Adam Novak

Support Github-style ``` code ``` code blocks

1

I have a schema defined in AVDL which makes heavy use of backtick-delimited preformatted code blocks for ASCII art. Avrodoc does not interpret these correctly at all. I think the...

Pull images from Docker Hub through a caching mirror

4

### Version of Singularity: What version of Singularity are you using? Run: ``` $ singularity version 3.5.3 ``` ### Expected behavior When I run `singularity pull out.sif docker://ubuntu`, I want...

`S3.Object.copy()` doesn't handle edge cases in VPCs with S3 Endpoints where `CopyObject` is disallowed

2

### Describe the bug In my project which uses Boto3, I observed that a `copy()` call on an `S3.Object` failed with this stacktrace: Traceback (most recent call last): File "/usr/local/bin/toil-cwl-runner",...

`InstanceProfile` "has" `Roles`, but it should "hasMany" `Roles`

4

An IAM instance profile can have a collection of roles attached to it. I think in the giant JSON that needs to be reflected as a `hasMany` and not a...

`elect`/`reserve`/`reservation` system's locked nodes are not actually locked, and other pods schedule on them

3

**What happened**: As noted in https://github.com/volcano-sh/volcano/issues/1901#issuecomment-1055588056, I'm trying to get large single pods to not be starved by smaller pods. I need Volcano to reserve some room for them on...

Expose hFILE_backend and hfile_init to allow custom hFILE implementations

1

I have a custom hFILE backend over C++ streams that I have written for vg: https://github.com/vgteam/vg/blob/39ac300bb735abf8350e3d2a7ec0356a0742fd56/src/stream/hfile_cppstream.cpp It has built just fine up until now, since vg ships htslib as a...

Here's the only place we use it: https://github.com/DataBiosphere/toil/blob/7db3435bfb76d329f02b5eeb5677df972684d66a/src/toil/jobStores/aws/jobStore.py#L494 We don't use it for exports, and we don't use it for the actual job-storing part of the job store, and we...

Ability to use a Kubernetes namespace other then the default one in the config

1

Similar to #3922, I have my default Kubernetes namespace as the `vg` one, and although I have access to the `toil` namespace, my Toil Kubernetes testing usually ends up in...

I have an AWS profile for `toil`, for our Toil AWS account, and a default one for the vg AWS account. I end up testing Toil stuff in the vg...

To avoid problems like https://github.com/DataBiosphere/toil/issues/2753, we should add an option for `apiDockerCall` to delete images it downloaded when the containers finish. It should be thread safe, somehow. ┆Issue is synchronized...