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seek4science / seek

For finding, sharing and exchanging Data, Models, Simulations and Processes in Science.
http://www.seek4science.org
BSD 3-Clause "New" or "Revised" License
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cwltool 3.0.20201203173111 not compatible with Docker container 20201203173111 #646

Closed stain closed 3 years ago

stain commented 3 years ago

7f9ae90 bumped the cwltool version in requirements.txt to 3.0.20201203173111 - however as the Debian 9 base image of Dockerfile (via ruby:2.6-stretch) is based on Python 3.5, building it will fail with:

Collecting cwltool==3.0.20201203173111 (from -r requirements.txt (line 1))
  Could not find a version that satisfies the requirement cwltool==3.0.20201203173111 (from -r requirements.txt (line 1)) (from versions: 0.1.20141118163626.cbb1b06, 0.1.20141118185349.d594c3e, 0.1.20141119031726.8dcd753, 0.1.20141125184103.2d72b5c

The last known Python 3.5 compatible cwltool is 3.0.20200807132242.

Python 3.5 was deprecated with 5 Sept 2020 which is around the same time.

Suggestion: Change Dockerfile with sed to force use of older cwltool==3.0.20200807132242 – or update to FROM ruby:2.6-buster ?

stain commented 3 years ago

Workaround in 8e37ef5d63d3ca824520115b775d5438c345b49b but given that Debian 10 was released in 2019-07-06 perhaps it's rather time to update the base image..

stain commented 3 years ago

@simleo point out:

The catch is that stretch does not support python 3.6, but switching to buster does not work either because it does not support openjdk 8 You get openjdk 11, which breaks Solr

stuzart commented 3 years ago

There is now a new Dockerfile on the master branch which uses buster and should solve the problems.

stuzart commented 3 years ago

$> docker run -it --rm fairdom/seek:workflow bash $> python --version Python 3.7.3