Dependency issues in module update after 1.8.0

[kmoad]

Hm - this is tricky: To hide the yaml warnings I had redirected stderr in a wrapper script. After install of 1.8.0, ocwrapper module update listed four things to update. Then nothing. For a really long time - until I clued in. Not sure I agree with the use of both stdout and stderr in the same breath? Then a slew of fun of our own making - a nasty permissions thing. Redo the install/update.Then a trial -expect nothing - run of oc module update: oc module update Newer versions of (cravat-converter, oldcravat-converter, vcf-converter) are available, but would break dependencies. You may use --strategy=force to force installation. No module updates are needed

I think we're good, but a little shakey. (I don't use oc, I'll pester she-who-does to try it asap)

Originally posted by @iceback in https://github.com/KarchinLab/open-cravat/issues/26#issuecomment-620345299

[kmoad]

@iceback New issue here for the dependency thing.

Could you send me the output of oc module ls -i. It'll probably be a quite a few lines. I'm going to recreate your installed modules and versions to see what's causing dependency issues.

[iceback]

Sure, give me a second

moduleListing.txt

[iceback]

Trouble today: 2020/04/28 12:07:31 cravat Input format could not be determined for file Batch1and3-joint.raw.SGS_regions.filteredInd.vcf.gz. Additional input format converters are available. View available converters in the store or with "oc module ls -a -t converter"

ocDriver module ls -a -t converter Name Title Type Installed Up to date Store latest ver Store data source ver Local ver Local data source ver Size 23andme-converter 23andMe Converter converter 1.3.1 15.7 kB ancestrydna-converter AncestryDNA Converter converter 1.3.1 27.4 kB cravat-converter Cravat Converter converter yes 1.1.2 None 9.2 kB dbsnp-converter dbSNP Converter converter 1.1.1 153 28.7 GB ftdna-converter FamilyTreeDNA Converter converter 1.3.1 28.4 kB oldcravat-converter OldCravat Converter converter yes 1.1.2 None 7.6 kB vcf-converter VCF Converter converter yes 1.4.2 None 48.9 kB

[kmoad]

It looks like a few modules only partially installed. One of them was vcf-converter, which is why the vcf file was not processed properly. The one's that partial installed have None as a version in moduleListing.txt. To fix it in your installation, run oc module uninstall XXXXX && oc module install XXXXX for the None version modules.

I expect this was caused when you cancelled the update. Normally, this would delete the module that was mid-install, but it seems like there was some corner case here that prevented it. We'll try to track it down and make the partial handling more robust next version.

[iceback]

Likely story😏. Will get those reloaded ASAP

On Apr 28, 2020, at 2:30 PM, Kyle Moad notifications@github.com wrote:

 It looks like a few modules only partially installed. One of them was vcf-converter, which is why the vcf file was not processed properly. The one's that partial installed have None as a version in moduleListing.txt. To fix it in your installation, run oc module uninstall XXXXX && oc module install XXXXX for the None version modules.

I expect this was caused when you cancelled the update. Normally, this would delete the module that was mid-install, but it seems like there was some corner case here that prevented it. We'll try to track it down and make the partial handling more robust next version.

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[iceback]

Yes! uninstalled, installed and things look good. Waiting for confirmation from the real user, but thanks for your help.