The format-checking test runs this CWL file, which assumes that a rev binary is available on the system, and does not provide one via container.
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$namespaces: |
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edam: "http://edamontology.org/" |
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cwlVersion: v1.2 |
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class: CommandLineTool |
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doc: "Reverse each line using the `rev` command" |
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inputs: |
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input: |
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type: File |
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inputBinding: {} |
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format: edam:format_2330 |
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outputs: |
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output: |
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type: File |
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outputBinding: |
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glob: output.txt |
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format: edam:format_2330 |
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baseCommand: rev |
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stdout: output.txt |
In Debian and Ubuntu (between 25.10 and 26.04), the rev binary which used to be in util-linux, an extremely essential package, is now in bsdextrautils, a less essential package. In particular, that package is not installed in the Docker container ubuntu:26.04. If you docker run -ti --rm ubuntu:26.04 dpkg --list you will see that it ships bsdutils, coreutils, and util-linux, but not bsdextrautils.
The test should probably be rewritten to not assume that all CWL host platforms ship a rev binary.
The format-checking test runs this CWL file, which assumes that a
revbinary is available on the system, and does not provide one via container.cwl-v1.2/tests/formattest.cwl
Lines 1 to 20 in 551d58d
In Debian and Ubuntu (between 25.10 and 26.04), the
revbinary which used to be inutil-linux, an extremely essential package, is now inbsdextrautils, a less essential package. In particular, that package is not installed in the Docker containerubuntu:26.04. If youdocker run -ti --rm ubuntu:26.04 dpkg --listyou will see that it shipsbsdutils,coreutils, andutil-linux, but notbsdextrautils.The test should probably be rewritten to not assume that all CWL host platforms ship a
revbinary.