Update cwltool version to match singularity/3.10.3

[qiyubio]

Hi, the current version of cwltool will report error on singularity/3.10.3 since the version become singularity-ce instead of singularity. Would you update the version to at least 3.1.20211014180718 or above? Thanks.

error:

Singularity is required to run this tool: invalid literal for int() with base 10: 's'

[yyoshiaki]

Hi, Thank you for reporting the issue. In my environment (singularity version 3.8.1-1.el7 cwltool 3.1.20210922203925), no error occurred at least. I will check other versions.

[qiyubio]

Thanks for your response. The error only came if the singularity --version output changed, I guess this is not completed related to the version of singularity, but more of which source of singularity was installed. The hpcng verion of singularity might work, but since they are going to change to apptainer, we switched to sylabs version, however, the sylabs' singularity are marking the version with community edition (ce), so that it will break the way that cwltool to check the singularity version.

[yyoshiaki]

Thank you for your detailed reports. Unfortunately, I'm not familiar with singularity, and the issue looks the matter around singularity and cwltool, so making an issue in cwltool repo may be better...

[qiyubio]

Just a reminder that the listed version of cwltool on the VIRTUS1/2 is out of date. It’s a known issue for cwltool, and fixed after version 3.1.20211014180718.

On Fri, Oct 14, 2022 at 10:30 PM Yoshiaki Yasumizu @.***> wrote:

Thank you for your detailed reports. Unfortunately, I'm not familiar with singularity, and the issue looks the matter around singularity and cwltool, so making an issue in cwltool repo https://github.com/common-workflow-language/cwltool may be better...

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[yyoshiaki]

Thank you, I confirmed that the latest cwltool (3.1.20221008225030) worked, and updated README.md.

[qiyubio]

Thanks you, I tested that cwltool/3.1.20221018083734 works too, and cwltool/3.1.20211014180718 will fail for VIRTUS/2.

[yyoshiaki]

Thank you!