Ben Booth

Kubernetes support

2

I was just curious about the amount of effort required to support Kubernetes. I know the README says Kubernetes is not supported, but does that mean it for sure doesn't...

Better CTRL+C handling

1

In normal spark shell, pressing CTRL+C once will attempt to cancel the currently running spark job. I know in the past pressing CTRL+C in Ammonite would use thread.stop() to kill...

Can startup time be improved?

7

I understand that this is a hard problem, and that Leiningen isn't any better at this, but I think the major deal-breaker for using boot CLI scripts is the SLOW...

Websocket implementation for connect_core_v1_get_namespaced_pod_exec

1

Currently there doesn't appear to be a websocket implementation for `connect_core_v1_get_namespaced_pod_exec`. It would be great to have one. The python k8s client has an implementation [here](https://github.com/kubernetes-client/python-base/blob/master/stream/ws_client.py). The `ws` crate could...

Allow use of any numeric type to store the R-tree instead of just Float

1

It would be nice if more numeric types were supported instead of just Float, e.g. Double, Int, Long, BigInt, BigDecimal. Can the numeric type be generalized? This would be useful...

add `thinColor` style for bigBed tracks

2

When I load bigBed tracks into JBrowse, I noticed that the `utrColor` style setting is not used. Instead, the entire feature is the same color, unlike the `ProcessedTranscript` glyph. This...

onclick handler with newWindow action opens two windows in FireFox

15

I'm using JBrowse 1.11.4, with FireFox 31. I have a set of CanvasFeatures tracks with a custom onclick handler that looks like: ``` "onClick" : { "action" : "newWindow", "url"...

Mango cannot load fasta files with pipes in the contigName

2

If I run mango-submit passing a .fasta file as reference: ``` /users/bbooth/src/mango/bin/mango-submit /data/seqdata/analysis/fakereads/S288C_reference_genome_R64-2-1_20150113/S288C_reference_sequence_R64-2-1_20150113.fsa.fasta -features /data/seqdata/analysis/fakereads//data/seqdata/analysis/fakereads/S288C_reference_genome_R64-2-1_20150113/saccharomyces_cerevisiae_R64-2-1_20150113.genes.gff3 ``` The fasta file has chromosome names with pipes, e.g.: ``` ref|NC_001141| ref|NC_001136| ref|NC_001135| ref|NC_001144|...

It would be nice if Ammonite had support for java remote debugging scripts. RIght now it is possible to attach to a running ammonite process but breakpoints don't work and...

Allow for ammonite-style import $file in scripts with using directives

4

Right now scala-cli requires passing in all scala source dependencies as arguments, including transitive dependencies. It would be nice to have ammonite-style `import $file` syntax, maybe with the existing `using`...