(Originally published on BiocodersHub.)
If you’re doing bioinformatics in Python, you’re probably using Biopython. Actually, Biopython is a good reason for using Python. But it can be formidable to newcomers: there’s a lot there and there’s not a huge amount of learning material. This then is …
It's all there in the documentation, but sometimes it's hard to find. This document gives you another place to look.
So how do I ...
Curiously, the identity of admin users is hardcoded into the Galaxy configuration file. (Which makes it secure, I guess, but separate from the …
Galaxy toolsheds
Relatively painless tool-sharing
This is a more recent innovation in Galaxy, which can make it a somewhat confused one: the concept of the toolshed has changed over its lifetime, the documentation is incomplete, and there's a slightly strange emphasis in the documentation that exists. So …
Toolsheds …
(Originally published on BiocodersHub)
Following several lengthy and passionate discussions in different venues on what language to use for teaching bioinformatics, I've started cutting and pasting my reply. And here it is.
You'll get a lot of different opinions on this because:
(Previously published on BiocodersHub.)
Previously I'd spoken about how Biopython represents sequence data with the Seq class. But there is also the SeqRecord class:
Odds and ends and the surprising.
If you are serving the installation with a proxy redirect (e.g. the galaxy server is running on port 7070 but is being redirect by Apache to appear at port 80 on /galaxy), while you can access Galaxy at both addresses, login will …
More things I done learned about Galaxy tool development
A pot-pouri of titbits that are probably documented somewhere, but weren't obvious to me.
This presents one way to create an optimized production Galaxy instance. Variations are certainly possible and some of the choices presented are/were dictated by local culture. Certain settings may be more suitable for production or development environments. Nonetheless, this presents a start-to-stop process for installation and setup.
Note: this …