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

[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 JavaScript files working in galaxy?

Thank you very much.

Steven
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[galaxy-dev] pyconfig.h missing

[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.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1


Cython/Plex/Scanners.c:8:22: fatal error: pyconfig.h: No such file or directory
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1



It seems that the python-dev package is missing. Should Galaxy have installed 
that (through the virtual environment) or does it need to be installed 
separately on the command line. If so, where would it have to go?


Thanks for any help.


Fiona


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

[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:
https://galaxyproject.org/admin/data-integration/
2. The data managers page:
https://galaxyproject.org/admin/tools/data-managers/
3. This biostars answer: https://biostar.usegalaxy.org/p/7176/
4. This page on custom genomes that seems to be user / history oriented:
https://galaxyproject.org/learn/custom-genomes/
5. This page on rsyncing from the Galaxy reference data collection:
https://galaxyproject.org/admin/use-galaxy-rsync/ - quick test gives me
rsync error though
6. This guide to using the human reference data:
https://biostar.usegalaxy.org/p/14777/
7. I hear the usegalaxy.org reference collection is available via cvmfs - I
think this was discussed in a Galaxy Admins meetup at some point.

None of this is comprehensive. There are 2 sets of questions for me (in my
role as Galaxy admin):

1. If I want to make reference genomes and common indices (like for HISAT
and BWA) available for e.g. human and mouse, what is the best way to do
this?

2. If I want to add a genome for a non-model organism (e.g. M. tuberculosis
or L. calcarifer) available, what is the best way to do this? Which data
manager should or could I use?

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

[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
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany


On Thu, Jul 6, 2017 at 8:30 AM, D K  wrote:
> 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, files
> previously added to a library still point to the old location.
> I found this question on biostars:
> https://biostar.usegalaxy.org/p/1119/
> Is the only way to do this sort of update to manually change such entries in
> the database?
>
> Thanks!
>
>
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[galaxy-dev] Moving Shared Data Library Folders

[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, files previously added to a library still point
to the old location.
I found this question on biostars:
https://biostar.usegalaxy.org/p/1119/
Is the only way to do this sort of update to manually change such entries
in the database?

Thanks!
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