Joe Slagel

Access token expires when accessing Google Cloud Storage (GS) objects

3

I’m currently using the GCS_OAUTH_TOKEN environment variable method to provide an OAuth access token to samtools in order to access GCS stored objects (see #390). Obtaining an access token is...

Significant number of critical vulnerabilities reported in dependencies

3

Running trivy against version 0.9.1 reports 25 critical vulnerabilities in dependent libraries used by bpipe. For example: - CVE-2017-17485 [https://avd.aquasec.com/nvd/cve-2017-17485](https://avd.aquasec.com/nvd/cve-2017-17485) - CVE-2016-6809 [https://avd.aquasec.com/nvd/cve-2016-6809]( https://avd.aquasec.com/nvd/cve-2016-6809) Would it be possible to update...

Allow make completions of intermediate targets if they are phony

4

Commit https://github.com/scop/bash-completion/commit/e0c08321795c8174fa2275d2683c4ffc1b36db5b appears to also fix an issue were intermediate targets were previously being included in completion when they probably shouldn't have. However there are use cases in which you...

Do you support custom application settings and data sections? does Illumina?

1

The V2 specification allows for [application settings ](https://support-docs.illumina.com/SHARE/SampleSheetv2/Content/SHARE/SampleSheetv2/SectionsApplications.htm )in the sample sheet. E.g for [BCL Convert](https://support-docs.illumina.com/SHARE/SampleSheetv2/Content/SHARE/SampleSheetv2/Settings_fNS_m2000_m1000.htm). Does sample-sheet support adding these application sections? and can you make your own application...

Noticed recently that I was having problems running an cwl and having docker install properly. Was using cwltool and the get.docker.com script seemed to be failing. Switched it over to...

Localization timestamp issue and docker container user

2

I'm using as inputs a bam file and its corresponding bam index file. When these files get localized the bam index file's timestamp sometimes will be newer than the bam...

Mounting a writable existing persistent disk?

2

I've had some good successes with mounting existing read-only persistent disks to the VM running a dsub job, and its very cool that one can do this. However I was...

Security concerns with using the '--ssh' option

4

I'm following up on an item reported by a [colleague](https://groups.google.com/g/gcp-life-sciences-discuss/c/Yoe9SiT7yHI) about and issue using `dsub` reporting an ssh error: ``` - name: 'Started running "ssh": listening on xx.xx.xxx:22 (22)' start-time:...

Since `dsub `is modeled after `qsub`, what about the idea of implementing interactive jobs similar to what `qsub` can do? As the qsub documentation says: > **-I** Declares that the...

dsub exit codes

2

Just wondering what one should expect if they were to run the following: `dsub --provider local --command 'exit 99' --logging /tmp/log` Right now dsub returns an error code of 1....