July 2016 - galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] cognoma
by Casey Greene 19 Jul '16

19 Jul '16

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

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jupyter + apache proxy + SSL
by Nikolay Aleksandrov Vazov 19 Jul '16

19 Jul '16

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%2Fjupy…'. 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

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cognoma
by Calvin Morrison 19 Jul '16

19 Jul '16

Hi guys, a recruiter hit me up recently and mentioned a local hackathon.. I took a look at their big biologist machine learning online service idea, but it sounded awfully fimiliar. Looks like the greenlab out of UPenn hasn't heard of galaxyproject, but I'm not doing a very good job explaining how galaxy could be leveraged to do exactly what I want... just seems like awful duplication on their part when expanding galaxy would be preferable. see my issue on it: https://github.com/cognoma/cognoma/issues/18#issuecomment-233335587 Their website: https://github.com/cognoma/cognoma/ A current doc outlining the project: https://docs.google.com/document/d/1QoLZwTmMhvu_tv3SO4bA3-XomV1y5BR0CWhh833… Any ideas I can spin them to help convince them that galaxy probably does almost everything they need, aside from integrating their tools? Calvin

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Implementing iRODS with Galaxy
by Katherine Beaulieu 18 Jul '16

18 Jul '16

Hi there, I have developed a tool that does the importing and exporting to Galaxy. Please see the attached link to the github repos for the two tools. Please keep in mind that this tool is still in development. As well, it has only been tested on a local instance of Galaxy and the authentication with iRODS has not quite been worked on. If you have any suggestions please let me know. https://github.com/AAFC-MBB/Galaxy/tree/dev/wrappers/irods_pull https://github.com/AAFC-MBB/Galaxy/tree/dev/wrappers/irods_push

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Suggestion for Structural Variant Analysis onto Galaxy Main
by Wong, Orlando 15 Jul '16

15 Jul '16

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!

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planemo shed_create bug? on planemo/server docker image
by Steve Cassidy 15 Jul '16

15 Jul '16

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

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New galaxy parameter type
by Katherine Beaulieu 15 Jul '16

15 Jul '16

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?

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package_cython_0_20_1
by Rathert, Philipp, Dr. 15 Jul '16

15 Jul '16

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_dependencie…> 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

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default number of concurrent jobs
by Ulf Schaefer 15 Jul '16

15 Jul '16

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 ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE **************************************************************************

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Get the username and password of a user
by Mohamed Kassam 15 Jul '16

15 Jul '16

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

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