[galaxy-dev] any introduce for how Mako and JavaScript work in galaxy?

2017-07-06 Thread Steven Shen
Hi everyone, I want to make some change for my local galaxy web, actually I can edit galaxy_path/static/scripts/bundled/*.js directly. It seems mako templates are used for galaxy, as well as many JavaScript files, but I don't know how they work. So is there any introduce for how mako and

[galaxy-dev] pyconfig.h missing

2017-07-06 Thread Fiona Mary Roche
Hi there, I am trying to install cutadapt (package_cutadapt_1_8, from iuc) on a newly installed 17.05 Galaxy on Ubuntu. Both cutadapt and cython (a dependency) fail with the following errors: cutadapt/_align.c:8:22: fatal error: pyconfig.h: No such file or directory compilation terminated.

[galaxy-dev] "Best practice" for maintaining genome list in Galaxy

2017-07-06 Thread Peter van Heusden
Hi there Is there current "best practice" for maintaining a collection of reference genome data in a Galaxy server? I.e. filling in the dbkeys.loc and all_fasta.loc table and associated data. I know of the following discussions on this topic: 1. The data integration page:

Re: [galaxy-dev] Moving Shared Data Library Folders

2017-07-06 Thread Devon Ryan
You end up needing to update the database, or at least I did a year or two ago when I last did something like this. Thankfully, if you moved things in a mostly predictable way you can do it with a bit of python (the path is stored in the "external_filename" field of the "dataset" table). Devon --

[galaxy-dev] Moving Shared Data Library Folders

2017-07-06 Thread D K
Is it possible to move the file locations of Shared data libraries that have already been added to the system? I just tried moving some of these files to a new location (e.g. /somewhere/files to /somewhere_else/libraries) and updating the galaxy.ini entry to point to the new location. However,