jar  (OBSOLETE_MODIFIED)     0
jars/jackson-annotations-2.10.2.jar     (OBSOLETE_MODIFIED)     0
jars/jackson-core-2.10.2.jar    (OBSOLETE_MODIFIED)     0
jars/jackson-databind-2.10.2.jar        (OBSOLETE_MODIFIED)     0
jars/lazyRatioViewer-0.1.0.jar  (NEW)   20200717171928

Do you know where the OBSOLETE_MODIFIED come from?

[tischi]

@lldelisle

What I meant is that you only do this:

  Fiji.app/ImageJ-linux64 --headless --update add-update-site BigDataProcessor https://sites.imagej.net/BigDataProcessor/
  Fiji.app/ImageJ-linux64 --headless --update update

By the way, I noticed that on a fresh installation of Fiji I got

You got this doing what? Doing this?
ImageJ --update list-from-site BigDataProcessor
I have never used this command, it seems to provide a rather verbose information about the update site. I don't think you need to worry about this...
@imagejan what do you think?

[lldelisle]

1. About a general update. If I create a fresh conda environment with the last fiji available today (20170530) and do:

ImageJ --headless --update add-update-site BigDataProcessor https://sites.imagej.net/BigDataProcessor/
ImageJ --headless --update update

It will update all the plugins and fiji which have been updated since the installation of Fiji in the conda recipe.
See what I get before adding BigDataProcessor:

$ ImageJ --headless --update list-updateable
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option PermSize=128m; support was removed in 8.0
Picked up _JAVA_OPTIONS: -Dawt.useSystemAAFontSettings=on
Java HotSpot(TM) 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release
Done: Checksummer
plugins/3D_Blob_Segmentation-3.0.1.jar  (UPDATEABLE)    20210915210749
plugins/3D_Objects_Counter-2.0.1.jar    (UPDATEABLE)    20170530201750
plugins/3D_Viewer-4.0.3.jar     (UPDATEABLE)    20200731193402
plugins/AnalyzeSkeleton_-3.4.2.jar      (UPDATEABLE)    20210915210749
plugins/Anisotropic_Diffusion_2D-2.0.1.jar      (UPDATEABLE)    20170530201750
plugins/Archipelago_Plugins-0.5.4.jar   (UPDATEABLE)    20170530201750
plugins/Arrow_-2.0.2.jar        (UPDATEABLE)    20170530201750
plugins/Auto_Threshold-1.17.2.jar       (UPDATEABLE)    20200731193402
plugins/BalloonSegmentation_-3.0.1.jar  (UPDATEABLE)    20170530201750
plugins/Bug_Submitter-2.1.1.jar (UPDATEABLE)    20170530201750
plugins/CPU_Meter-2.0.1.jar     (UPDATEABLE)    20170530201750
plugins/Calculator_Plus-2.0.1.jar       (UPDATEABLE)    20170530201750
plugins/Cell_Counter-3.0.0.jar  (UPDATEABLE)    20200731193402
plugins/Colocalisation_Analysis-3.0.5.jar       (UPDATEABLE)    20210915210749
plugins/Color_Histogram-2.0.7.jar       (UPDATEABLE)    20170530201750
plugins/Color_Inspector_3D-2.5.0.jar    (UPDATEABLE)    20200731193402
plugins/Colour_Deconvolution-3.0.3.jar  (UPDATEABLE)    20200731193402
plugins/CorrectBleach_-2.0.3.jar        (UPDATEABLE)    20200731193402
plugins/Correct_3D_Drift-1.0.6.jar      (UPDATEABLE)    20200731193402
plugins/Descriptor_based_registration-2.1.7.jar (UPDATEABLE)    20200611133920
plugins/Dichromacy_-2.1.2.jar   (UPDATEABLE)    20200731193402
plugins/Directionality_-2.3.0.jar       (UPDATEABLE)    20181204141527
plugins/Examples/CoverMaker/Prepare_Cover_Maker_Database.py     (UPDATEABLE)    20220211201246
plugins/Examples/Multithreaded_Image_Processing_in_Javascript.js        (UPDATEABLE)    20220211201246
plugins/Examples/The_Hue_Game.bsh       (UPDATEABLE)    20220211201246
plugins/FS_Align_TrakEM2-2.0.3.jar      (UPDATEABLE)    20180706220210
plugins/Feature_Detection-2.0.2.jar     (UPDATEABLE)    20170530201750
plugins/Fiji_Archipelago-2.0.1.jar      (UPDATEABLE)    20210915210749
plugins/Fiji_Developer-2.0.7.jar        (UPDATEABLE)    20180706220210
plugins/Fiji_Package_Maker-2.1.1.jar    (UPDATEABLE)    20170530201750
plugins/Fiji_Plugins-3.1.1.jar  (UPDATEABLE)    20170530201750
plugins/FlowJ_-2.0.1.jar        (UPDATEABLE)    20200731193402
plugins/Graph_Cut-1.0.2.jar     (UPDATEABLE)    20210915210749
plugins/Gray_Morphology-2.3.5.jar       (UPDATEABLE)    20200731193402
plugins/H5J_Loader_Plugin-1.1.0.jar     (UPDATEABLE)    20210915210749
plugins/Helmholtz_Analysis-2.0.2.jar    (UPDATEABLE)    20170530201750
plugins/IJ_Robot-2.0.1.jar      (UPDATEABLE)    20170530201750
plugins/IO_-4.1.0.jar   (UPDATEABLE)    20200731193402
plugins/Image_5D-2.0.2.jar      (UPDATEABLE)    20170530201750
plugins/Image_Expression_Parser-3.0.1.jar       (UPDATEABLE)    20210915210749
plugins/Interactive_3D_Surface_Plot-3.0.0.jar   (UPDATEABLE)    20170530201750
plugins/IsoData_Classifier-2.0.1.jar    (UPDATEABLE)    20170530201750
plugins/JRuby/imagej.rb (UPDATEABLE)    20220211201246
plugins/Kuwahara_Filter-2.0.1.jar       (UPDATEABLE)    20170530201750
plugins/KymographBuilder-2.1.1.jar      (UPDATEABLE)    20181204141527
plugins/LSM_Reader-4.1.2.jar    (UPDATEABLE)    20170530201750
plugins/LSM_Toolbox-4.1.2.jar   (UPDATEABLE)    20210915210749
plugins/Lasso_and_Blow_Tool-2.0.2.jar   (UPDATEABLE)    20170530201750
plugins/Linear_Kuwahara-2.0.1.jar       (UPDATEABLE)    20170530201750
plugins/LocalThickness_-4.0.3.jar       (UPDATEABLE)    20200731193402
plugins/MTrack2_-2.0.1.jar      (UPDATEABLE)    20170530201750
plugins/M_I_P-2.0.1.jar (UPDATEABLE)    20170530201750
plugins/Manual_Tracking-2.1.1.jar       (UPDATEABLE)    20170530201750
plugins/Multi_Kymograph-3.0.1.jar       (UPDATEABLE)    20170530201750
plugins/PIV_analyser-1.1.2.jar  (UPDATEABLE)    20170530201750
plugins/QuickPALM_-1.1.2.jar    (UPDATEABLE)    20170530201750
plugins/RATS_-2.0.2.jar (UPDATEABLE)    20171226155229
plugins/Reconstruct_Reader-2.0.4.jar    (UPDATEABLE)    20180706220210
plugins/SPIM_Opener-2.0.2.jar   (UPDATEABLE)    20170530201750
plugins/SPIM_Registration-5.0.22.jar    (UPDATEABLE)    20210915210749
plugins/Samples_-2.0.2.jar      (UPDATEABLE)    20170530201750
plugins/Scripts/Image/Hyperstacks/Temporal-Color_Code.ijm       (UPDATEABLE)    20220211201246
plugins/Scripts/Plugins/Utilities/Record_Window.py      (UPDATEABLE)    20220211201246
plugins/Series_Labeler-2.0.1.jar        (UPDATEABLE)    20170530201750
plugins/Sholl_Analysis-0.0.0-STUB.jar   (UPDATEABLE)    20210915210749
plugins/Simple_Neurite_Tracer-0.0.0-STUB.jar    (UPDATEABLE)    20210915210749
plugins/Siox_Segmentation-1.0.5.jar     (UPDATEABLE)    20210915210749
plugins/Skeletonize3D_-2.1.1.jar        (UPDATEABLE)    20170530201750
plugins/SplineDeformationGenerator_-2.0.2.jar   (UPDATEABLE)    20171226155229
plugins/Stack_Manipulation-2.1.2.jar    (UPDATEABLE)    20190603111541
plugins/Statistical_Region_Merging-2.0.1.jar    (UPDATEABLE)    20170530201750
plugins/Stitching_-3.1.8.jar    (UPDATEABLE)    20210907125640
plugins/Sync_Win-1.7-fiji4.jar  (UPDATEABLE)    20210915210749
plugins/Thread_Killer-2.0.1.jar (UPDATEABLE)    20170530201750
plugins/Time_Lapse-2.1.1.jar    (UPDATEABLE)    20200731193402
plugins/Time_Stamper-2.1.0.jar  (UPDATEABLE)    20171226155229
plugins/ToAST_-25.0.2.jar       (UPDATEABLE)    20170530201750
plugins/TopoJ_-2.0.1.jar        (UPDATEABLE)    20170530201750
plugins/TrackMate_-0.0.0-STUB.jar       (UPDATEABLE)    20210915210749
plugins/Trainable_Segmentation-3.3.2.jar        (UPDATEABLE)    20220114124145
plugins/TrakEM2_-1.3.6.jar      (UPDATEABLE)    20210915210749
plugins/TrakEM2_Archipelago-2.0.3.jar   (UPDATEABLE)    20180706220210
plugins/VIB_-3.0.3.jar  (UPDATEABLE)    20200731193402
plugins/Vaa3d_Reader-2.0.3.jar  (UPDATEABLE)    20200731193402
plugins/Vaa3d_Writer-1.0.3.jar  (UPDATEABLE)    20210915210749
plugins/Video_Editing-2.0.1.jar (UPDATEABLE)    20170530201750
plugins/View5D_-2.3.6.jar       (UPDATEABLE)    20210915210749
plugins/Volume_Calculator-2.0.2.jar     (UPDATEABLE)    20170530201750
plugins/Volume_Viewer-2.01.2.jar        (UPDATEABLE)    20170530201750
plugins/bUnwarpJ_-2.6.13.jar    (UPDATEABLE)    20200731193402
plugins/bigdataviewer_fiji-6.2.2.jar    (UPDATEABLE)    20211203143546
plugins/bigwarp_fiji-7.0.5.jar  (UPDATEABLE)    20220201121025
plugins/bio-formats_plugins-6.9.0.jar   (UPDATEABLE)    20220224113621
plugins/blockmatching_-2.1.3.jar        (UPDATEABLE)    20180706220210
plugins/level_sets-1.0.2.jar    (UPDATEABLE)    20170530201750
plugins/mpicbg_-1.4.1.jar       (UPDATEABLE)    20200825115610
plugins/panorama_-3.0.2.jar     (UPDATEABLE)    20170530201750
plugins/register_virtual_stack_slices-3.0.5.jar (UPDATEABLE)    20210915210749
plugins/registration_3d-2.0.1.jar       (UPDATEABLE)    20170530201750
plugins/trakem2_tps-1.1.4.jar   (UPDATEABLE)    20180526000053
plugins/z_spacing-1.1.1.jar     (UPDATEABLE)    20181204141527
jars/T2-NIT-1.1.3.jar   (UPDATEABLE)    20210915210749
jars/T2-TreelineGraph-1.1.3.jar (UPDATEABLE)    20200731193402
jars/VIB-lib-2.2.0.jar  (UPDATEABLE)    20210915210749
jars/VectorString-2.0.2.jar     (UPDATEABLE)    20181204141527
jars/ant-1.9.7.jar      (UPDATEABLE)    20200731193402
jars/ant-launcher-1.9.7.jar     (UPDATEABLE)    20200731193402
jars/asm-7.1.jar        (UPDATEABLE)    20200731193402
jars/asm-analysis-7.1.jar       (UPDATEABLE)    20200731193402
jars/asm-commons-7.1.jar        (UPDATEABLE)    20200731193402
jars/asm-tree-7.1.jar   (UPDATEABLE)    20200731193402
jars/asm-util-7.1.jar   (UPDATEABLE)    20200731193402
jars/autocomplete-3.1.0.jar     (UPDATEABLE)    20200731193402
jars/batik-anim-1.13.jar        (UPDATEABLE)    20200731193402
jars/batik-awt-util-1.13.jar    (UPDATEABLE)    20200731193402
jars/batik-bridge-1.13.jar      (UPDATEABLE)    20200731193402
jars/batik-css-1.13.jar (UPDATEABLE)    20200731193402
jars/batik-dom-1.13.jar (UPDATEABLE)    20200731193402
jars/batik-ext-1.13.jar (UPDATEABLE)    20200731193402
jars/batik-gvt-1.13.jar (UPDATEABLE)    20200731193402
jars/batik-parser-1.13.jar      (UPDATEABLE)    20200731193402
jars/batik-script-1.13.jar      (UPDATEABLE)    20200731193402
jars/batik-svg-dom-1.13.jar     (UPDATEABLE)    20200731193402
jars/batik-svggen-1.13.jar      (UPDATEABLE)    20200731193402
jars/batik-util-1.13.jar        (UPDATEABLE)    20200731193402
jars/batik-xml-1.13.jar (UPDATEABLE)    20200731193402
jars/bigdataviewer-core-10.2.2.jar      (UPDATEABLE)    20211201154914
jars/bigdataviewer-vistools-1.0.0-beta-29.jar   (UPDATEABLE)    20211201154914
jars/bio-formats/formats-api-6.9.0.jar  (UPDATEABLE)    20220224113621
jars/bio-formats/formats-bsd-6.9.0.jar  (UPDATEABLE)    20220224113621
jars/bio-formats/formats-gpl-6.9.0.jar  (UPDATEABLE)    20220224113621
jars/bio-formats/jxrlib-all-0.2.4.jar   (UPDATEABLE)    20200721100103
jars/bio-formats/metakit-5.3.3.jar      (UPDATEABLE)    20210823155303
jars/bio-formats/ome-common-6.0.7.jar   (UPDATEABLE)    20210823155303
jars/bio-formats/ome-mdbtools-5.3.2.jar (UPDATEABLE)    20180903142856
jars/bio-formats/ome-poi-5.3.4.jar      (UPDATEABLE)    20210823155303
jars/bio-formats/ome-xml-6.2.3.jar      (UPDATEABLE)    20210823155303
jars/bio-formats/specification-6.2.3.jar        (UPDATEABLE)    20210823155303
jars/bio-formats/turbojpeg-6.9.0.jar    (UPDATEABLE)    20220224113621
jars/bytelist-1.0.15.jar        (UPDATEABLE)    20181204141527
jars/commons-codec-1.14.jar     (UPDATEABLE)    20200731193402
jars/commons-compress-1.20.jar  (UPDATEABLE)    20200731193402
jars/commons-lang3-3.10.jar     (UPDATEABLE)    20200731193402
jars/commons-logging-1.2.jar    (UPDATEABLE)    20180526000053
jars/ffmpeg-4.1-1.4.4.jar       (UPDATEABLE)    20190524140906
jars/fiji-2.3.1.jar     (UPDATEABLE)    20210915210749
jars/fiji-compat-0.0.0-STUB.jar (UPDATEABLE)    20200731193402
jars/fiji-lib-2.1.3.jar (UPDATEABLE)    20210915210749
jars/groovy-3.0.4.jar   (UPDATEABLE)    20200731193402
jars/gson-2.8.6.jar     (UPDATEABLE)    20200731193402
jars/guava-21.0.jar     (UPDATEABLE)    20170530201750
jars/ij-1.53f.jar       (UPDATEABLE)    20210915210749
jars/ij1-patcher-1.2.1.jar      (UPDATEABLE)    20210915210749
jars/imagej-2.3.0.jar   (UPDATEABLE)    20210915210749
jars/imagej-common-0.34.1.jar   (UPDATEABLE)    20210915210749
jars/imagej-deprecated-0.1.4.jar        (UPDATEABLE)    20210915210749
jars/imagej-launcher-6.0.1.jar  (UPDATEABLE)    20210915210749
jars/imagej-legacy-0.38.0.jar   (UPDATEABLE)    20210915210749
jars/imagej-notebook-0.7.1.jar  (UPDATEABLE)    20210915210749
jars/imagej-ops-0.45.8.jar      (UPDATEABLE)    20210915210749
jars/imagej-plugins-commands-0.8.1.jar  (UPDATEABLE)    20210915210749
jars/imagej-plugins-tools-0.3.1.jar     (UPDATEABLE)    20210915210749
jars/imagej-plugins-uploader-ssh-0.3.2.jar      (UPDATEABLE)    20210915210749
jars/imagej-plugins-uploader-webdav-0.3.2.jar   (UPDATEABLE)    20200731193402
jars/imagej-scripting-0.8.2.jar (UPDATEABLE)    20210915210749
jars/imagej-ui-awt-0.3.1.jar    (UPDATEABLE)    20210915210749
jars/imagej-ui-swing-0.23.3.jar (UPDATEABLE)    20210929092044
jars/imagej-updater-0.10.5.jar  (UPDATEABLE)    20200731193402
jars/imglib2-5.12.0.jar (UPDATEABLE)    20210915210749
jars/imglib2-algorithm-0.12.1.jar       (UPDATEABLE)    20211221103301
jars/imglib2-algorithm-fft-0.2.0.jar    (UPDATEABLE)    20180526000053
jars/imglib2-algorithm-gpl-0.2.5.jar    (UPDATEABLE)    20201027145432
jars/imglib2-ij-2.0.0-beta-46.jar       (UPDATEABLE)    20200731193402
jars/imglib2-realtransform-3.1.2.jar    (UPDATEABLE)    20220203093610
jars/imglib2-roi-0.11.0.jar     (UPDATEABLE)    20210915210749
jars/imglib2-ui-2.0.1.jar       (UPDATEABLE)    20200731193402
jars/invokebinder-1.10.jar      (UPDATEABLE)    20181204141527
jars/itextpdf-5.5.13.1.jar      (UPDATEABLE)    20200731193402
jars/javacpp-1.4.4.jar  (UPDATEABLE)    20190524140906
jars/javassist-3.27.0-GA.jar    (UPDATEABLE)    20200731193402
jars/jcodings-1.0.55.jar        (UPDATEABLE)    20210915210749
jars/jcommon-1.0.24.jar (UPDATEABLE)    20170530201750
jars/jffi-1.2.19-native.jar     (UPDATEABLE)    20200731193402
jars/jffi-1.2.20.jar    (UPDATEABLE)    20200731193402
jars/jfreechart-1.5.0.jar       (UPDATEABLE)    20171226155229
jars/jgrapht-0.0.0-STUB.jar     (UPDATEABLE)    20200731193402
jars/jgraphx-4.1.0.jar  (UPDATEABLE)    20200731193402
jars/jhdf5-14.12.6.jar  (UPDATEABLE)    20171226155229
jars/jitk-tps-3.0.2.jar (UPDATEABLE)    20220201121025
jars/jna-4.5.2.jar      (UPDATEABLE)    20181204141527
jars/jnr-constants-0.9.12.jar   (UPDATEABLE)    20200731193402
jars/jnr-enxio-0.16.jar (UPDATEABLE)    20181204141527
jars/jnr-ffi-2.1.10.jar (UPDATEABLE)    20200731193402
jars/jnr-netdb-1.1.6.jar        (UPDATEABLE)    20181204141527
jars/jnr-posix-3.0.50.jar       (UPDATEABLE)    20200731193402
jars/jnr-unixsocket-0.17.jar    (UPDATEABLE)    20181204141527
jars/joda-time-2.10.6.jar       (UPDATEABLE)    20200731193402
jars/joni-2.1.29.jar    (UPDATEABLE)    20201016171405
jars/jruby-core-9.1.17.0.jar    (UPDATEABLE)    20181204141527
jars/jruby-stdlib-9.1.17.0.jar  (UPDATEABLE)    20181204141527
jars/jsch-0.1.55.jar    (UPDATEABLE)    20181204141527
jars/jython-shaded-0.0.0-STUB.jar       (UPDATEABLE)    20200731193402
jars/jzlib-1.1.3.jar    (UPDATEABLE)    20170530201750
jars/kryo-4.0.2.jar     (UPDATEABLE)    20210915210749
jars/languagesupport-3.1.0.jar  (UPDATEABLE)    20200731193402
jars/legacy-imglib1-1.1.9.jar   (UPDATEABLE)    20210915210749
jars/linux64/ffmpeg-4.1-1.4.4-linux-x86_64.jar  (UPDATEABLE)    20190524140906
jars/log4j-0.0.0-STUB.jar       (UPDATEABLE)    20220201121025
jars/logback-classic-1.2.3.jar  (UPDATEABLE)    20170530201750
jars/logback-core-1.2.3.jar     (UPDATEABLE)    20170530201750
jars/mapdb-0.0.0-STUB.jar       (UPDATEABLE)    20200731193402
jars/metadata-extractor-2.11.0.jar      (UPDATEABLE)    20200731193402
jars/miglayout-swing-5.2.jar    (UPDATEABLE)    20200731193402
jars/minimaven-2.2.2.jar        (UPDATEABLE)    20200731193402
jars/minlog-1.3.0.jar   (UPDATEABLE)    20210915210749
jars/mpicbg-1.4.1.jar   (UPDATEABLE)    20200825115610
jars/native-lib-loader-2.3.6.jar        (UPDATEABLE)    20210915210749
jars/netcdf-0.0.0-STUB.jar      (UPDATEABLE)    20210915210749
jars/objenesis-2.5.1.jar        (UPDATEABLE)    20210915210749
jars/op-finder-0.1.4.jar        (UPDATEABLE)    20200731193402
jars/opencsv-5.2.jar    (UPDATEABLE)    20210915210749
jars/options-1.4.jar    (UPDATEABLE)    20181204141527
jars/pal-optimization-2.0.1.jar (UPDATEABLE)    20170530201750
jars/parsington-2.0.0.jar       (UPDATEABLE)    20200731193402
jars/perf4j-0.9.16.jar  (UPDATEABLE)    20200731193402
jars/postgresql-42.2.12.jar     (UPDATEABLE)    20200731193402
jars/rsyntaxtextarea-3.1.1.jar  (UPDATEABLE)    20200731193402
jars/scifio-0.42.0.jar  (UPDATEABLE)    20210508213753
jars/scifio-bf-compat-4.1.0.jar (UPDATEABLE)    20200731193402
jars/scifio-cli-0.6.1.jar       (UPDATEABLE)    20200731193402
jars/scifio-hdf5-0.2.1.jar      (UPDATEABLE)    20200731193402
jars/scifio-jai-imageio-1.1.1.jar       (UPDATEABLE)    20210915210749
jars/scifio-lifesci-0.9.0.jar   (UPDATEABLE)    20200731193402
jars/scifio-ome-xml-0.16.1.jar  (UPDATEABLE)    20210915210749
jars/scijava-common-2.87.0.jar  (UPDATEABLE)    20210915210749
jars/scijava-config-2.0.2.jar   (UPDATEABLE)    20170530201750
jars/scijava-plugins-commands-0.2.3.jar (UPDATEABLE)    20210915210749
jars/scijava-plugins-platforms-0.3.1.jar        (UPDATEABLE)    20210915210749
jars/scijava-plugins-text-markdown-0.1.3.jar    (UPDATEABLE)    20170530201750
jars/scijava-plugins-text-plain-0.1.3.jar       (UPDATEABLE)    20170530201750
jars/scijava-ui-awt-0.1.7.jar   (UPDATEABLE)    20210915210749
jars/scijava-ui-swing-0.13.3.jar        (UPDATEABLE)    20210915210749
jars/script-editor-0.7.4.jar    (UPDATEABLE)    20220310111006
jars/scripting-beanshell-0.3.4.jar      (UPDATEABLE)    20200731193402
jars/scripting-clojure-0.1.6.jar        (UPDATEABLE)    20170530201750
jars/scripting-groovy-0.3.0.jar (UPDATEABLE)    20200731193402
jars/scripting-java-0.4.1.jar   (UPDATEABLE)    20200731193402
jars/scripting-javascript-0.5.0.jar     (UPDATEABLE)    20200731193402
jars/scripting-jruby-0.3.1.jar  (UPDATEABLE)    20210915210749
jars/scripting-jython-1.0.0.jar (UPDATEABLE)    20200731193402
jars/scripting-renjin-0.2.3.jar (UPDATEABLE)    20200731193402
jars/scripting-scala-0.2.2.jar  (UPDATEABLE)    20200731193402
jars/slf4j-api-1.7.30.jar       (UPDATEABLE)    20200731193402
jars/snakeyaml-1.26.jar (UPDATEABLE)    20200731193402
jars/spim_data-2.2.4.jar        (UPDATEABLE)    20200731193402
jars/swing-checkbox-tree-1.0.2.jar      (UPDATEABLE)    20170530201750
jars/ui-behaviour-2.0.3.jar     (UPDATEABLE)    20210320233234
jars/weave_jy2java-2.1.1.jar    (UPDATEABLE)    20210915210749
jars/weka-dev-3.9.4.jar (UPDATEABLE)    20200731193402
jars/xmlgraphics-commons-2.4.jar        (UPDATEABLE)    20200731193402
jars/xmpcore-5.1.3.jar  (UPDATEABLE)    20200731193402
jars/xz-1.8.jar (UPDATEABLE)    20200731193402
jars/yecht-0.0.0-STUB.jar       (UPDATEABLE)    20200731193402

Then If I add BigDataProcessor with:

$ ImageJ --headless --update add-update-site BigDataProcessor http://sites.imagej.net/BigDataProcessor/
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option PermSize=128m; support was removed in 8.0
Picked up _JAVA_OPTIONS: -Dawt.useSystemAAFontSettings=on
Java HotSpot(TM) 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release
Done: Checksummer

Then I get:

$ ImageJ --headless --update list-updateable
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option PermSize=128m; support was removed in 8.0
Picked up _JAVA_OPTIONS: -Dawt.useSystemAAFontSettings=on
Java HotSpot(TM) 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release
Done: Checksummer
plugins/3D_Blob_Segmentation-3.0.1.jar  (UPDATEABLE)    20210915210749
plugins/3D_Objects_Counter-2.0.1.jar    (UPDATEABLE)    20170530201750
plugins/3D_Viewer-4.0.3.jar     (UPDATEABLE)    20200731193402
plugins/AnalyzeSkeleton_-3.4.2.jar      (UPDATEABLE)    20210915210749
plugins/Anisotropic_Diffusion_2D-2.0.1.jar      (UPDATEABLE)    20170530201750
plugins/Archipelago_Plugins-0.5.4.jar   (UPDATEABLE)    20170530201750
plugins/Arrow_-2.0.2.jar        (UPDATEABLE)    20170530201750
plugins/Auto_Threshold-1.17.2.jar       (UPDATEABLE)    20200731193402
plugins/BalloonSegmentation_-3.0.1.jar  (UPDATEABLE)    20170530201750
plugins/Bug_Submitter-2.1.1.jar (UPDATEABLE)    20170530201750
plugins/CPU_Meter-2.0.1.jar     (UPDATEABLE)    20170530201750
plugins/Calculator_Plus-2.0.1.jar       (UPDATEABLE)    20170530201750
plugins/Cell_Counter-3.0.0.jar  (UPDATEABLE)    20200731193402
plugins/Colocalisation_Analysis-3.0.5.jar       (UPDATEABLE)    20210915210749
plugins/Color_Histogram-2.0.7.jar       (UPDATEABLE)    20170530201750
plugins/Color_Inspector_3D-2.5.0.jar    (UPDATEABLE)    20200731193402
plugins/Colour_Deconvolution-3.0.3.jar  (UPDATEABLE)    20200731193402
plugins/CorrectBleach_-2.0.3.jar        (UPDATEABLE)    20200731193402
plugins/Correct_3D_Drift-1.0.6.jar      (UPDATEABLE)    20200731193402
plugins/Descriptor_based_registration-2.1.7.jar (UPDATEABLE)    20200611133920
plugins/Dichromacy_-2.1.2.jar   (UPDATEABLE)    20200731193402
plugins/Directionality_-2.3.0.jar       (UPDATEABLE)    20181204141527
plugins/Examples/CoverMaker/Prepare_Cover_Maker_Database.py     (UPDATEABLE)    20220211201246
plugins/Examples/Multithreaded_Image_Processing_in_Javascript.js        (UPDATEABLE)    20220211201246
plugins/Examples/The_Hue_Game.bsh       (UPDATEABLE)    20220211201246
plugins/FS_Align_TrakEM2-2.0.3.jar      (UPDATEABLE)    20180706220210
plugins/Feature_Detection-2.0.2.jar     (UPDATEABLE)    20170530201750
plugins/Fiji_Archipelago-2.0.1.jar      (UPDATEABLE)    20210915210749
plugins/Fiji_Developer-2.0.7.jar        (UPDATEABLE)    20180706220210
plugins/Fiji_Package_Maker-2.1.1.jar    (UPDATEABLE)    20170530201750
plugins/Fiji_Plugins-3.1.1.jar  (UPDATEABLE)    20170530201750
plugins/FlowJ_-2.0.1.jar        (UPDATEABLE)    20200731193402
plugins/Graph_Cut-1.0.2.jar     (UPDATEABLE)    20210915210749
plugins/Gray_Morphology-2.3.5.jar       (UPDATEABLE)    20200731193402
plugins/H5J_Loader_Plugin-1.1.0.jar     (UPDATEABLE)    20210915210749
plugins/Helmholtz_Analysis-2.0.2.jar    (UPDATEABLE)    20170530201750
plugins/IJ_Robot-2.0.1.jar      (UPDATEABLE)    20170530201750
plugins/IO_-4.1.0.jar   (UPDATEABLE)    20200731193402
plugins/Image_5D-2.0.2.jar      (UPDATEABLE)    20170530201750
plugins/Image_Expression_Parser-3.0.1.jar       (UPDATEABLE)    20210915210749
plugins/Interactive_3D_Surface_Plot-3.0.0.jar   (UPDATEABLE)    20170530201750
plugins/IsoData_Classifier-2.0.1.jar    (UPDATEABLE)    20170530201750
plugins/JRuby/imagej.rb (UPDATEABLE)    20220211201246
plugins/Kuwahara_Filter-2.0.1.jar       (UPDATEABLE)    20170530201750
plugins/KymographBuilder-2.1.1.jar      (UPDATEABLE)    20181204141527
plugins/LSM_Reader-4.1.2.jar    (UPDATEABLE)    20170530201750
plugins/LSM_Toolbox-4.1.2.jar   (UPDATEABLE)    20210915210749
plugins/Lasso_and_Blow_Tool-2.0.2.jar   (UPDATEABLE)    20170530201750
plugins/Linear_Kuwahara-2.0.1.jar       (UPDATEABLE)    20170530201750
plugins/LocalThickness_-4.0.3.jar       (UPDATEABLE)    20200731193402
plugins/MTrack2_-2.0.1.jar      (UPDATEABLE)    20170530201750
plugins/M_I_P-2.0.1.jar (UPDATEABLE)    20170530201750
plugins/Manual_Tracking-2.1.1.jar       (UPDATEABLE)    20170530201750
plugins/Multi_Kymograph-3.0.1.jar       (UPDATEABLE)    20170530201750
plugins/PIV_analyser-1.1.2.jar  (UPDATEABLE)    20170530201750
plugins/QuickPALM_-1.1.2.jar    (UPDATEABLE)    20170530201750
plugins/RATS_-2.0.2.jar (UPDATEABLE)    20171226155229
plugins/Reconstruct_Reader-2.0.4.jar    (UPDATEABLE)    20180706220210
plugins/SPIM_Opener-2.0.2.jar   (UPDATEABLE)    20170530201750
plugins/SPIM_Registration-5.0.22.jar    (UPDATEABLE)    20210915210749
plugins/Samples_-2.0.2.jar      (UPDATEABLE)    20170530201750
plugins/Scripts/Image/Hyperstacks/Temporal-Color_Code.ijm       (UPDATEABLE)    20220211201246
plugins/Scripts/Plugins/Utilities/Record_Window.py      (UPDATEABLE)    20220211201246
plugins/Series_Labeler-2.0.1.jar        (UPDATEABLE)    20170530201750
plugins/Sholl_Analysis-0.0.0-STUB.jar   (UPDATEABLE)    20210915210749
plugins/Simple_Neurite_Tracer-0.0.0-STUB.jar    (UPDATEABLE)    20210915210749
plugins/Siox_Segmentation-1.0.5.jar     (UPDATEABLE)    20210915210749
plugins/Skeletonize3D_-2.1.1.jar        (UPDATEABLE)    20170530201750
plugins/SplineDeformationGenerator_-2.0.2.jar   (UPDATEABLE)    20171226155229
plugins/Stack_Manipulation-2.1.2.jar    (UPDATEABLE)    20190603111541
plugins/Statistical_Region_Merging-2.0.1.jar    (UPDATEABLE)    20170530201750
plugins/Stitching_-3.1.8.jar    (UPDATEABLE)    20210907125640
plugins/Sync_Win-1.7-fiji4.jar  (UPDATEABLE)    20210915210749
plugins/Thread_Killer-2.0.1.jar (UPDATEABLE)    20170530201750
plugins/Time_Lapse-2.1.1.jar    (UPDATEABLE)    20200731193402
plugins/Time_Stamper-2.1.0.jar  (UPDATEABLE)    20171226155229
plugins/ToAST_-25.0.2.jar       (UPDATEABLE)    20170530201750
plugins/TopoJ_-2.0.1.jar        (UPDATEABLE)    20170530201750
plugins/TrackMate_-0.0.0-STUB.jar       (UPDATEABLE)    20210915210749
plugins/Trainable_Segmentation-3.3.2.jar        (UPDATEABLE)    20220114124145
plugins/TrakEM2_-1.3.6.jar      (UPDATEABLE)    20210915210749
plugins/TrakEM2_Archipelago-2.0.3.jar   (UPDATEABLE)    20180706220210
plugins/VIB_-3.0.3.jar  (UPDATEABLE)    20200731193402
plugins/Vaa3d_Reader-2.0.3.jar  (UPDATEABLE)    20200731193402
plugins/Vaa3d_Writer-1.0.3.jar  (UPDATEABLE)    20210915210749
plugins/Video_Editing-2.0.1.jar (UPDATEABLE)    20170530201750
plugins/View5D_-2.3.6.jar       (UPDATEABLE)    20210915210749
plugins/Volume_Calculator-2.0.2.jar     (UPDATEABLE)    20170530201750
plugins/Volume_Viewer-2.01.2.jar        (UPDATEABLE)    20170530201750
plugins/bUnwarpJ_-2.6.13.jar    (UPDATEABLE)    20200731193402
plugins/bigdataviewer_fiji-6.2.2.jar    (UPDATEABLE)    20211203143546
plugins/bigwarp_fiji-7.0.5.jar  (UPDATEABLE)    20220201121025
plugins/bio-formats_plugins-6.9.0.jar   (UPDATEABLE)    20220224113621
plugins/blockmatching_-2.1.3.jar        (UPDATEABLE)    20180706220210
plugins/level_sets-1.0.2.jar    (UPDATEABLE)    20170530201750
plugins/mpicbg_-1.4.1.jar       (UPDATEABLE)    20200825115610
plugins/panorama_-3.0.2.jar     (UPDATEABLE)    20170530201750
plugins/register_virtual_stack_slices-3.0.5.jar (UPDATEABLE)    20210915210749
plugins/registration_3d-2.0.1.jar       (UPDATEABLE)    20170530201750
plugins/trakem2_tps-1.1.4.jar   (UPDATEABLE)    20180526000053
plugins/z_spacing-1.1.1.jar     (UPDATEABLE)    20181204141527
jars/T2-NIT-1.1.3.jar   (UPDATEABLE)    20210915210749
jars/T2-TreelineGraph-1.1.3.jar (UPDATEABLE)    20200731193402
jars/VIB-lib-2.2.0.jar  (UPDATEABLE)    20210915210749
jars/VectorString-2.0.2.jar     (UPDATEABLE)    20181204141527
jars/ant-1.9.7.jar      (UPDATEABLE)    20200731193402
jars/ant-launcher-1.9.7.jar     (UPDATEABLE)    20200731193402
jars/asm-7.1.jar        (UPDATEABLE)    20200731193402
jars/asm-analysis-7.1.jar       (UPDATEABLE)    20200731193402
jars/asm-commons-7.1.jar        (UPDATEABLE)    20200731193402
jars/asm-tree-7.1.jar   (UPDATEABLE)    20200731193402
jars/asm-util-7.1.jar   (UPDATEABLE)    20200731193402
jars/autocomplete-3.1.0.jar     (UPDATEABLE)    20200731193402
jars/batik-anim-1.13.jar        (UPDATEABLE)    20200731193402
jars/batik-awt-util-1.13.jar    (UPDATEABLE)    20200731193402
jars/batik-bridge-1.13.jar      (UPDATEABLE)    20200731193402
jars/batik-css-1.13.jar (UPDATEABLE)    20200731193402
jars/batik-dom-1.13.jar (UPDATEABLE)    20200731193402
jars/batik-ext-1.13.jar (UPDATEABLE)    20200731193402
jars/batik-gvt-1.13.jar (UPDATEABLE)    20200731193402
jars/batik-parser-1.13.jar      (UPDATEABLE)    20200731193402
jars/batik-script-1.13.jar      (UPDATEABLE)    20200731193402
jars/batik-svg-dom-1.13.jar     (UPDATEABLE)    20200731193402
jars/batik-svggen-1.13.jar      (UPDATEABLE)    20200731193402
jars/batik-util-1.13.jar        (UPDATEABLE)    20200731193402
jars/batik-xml-1.13.jar (UPDATEABLE)    20200731193402
jars/bigdataviewer-core-10.2.2.jar      (UPDATEABLE)    20211201154914
jars/bigdataviewer-vistools-1.0.0-beta-29.jar   (UPDATEABLE)    20211201154914
jars/bio-formats/formats-api-6.9.0.jar  (UPDATEABLE)    20220224113621
jars/bio-formats/formats-bsd-6.9.0.jar  (UPDATEABLE)    20220224113621
jars/bio-formats/formats-gpl-6.9.0.jar  (UPDATEABLE)    20220224113621
jars/bio-formats/jxrlib-all-0.2.4.jar   (UPDATEABLE)    20200721100103
jars/bio-formats/metakit-5.3.3.jar      (UPDATEABLE)    20210823155303
jars/bio-formats/ome-common-6.0.7.jar   (UPDATEABLE)    20210823155303
jars/bio-formats/ome-mdbtools-5.3.2.jar (UPDATEABLE)    20180903142856
jars/bio-formats/ome-poi-5.3.4.jar      (UPDATEABLE)    20210823155303
jars/bio-formats/ome-xml-6.2.3.jar      (UPDATEABLE)    20210823155303
jars/bio-formats/specification-6.2.3.jar        (UPDATEABLE)    20210823155303
jars/bio-formats/turbojpeg-6.9.0.jar    (UPDATEABLE)    20220224113621
jars/bytelist-1.0.15.jar        (UPDATEABLE)    20181204141527
jars/commons-codec-1.14.jar     (UPDATEABLE)    20200731193402
jars/commons-compress-1.20.jar  (UPDATEABLE)    20200731193402
jars/commons-lang3-3.10.jar     (UPDATEABLE)    20200731193402
jars/commons-logging-1.2.jar    (UPDATEABLE)    20180526000053
jars/ffmpeg-4.1-1.4.4.jar       (UPDATEABLE)    20190524140906
jars/fiji-2.3.1.jar     (UPDATEABLE)    20210915210749
jars/fiji-compat-0.0.0-STUB.jar (UPDATEABLE)    20200731193402
jars/fiji-lib-2.1.3.jar (UPDATEABLE)    20210915210749
jars/groovy-3.0.4.jar   (UPDATEABLE)    20200731193402
jars/gson-2.8.6.jar     (UPDATEABLE)    20200731193402
jars/guava-21.0.jar     (UPDATEABLE)    20170530201750
jars/ij-1.53f.jar       (UPDATEABLE)    20210915210749
jars/ij1-patcher-1.2.1.jar      (UPDATEABLE)    20210915210749
jars/imagej-2.3.0.jar   (UPDATEABLE)    20210915210749
jars/imagej-common-0.34.1.jar   (UPDATEABLE)    20210915210749
jars/imagej-deprecated-0.1.4.jar        (UPDATEABLE)    20210915210749
jars/imagej-launcher-6.0.1.jar  (UPDATEABLE)    20210915210749
jars/imagej-legacy-0.38.0.jar   (UPDATEABLE)    20210915210749
jars/imagej-notebook-0.7.1.jar  (UPDATEABLE)    20210915210749
jars/imagej-ops-0.45.8.jar      (UPDATEABLE)    20210915210749
jars/imagej-plugins-commands-0.8.1.jar  (UPDATEABLE)    20210915210749
jars/imagej-plugins-tools-0.3.1.jar     (UPDATEABLE)    20210915210749
jars/imagej-plugins-uploader-ssh-0.3.2.jar      (UPDATEABLE)    20210915210749
jars/imagej-plugins-uploader-webdav-0.3.2.jar   (UPDATEABLE)    20200731193402
jars/imagej-scripting-0.8.2.jar (UPDATEABLE)    20210915210749
jars/imagej-ui-awt-0.3.1.jar    (UPDATEABLE)    20210915210749
jars/imagej-ui-swing-0.23.3.jar (UPDATEABLE)    20210929092044
jars/imagej-updater-0.10.5.jar  (UPDATEABLE)    20200731193402
jars/imglib2-5.12.0.jar (UPDATEABLE)    20210915210749
jars/imglib2-algorithm-0.12.1.jar       (UPDATEABLE)    20211221103301
jars/imglib2-algorithm-fft-0.2.0.jar    (UPDATEABLE)    20180526000053
jars/imglib2-algorithm-gpl-0.2.5.jar    (UPDATEABLE)    20201027145432
jars/imglib2-ij-2.0.0-beta-46.jar       (UPDATEABLE)    20200731193402
jars/imglib2-realtransform-3.1.2.jar    (UPDATEABLE)    20220203093610
jars/imglib2-roi-0.11.0.jar     (UPDATEABLE)    20210915210749
jars/imglib2-ui-2.0.1.jar       (UPDATEABLE)    20200731193402
jars/invokebinder-1.10.jar      (UPDATEABLE)    20181204141527
jars/itextpdf-5.5.13.1.jar      (UPDATEABLE)    20200731193402
jars/javacpp-1.4.4.jar  (UPDATEABLE)    20190524140906
jars/javassist-3.27.0-GA.jar    (UPDATEABLE)    20200731193402
jars/jcodings-1.0.55.jar        (UPDATEABLE)    20210915210749
jars/jcommon-1.0.24.jar (UPDATEABLE)    20170530201750
jars/jffi-1.2.19-native.jar     (UPDATEABLE)    20200731193402
jars/jffi-1.2.20.jar    (UPDATEABLE)    20200731193402
jars/jfreechart-1.5.0.jar       (UPDATEABLE)    20171226155229
jars/jgrapht-0.0.0-STUB.jar     (UPDATEABLE)    20200731193402
jars/jgraphx-4.1.0.jar  (UPDATEABLE)    20200731193402
jars/jhdf5-14.12.6.jar  (UPDATEABLE)    20171226155229
jars/jitk-tps-3.0.2.jar (UPDATEABLE)    20220201121025
jars/jna-4.5.2.jar      (UPDATEABLE)    20181204141527
jars/jnr-constants-0.9.12.jar   (UPDATEABLE)    20200731193402
jars/jnr-enxio-0.16.jar (UPDATEABLE)    20181204141527
jars/jnr-ffi-2.1.10.jar (UPDATEABLE)    20200731193402
jars/jnr-netdb-1.1.6.jar        (UPDATEABLE)    20181204141527
jars/jnr-posix-3.0.50.jar       (UPDATEABLE)    20200731193402
jars/jnr-unixsocket-0.17.jar    (UPDATEABLE)    20181204141527
jars/joda-time-2.10.6.jar       (UPDATEABLE)    20200731193402
jars/joni-2.1.29.jar    (UPDATEABLE)    20201016171405
jars/jruby-core-9.1.17.0.jar    (UPDATEABLE)    20181204141527
jars/jruby-stdlib-9.1.17.0.jar  (UPDATEABLE)    20181204141527
jars/jsch-0.1.55.jar    (UPDATEABLE)    20181204141527
jars/jython-shaded-0.0.0-STUB.jar       (UPDATEABLE)    20200731193402
jars/jzlib-1.1.3.jar    (UPDATEABLE)    20170530201750
jars/kryo-4.0.2.jar     (UPDATEABLE)    20210915210749
jars/languagesupport-3.1.0.jar  (UPDATEABLE)    20200731193402
jars/legacy-imglib1-1.1.9.jar   (UPDATEABLE)    20210915210749
jars/linux64/ffmpeg-4.1-1.4.4-linux-x86_64.jar  (UPDATEABLE)    20190524140906
jars/log4j-0.0.0-STUB.jar       (UPDATEABLE)    20220201121025
jars/logback-classic-1.2.3.jar  (UPDATEABLE)    20170530201750
jars/logback-core-1.2.3.jar     (UPDATEABLE)    20170530201750
jars/mapdb-0.0.0-STUB.jar       (UPDATEABLE)    20200731193402
jars/metadata-extractor-2.11.0.jar      (UPDATEABLE)    20200731193402
jars/miglayout-swing-5.2.jar    (UPDATEABLE)    20200731193402
jars/minimaven-2.2.2.jar        (UPDATEABLE)    20200731193402
jars/minlog-1.3.0.jar   (UPDATEABLE)    20210915210749
jars/mpicbg-1.4.1.jar   (UPDATEABLE)    20200825115610
jars/native-lib-loader-2.3.6.jar        (UPDATEABLE)    20210915210749
jars/netcdf-0.0.0-STUB.jar      (UPDATEABLE)    20210915210749
jars/objenesis-2.5.1.jar        (UPDATEABLE)    20210915210749
jars/op-finder-0.1.4.jar        (UPDATEABLE)    20200731193402
jars/opencsv-5.2.jar    (UPDATEABLE)    20210915210749
jars/options-1.4.jar    (UPDATEABLE)    20181204141527
jars/pal-optimization-2.0.1.jar (UPDATEABLE)    20170530201750
jars/parsington-2.0.0.jar       (UPDATEABLE)    20200731193402
jars/perf4j-0.9.16.jar  (UPDATEABLE)    20200731193402
jars/postgresql-42.2.12.jar     (UPDATEABLE)    20200731193402
jars/rsyntaxtextarea-3.1.1.jar  (UPDATEABLE)    20200731193402
jars/scifio-0.42.0.jar  (UPDATEABLE)    20210508213753
jars/scifio-bf-compat-4.1.0.jar (UPDATEABLE)    20200731193402
jars/scifio-cli-0.6.1.jar       (UPDATEABLE)    20200731193402
jars/scifio-hdf5-0.2.1.jar      (UPDATEABLE)    20200731193402
jars/scifio-jai-imageio-1.1.1.jar       (UPDATEABLE)    20210915210749
jars/scifio-lifesci-0.9.0.jar   (UPDATEABLE)    20200731193402
jars/scifio-ome-xml-0.16.1.jar  (UPDATEABLE)    20210915210749
jars/scijava-common-2.87.0.jar  (UPDATEABLE)    20210915210749
jars/scijava-config-2.0.2.jar   (UPDATEABLE)    20170530201750
jars/scijava-plugins-commands-0.2.3.jar (UPDATEABLE)    20210915210749
jars/scijava-plugins-platforms-0.3.1.jar        (UPDATEABLE)    20210915210749
jars/scijava-plugins-text-markdown-0.1.3.jar    (UPDATEABLE)    20170530201750
jars/scijava-plugins-text-plain-0.1.3.jar       (UPDATEABLE)    20170530201750
jars/scijava-ui-awt-0.1.7.jar   (UPDATEABLE)    20210915210749
jars/scijava-ui-swing-0.13.3.jar        (UPDATEABLE)    20210915210749
jars/script-editor-0.7.4.jar    (UPDATEABLE)    20220310111006
jars/scripting-beanshell-0.3.4.jar      (UPDATEABLE)    20200731193402
jars/scripting-clojure-0.1.6.jar        (UPDATEABLE)    20170530201750
jars/scripting-groovy-0.3.0.jar (UPDATEABLE)    20200731193402
jars/scripting-java-0.4.1.jar   (UPDATEABLE)    20200731193402
jars/scripting-javascript-0.5.0.jar     (UPDATEABLE)    20200731193402
jars/scripting-jruby-0.3.1.jar  (UPDATEABLE)    20210915210749
jars/scripting-jython-1.0.0.jar (UPDATEABLE)    20200731193402
jars/scripting-renjin-0.2.3.jar (UPDATEABLE)    20200731193402
jars/scripting-scala-0.2.2.jar  (UPDATEABLE)    20200731193402
jars/slf4j-api-1.7.30.jar       (UPDATEABLE)    20200731193402
jars/snakeyaml-1.26.jar (UPDATEABLE)    20200731193402
jars/spim_data-2.2.4.jar        (UPDATEABLE)    20200731193402
jars/swing-checkbox-tree-1.0.2.jar      (UPDATEABLE)    20170530201750
jars/ui-behaviour-2.0.3.jar     (UPDATEABLE)    20210320233234
jars/weave_jy2java-2.1.1.jar    (UPDATEABLE)    20210915210749
jars/weka-dev-3.9.4.jar (UPDATEABLE)    20200731193402
jars/xmlgraphics-commons-2.4.jar        (UPDATEABLE)    20200731193402
jars/xmpcore-5.1.3.jar  (UPDATEABLE)    20200731193402
jars/xz-1.8.jar (UPDATEABLE)    20200731193402
jars/yecht-0.0.0-STUB.jar       (UPDATEABLE)    20200731193402

The goal of a conda recipe is to be able to easily reinstall a given version of each tool and plugin so I cannot do this in a bioconda recipe. That's why I need to add only the files related to BigDataProcessor.

2. Regarding the OBSOLETE_MODIFIED.
   This is with a fresh installation of ImageJ (not the 20170530 from conda but the one available at https://downloads.imagej.net/fiji/latest/fiji-linux64.zip which may be fiji-2.1.1).
   I did:

$ Fiji.app/ImageJ-linux64 --update add-update-site BigDataProcessor http://sites.imagej.net/BigDataProcessor/
$ Fiji.app/ImageJ-linux64 --update list-from-site BigDataProcessor

[tischi]

The goal of a conda recipe is to be able to easily reinstall a given version of each tool and plugin so I cannot do this in a bioconda recipe. That's why I need to add only the files related to BigDataProcessor.

I see, so you need to somehow download a fixed version of both Fiji and of the BigDataProcessor update site, correct?
In fact, I do not know how to achieve this, I only know how to download the latest versions of both.

@haesleinhuepf @imagejan do you maybe know how to install via command line a specific version of Fiji and a specific version of an update site?

[lldelisle]

Hi,
I just solved the OBSOLETE_MODIFIED, it was due to certificate on https://downloads.imagej.net/ that my HPC consider as expired...
Sorry.

[imagejan]

The BigDataProcessor update site (same as any other update site) is supposed to work with an up-to-date Fiji, not with the one from 2017. I doubt that installing just the BDP-related files will make much sense.

The problem is possible the outdated Fiji available from conda, maybe this can be updated? I suggest discussing this on forum.image.sc.

To my knowledge, the updater is currently not really suitable to achieve the goal of getting a specific version of all Fiji components from a given point in time.

If you need a reproducible Fiji installation, I'd suggest building bigdataprocessor2 with maven, where all dependencies are pinned to specific versions that are guaranteed to work together by the inherited bill of materials (BOM), pom-scijava.

I'll ping @ctrueden here, as I'm sure he'll be able to give better advice than me.