Robert Syme

No probs. Do you just want those that are topics (is_a: EDAM:0000003)? If so: ["Nucleic acids", "Sequence", "Structure", "Phylogenetics", "Microarrays", "Proteomics", "Literature and documentation", "Data handling", "Sequencing and mapping", "Classification",...

https://github.com/michaelbarton/bioinformatics-career-survey/pull/3

Yeah, the topics are a bit vauge. I'll pull them out when I get home in a couple of hours. I'll also pull request on the correct branch next time,...

Rather than send a pull request, I've put the topics and sub-topics up at https://gist.github.com/1341255 for discussion and forking. Note that there are topics with no subtopics (Laboratory resources, Classification...

Sorry for the very slow response. The prof has been on my back to get a paper finished. Everything is up at https://gist.github.com/1341255 These are all the is_a relations flowing...

We could check the response code and retry the image fetch on 500 or even 5XX, but the challenge is that there might be other reasons why biocontainers might return...

What are the names of your assemblies? I ran into a similar problem when I had "." or "-" in my assembly names.

It looks like an issue with kyotocabinet when ussing gcc 6/7: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=811627 One possible workaround would be to include that patch from here: http://pkgs.fedoraproject.org/cgit/rpms/kyotocabinet.git/commit/?h=f24&id=988ed3a17b1a5ba659c4f3758b5a262859b0e4e1 ``` --- kyotocabinet-1.2.76/kcdbext.h 2016-05-25 11:32:53.591866016 +0200...

I ran into the same troubles. It looks to be because of gcc versions (6/7) being less lenient about these type conversions. Workaround in a comment here: https://github.com/glennhickey/progressiveCactus/issues/76#issuecomment-334714835 Note that...

One option would be to use hal2assemblyHub.py tool is provided in the HAL toolkit. Manual here: [github.com/ComparativeGenomicsToolkit/hal/assemblyHub](https://github.com/ComparativeGenomicsToolkit/hal/tree/master/assemblyHub) and more step-by-step instructions here: [bioinf.uni-greifswald.de/augustus/binaries/tutorial-cgp/cactus.html](http://bioinf.uni-greifswald.de/augustus/binaries/tutorial-cgp/cactus.html)