Sam Hokin

run `./gradlew install --warning-mode all` in bio/sources and you get: The following annotation processors were detected on the compile classpath: 'org.apache.logging.log4j.core.config.plugins.processor.PluginProcessor'. Detecting annotation processors on the compile classpath is deprecated...

create-attribute-indexes is bombing on lack of a key for Intron

2

All of a sudden the create-attribute-indexes post-process is crashing on what appears to be the lack of a key for the Intron class. Even though it's declared in the core...

Problem updating Manhattan plot data using CanvasXpress.updateData(data)

3

Hiya! I've used updateData(data) to update a heatmap, and now I'm trying to do so with a Manhattan scatter plot. I have a selector that determines which data to plot,...

routes.rb posts to /#{job.id}; should post to REQUEST_URI/{#job.id}

14

https://github.com/wurmlab/sequenceserver/blob/c466156ca469d0f4d20ac21c46155f9d7b89e0ba/lib/sequenceserver/routes.rb#L101 We've had to hack this line in routes.rb to post to a custom URL because this posts to / , while our deployments serve sequenceserver under a proxied sub-url...

As far as I can tell it didn't cause any harm. But thought I'd report it FYI. Cheers! ``` shokin@morangie:~/weka-3-8-4$ java -jar weka.jar WARNING: An illegal reflective access operation has...

Update groovy-electric for latest groovy-mode

4

My version: This is GNU Emacs 24.5.1 (x86_64-pc-linux-gnu, GTK+ Version 3.18.9) of 2016-04-17 on lgw01-04, modified by Debian ``` Leaving directory `/home/sam/.emacs.d/elpa/s-20170428.1026' Compiling file /home/sam/.emacs.d/elpa/s-20170428.1026/s-pkg.el at Mon Jul 24 07:02:57...

Cuffdiff bug: FPKM is way above range conf_lo to conf_hi (and is wrong)

1

I've run Cuffdiff v2.1.1 (4046M) on DNAnexus for an experiment a couple of times, keeping or removing other conditions, to see if this is reproducible and it is. Here's a...

Fixes the problem with simple objects in jsonobjects queries.

1

## Details This is an update to the routine that creates unique IDs for simple objects in the front of path queries for _jsonobjects_ output. The previous code led to...

## Details This is a correction of Strain definition which should NOT be a BioEntity. It is simply an Organism sub-type and is not a genomic feature. In addition to...

Heya, thanks for doing the refactor work on libsvm! It'll come in handy for my project. I thought I'd post up the gradle equivalent of your pom repo declarations for...