Dan Leehr

Shell-unsafe characters in .netrc file are not escaped

3

If I have a password with characters such as `$` or `%` in my .netrc file, docker-volume-netshare does not correctly provide the password to mount.cifs command. I've found that I...

Time estimate

10

I'm teaching shell at GCB Academy's [Introduction to Scientific Computing for Genomics](https://genome.duke.edu/gcb-academy#iscg) next week and was very excited to see this lesson in such good shape. We have 3.5 hours...

``` $ pod spec lint -> DLSFTPClient (1.0.0) - NOTE | [iOS] [xcodebuild] DLSFTPClient/DLSFTPClient/Classes/DLSFTPConnection.m:356:93: warning: implicit conversion loses integer precision: 'unsigned long' to 'unsigned int' [-Wshorten-64-to-32] - NOTE | [iOS]...

I'M A COP YOU IDIOT

1

Could be used for assertions

Jobs with many parallel tasks cause GKE cluster failures

16

When testing a moderately parallelized job on GKE (24 exome samples, 48 files), the cluster API becomes unresponsive and triggers failures in the workflow. It's not failing because of the...

The [KubernetesJobBuilder.container_args](https://github.com/Duke-GCB/calrissian/blob/master/calrissian/job.py#L116-L133) method builds up a simple command-line array connecting stdout, stdin, and stderr. This method should address the same concerns as [cwltool's JobBase._execute](https://github.com/common-workflow-language/cwltool/blob/bbe20f54deea92d9c9cd38cb1f23c4423133d3de/cwltool/job.py#L234), doing the following: - [x] check...

CWL 1.0 CT173 Test Docker ENTRYPOINT usage

5

``` Got workflow error Traceback (most recent call last): File "/usr/local/lib/python3.6/site-packages/cwltool/command_line_tool.py", line 733, in collect_output raise WorkflowException("Did not find output file with glob pattern: '{}'".format(globpatterns)) cwltool.errors.WorkflowException: Did not find output...

The conformance tests should run automatically under a CI platform, like the other implementations listed on https://ci.commonwl.org. Calrissian uses CircleCI for running automated tests. Through much trial and error I...

``` Got workflow error Traceback (most recent call last): File "/usr/local/lib/python3.6/site-packages/cwltool/executors.py", line 264, in runner job.run(runtime_context) File "/usr/local/lib/python3.6/site-packages/calrissian/job.py", line 553, in run self.check_requirements() File "/usr/local/lib/python3.6/site-packages/calrissian/job.py", line 390, in check_requirements raise...

Implement other docker runtime features

2

As noted in https://github.com/Duke-GCB/calrissian/blob/b4526afa79ab4d0a5e766d068dbd3acf0ba20d4b/calrissian/job.py#L253 [DockerCommandLineJob.create_runtime()](https://github.com/common-workflow-language/cwltool/blob/bbe20f54deea92d9c9cd38cb1f23c4423133d3de/cwltool/docker.py#L279) builds up some additional docker command flags (read-only container filesystem, custom network access, matching user, etc) Some of these may be necessary/appropriate. Should research/triage/implement as...