Re: [galaxy-dev] cognoma
by Casey Greene
Thank you for your interest in the cognoma project [
http://dev.list.galaxyproject.org/cognoma-td4669691.html ]. As it turns
out, we have heard of Galaxy. It would be hard to be in computational
biology and unaware of Galaxy. We appreciate the galaxy project's
contributions to web-based workflows in bioinformatics. For the use case
and target audience that we aim to serve, galaxy seemed less suited than
alternative light weight and modular approaches.
Of course, we appreciate your enthusiasm for galaxy and cognoma! If you
feel passionately that galaxy is the right framework, the easiest way to
demonstrate that is by delivering a galaxy-cognoma solution.
Thanks!
Casey
5 years, 2 months
jupyter + apache proxy + SSL
by Nikolay Aleksandrov Vazov
Hi,
I am trying to set up galaxy server with IE jupyter with apache proxy and SSL enbled.
Does anybody have a similar setup? I am using
== galaxy.ini
dynamic_proxy_manage=False ('True' gives the same error)
dynamic_proxy=node
dynamic_proxy_session_map=database/session_map.sqlite
#dynamic_proxy_bind_port=8800
#dynamic_proxy_bind_ip=0.0.0.0
dynamic_proxy_external_proxy=True
dynamic_proxy_prefix=gie_proxy
== httpd.conf
ProxyPass /gie_proxy/jupyter/ipython/api/kernels ws://localhost:8800/gie_proxy/jupyter/ipython/api/kernels
VirtualHost _default_:80>
RewriteEngine on
ReWriteCond %{SERVER_PORT} !^443$
RewriteRule ^/(.*) https://%{HTTP_HOST}/$1 [NC,R,L]
</VirtualHost>
It works fine with HTTP but not HTTPS and, naturally, I get
jquery.js:10261 Mixed Content: The page at 'https://mydomain.xx/' was loaded over HTTPS, but requested an insecure XMLHttpRequest endpoint 'http://mydomain.xx/gie_proxy/jupyter/ipython/login?next=%2Fgie_proxy%2Fju...'. This request has been blocked; the content must be served over HTTPS.
Is there a way to modify the container config such that it runs on a https, or is there a galaxy configuration routine I can use?
Thank you
Nikolay
===============
Nikolay Vazov, PhD
Department for Research Computing, University of Oslo
5 years, 2 months
Suggestion for Structural Variant Analysis onto Galaxy Main
by Wong, Orlando
Hello Galaxy dev
I would like to suggest the idea of adding structural variant analysis tools for large structural variations for detecting long insertions, inversions or translocations on to the Galaxy Main. Currently, there are tools for detecting small variants, less than 50 bp for small indels. There are some of these structural variant analysis tools available on the Galaxy toolshed, but none are available on Galaxy Main or any of the other public galaxy servers listed on the wiki. I think it would be a great addition to Galaxy main, if it is possible. Thank you!
5 years, 2 months
planemo shed_create bug? on planemo/server docker image
by Steve Cassidy
I’m just getting my head around tool dependencies and in doing so trying to push my tools to a local toolshed which I can handily run with the planemo/server docker image via Kitematic.
That toolshed is set up with an admin user planemo(a)test.com<mailto:planemo@test.com> so I have a stanza in my .planemo.yml:
shed_username: "stevecassidy"
sheds:
http://localhost:32768/:
key: ""
email: "planemo(a)test.com<mailto:planemo@test.com>"
password: "planemo"
Now I try to create a repository in the toolshed with planemo:
$ planemo shed_create --shed_target http://localhost:32768/
Repository created
cd '/Users/steve/projects/hcsvlab-galaxy/tools/alveo' && git rev-parse HEAD
cd '/Users/steve/projects/hcsvlab-galaxy/tools/alveo' && git diff --quiet
Repository [alveoimport] does not exist in the targeted Tool Shed.
Note the conflicting messages here. The repository is created (and I can confirm that it is there) but then I get the message that the repo does not exist in the Toolshed. After a bit of digging it turns out that this is because the repo is owned by the user ‘planemo’ rather than my username as declared in .planemo.yml. If I add —owner plane to the command then it works fine.
So I’m not sure if this is a bug in the shed_create code or a weird interaction with the setup on planemo/server.
Steve
—
Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy
5 years, 2 months
New galaxy parameter type
by Katherine Beaulieu
Hi everyone,
I am looking to implement a new parameter type for galaxy tool development.
Does anyone know what would be involved in doing something like this or
perhaps what files would need to be edited?
5 years, 2 months
package_cython_0_20_1
by Rathert, Philipp, Dr.
Dear all,
I am trying to install package_cython_0_20_1 but I always get the following error.
It looks like the link is broken.
Any ideas how to get this installed?
Thanks for the help.
Cheers,
Philipp
Name Version Type Status Error
cython <http://129.69.102.30:8080/admin_toolshed/manage_repository_tool_dependenc...> 0.20.1 package Error File "lib/tool_shed/galaxy_install/install_manager.py", line 124, in install_and_build_package_via_fabric
tool_dependency = self.install_and_build_package( install_environment, tool_dependency, actions_dict )
File "lib/tool_shed/galaxy_install/install_manager.py", line 82, in install_and_build_package
initial_download=True )
File "lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 31, in execute_step
initial_download=initial_download )
File "lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 688, in execute_step
dir = self.url_download( work_dir, downloaded_filename, url, extract=True, checksums=checksums )
File "lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 184, in url_download
raise Exception( err_msg )
Error downloading from URLhttp://cython.org/release/Cython-0.20.1.tar.gz
:
HTTP Error 404: Not Found
5 years, 2 months
default number of concurrent jobs
by Ulf Schaefer
Hi all
I installed an out-of-the-box Galaxy instance on my local machine as per
the instructions (https://wiki.galaxyproject.org/Admin/GetGalaxy). I
have made minimal adjustments beyond making myself an admin.
When I run a workflow in batch mode on 10 data sets it appears to
running 5 concurrent jobs. Why? Does anyone know where that is
configured? Is it dynamically determined based on the number of cores I
have (n=4)?
Thanks for any advice
Ulf
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5 years, 2 months
Get the username and password of a user
by Mohamed Kassam
Dear all,
I would like to know if there is ana api which I can get the password and
username of a user directly for my python code. I would like to send these
infromation to an another server for connection.
Thanks in advance
5 years, 2 months
