Juan Medina

Scrollable Horizontal Bar Chart

12

Would like to see what other developers think about making barcharts with many categories brushable. Something like:  http://bl.ocks.org/nbremer/4c015860931fb6a13afc7bac51f40b43 I've found myself having very cluttered charts and this would certainly...

Do not submit empty jobs

3

Thanks again for such a great tool. Here I'm proposing a change, which I don't think its production ready, for a `leader.py` `TODO` item. When Toil finishes jobs, it walks...

Could toil also store requested cores data for stats purposes?

2

I'm not aware if recent versions do this already, but it would be nice to store stats about the number of cpus requested by jobs. Doing `clock / cores` could...

Fastest way to run svaba

1

First thank you for such a great tool. Let's say IO throughput is >5gb/s, total ram is 500GB, and you have up to 32 cpus, what is the fastest way...

disregard checks stateful status

5

I'd like to always run the checks regardless the condition of the previous $output, is this possible? It seems that the check class has a override option, but I don't...

Pass parameters to bpipe.config

2

I'm using LSF, several of my `bsub` jobs require variable parameters that can be a result of a previous step (e.g the number of nodes `-J jobName[1-$JOBS]`). It would be...

Toil submits all jobs twice, initially to do work then to (clean up?) -- second submission should only request 1 core

1

Hi all, I've noticed that my Toil (3.19.0) pipelines submit all jobs twice (as also noted by other people https://github.com/DataBiosphere/toil/issues/2730#issuecomment-509018961, @ionox0). In the first submission, the job does the work....

Add random exponential backoff to with_retries: Toil goes rogue if with_retries fails, pipeline should exit

5

When an operation completely fails using [`with_retries`](https://github.com/DataBiosphere/toil/blob/2a24f4adb75d5254f70f60746838508987a6b0e1/src/toil/batchSystems/abstractGridEngineBatchSystem.py#L36), Toil does not exit. Instead it remains as a rogue pipeline: ``` Cannot connect to LSF. Please wait ... ls_info: A socket operation...

I installed SGA following these steps: ``` wget https://github.com/jts/sga/archive/v0.10.14.tar.gz ./autogen.sh ./configure --with-sparsehash=/path/to/sparsehash/2.0.3 \ --with-bamtools=/path/to/bamtools/2.4.0 \ --prefix=/path/to/sga/0.10.14 make && make install ``` However: ``` $ ls /path/to/sga/0.10.14/bin sga sga-astat.py sga-bam2de.pl sga-mergeDriver.pl...

What about a new release?

1

`0.6.8` was released in 2016, perhaps time for a new release? There have been several bug fixes that would be great to see in a new release. Please let me...