Open ksuderman opened 1 week ago
The fix is against release 24.0 actually so we won't have to wait for the next release.
True, but the branch won't be tagged so we won't get a Docker image built automatically (except for the 24.0-auto image). According to John D 24.1.1 will be released in a few days so it should be ok to wait until then.
Hi @ksuderman have you released the24.1.1
version with the objects
folder permission bug fixed?
Hi @Anik, I did not see a notification about the release, but I see galaxy-min:24.1.1 on quay.io. I am testing it now and will report back.
Our tests are passing and #481 will be merged shortly.
Alright. This morning I pulled the 24.1.1 that was available and still the permission denied issue persisted in the object folder. So, I was wondering if the issue was resolved or not.
Is that with Kraken? I will try to reproduce using that.
Yes, it is with Kraken. I also tried with Diamond database builder and faced the same error of permission denied.
Hi @ksuderman could you reproduce and resolve the error? Please let me know.
Yes I am able to reproduce, at least I think it is the same problem you are experiencing. To be sure though, it is the data_manager_build_kraken2_database
tool that is the problem and not kraken2
itself?
I think this is a separate, but related, bug. I am trying to get a few more data points before reaching out to the backend team to find a solution.
However, is there a reason you are trying to build the Kraken2 database manually rather than using the ones available on CVMFS? I see you have refdata.enabled=false
in your values.yaml
, at least the values shared on the GalaxyHelp channel. It looks like the database you want to use is available as part of the default reference data included on CVMFS.
refdata:
enabled: true
type: cvmfs
cvmfs:
deploy: true # unless you are deploying CVMFS separately from Galaxy
Hi @ksuderman thanks for reproducing the error. Yes, the problem is with the kraken2 database builder tool. Kraken2 itself works fine (or would work fine if there is a database). Regarding your second question, I need to build the database using the Prebuilt RefSeq indexes which are available and getting updated once or twice a year. Also, there is an option of building a custom database with reference genomes other than NCBI. I am not using that at the moment. I am just trying to build it from the available ones and getting the error. For the time being, I can try to change the value file and use your suggestion.
Galaxy 24.1.1 will include the fix that will allow us to remove read permission for the entire objects directory.