galaxy-dev September 2016

galaxy-dev@lists.galaxyproject.org

39 participants
59 discussions

Galaxy Docker 16.07
by Björn Grüning 04 Sep '16

04 Sep '16

Hi all! We are proud to present you the next release of our Galaxy Docker Image. https://github.com/bgruening/docker-galaxy-stable/releases/tag/16.07 https://registry.hub.docker.com/u/bgruening/galaxy-stable/ A few highlights: * based on Galaxy 16.07, with all it's new features and enhancements * SFTP Integration (by Alexander Lenail) * enhanced SLURM documentation (by Marius van den Beek) * initial Docker compose support Moreover, our workshop slides with a general Docker introduction and how to manage the Galaxy Docker container is available here: https://galaxy.slides.com/bgruening/the-galaxy-docker-project/live#/ Don't forget to checkout our general readme file: https://github.com/bgruening/docker-galaxy-stable/blob/master/README.md Thanks to all contributors [1] and enjoy this release! Bjoern [1] https://github.com/bgruening/docker-galaxy-stable/graphs/contributors

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Re: [galaxy-dev] how to create users through Galaxy API?
by Martin Čech 03 Sep '16

03 Sep '16

Hi, you specify username, password and email in the body (payload) of the POST as Key:Value pairs. Code from the API method: ( https://galaxy-central.readthedocs.org/en/latest/_modules/galaxy/webapps/ga…) username = payload[ 'username' ] email = payload[ 'email' ] password = payload[ 'password' ] There are also other conditions that need to be fulfilled (e.g. user creation has to be turned on in the configuration) - you will find these when you look at the source code of the method (because the documentation is not perfect yet, sorry). M. On Sun, Dec 29, 2013 at 11:22 PM, xlwang <xlwang_0903(a)163.com> wrote: > hi, > I still have some confusion. > post /api/users , when i use postman, it seems like this: > > > No other parameters? How to confirm the new user's information?Such as > user name, password. > Can you give me a example please?Thank you! > > At 2013-12-30 06:04:15,"Martin Čech" <marten(a)bx.psu.edu> wrote: > > Hello, > > to create a user through API you send a POST request to /api/users > > More information about User API here: > > > https://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.… > > Martin > > > On Fri, Dec 27, 2013 at 5:11 AM, xlwang <xlwang_0903(a)163.com> wrote: > >> hello, >> I want to create users through Galaxy API.For example, I can get users >> information through url like this(use postman): >> http://localhost:8080/api/users?key=my_key >> But how to create a user? >> >> >> >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> > > > >

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Send repeat parameter to code file for multiple select list
by Katherine Beaulieu 03 Sep '16

03 Sep '16

Hello Galaxy Community, I was wondering if anyone had ever come across a situation where they have had to pass the contents of a repeat parameter to a code file in a Galaxy tool config? Is there any way to do this? Katherine

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Testtoolshed status
by Steve Cassidy 02 Sep '16

02 Sep '16

I’m getting a 500 response from the testtoolshed when I try to upload a tool via planemo: ➜ alveo-galaxy-tools git:(master) ✗ planemo shed_update --shed_target testtoolshed apitools cd '/Users/steve/projects/alveo-galaxy-tools/apitools' && git rev-parse HEAD cd '/Users/steve/projects/alveo-galaxy-tools/apitools' && git diff --quiet Could not update alveoimport Unexpected HTTP status code: 500: <html> <head><title>Internal Server Error</title></head> <body> <h1>Internal Server Error</h1> <p>The server has either erred or is incapable of performing the requested operation. <br/> </p> <hr noshade> <div align="right">WSGI Server</div> </body> </html> Repository metadata updated successfully for repository alveoimport. Failed to update a repository. In addition, I just got a “Tool Shed could not be reached” message via the web interface, so i’m wondering if something is up. Thanks, Steve — Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy

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Introducing Conda as a new standard for Galaxy tool dependencies
by Björn Grüning 01 Sep '16

01 Sep '16

Hi all, Galaxy 16.07 was just released: https://docs.galaxyproject.org/en/master/releases/16.07_announce.html and the IUC has some news to share with you. For a more readable version please see: https://docs.galaxyproject.org/en/master/admin/conda_faq.html ---- Galaxy tools (also called wrappers) traditionally use Tool Shed package recipes to install their dependencies. At the tool’s installation time the recipe is downloaded and executed in order to provide the underlying software executables. Introduction of these Galaxy-specific recipes was a necessary step at the time, however nowadays there are other more mature and stable options to install software in a similar manner. The Galaxy community has taken steps to improve the tool dependency system in order to enable new features and expand its reach. This document aims to describe these and answer the FAQ. It is a pleasure to announce the adoption of a new standard for tool dependencies in Galaxy which has been integrated over the last six months: Conda packages! Not only do Conda packages make tool dependencies more reliable and stable, they are also easier to test and faster to develop than the traditional Tool Shed package recipes . Conda is a package manager like apt-get, yum, pip, brew or guix. We don’t want to argue about the relative merits of various package managers here, in fact Galaxy supports multiple package managers and we welcome community contributions (such as implementing a Guix package manager or enhancing the existing brew support to bring it on par with Conda). As a community, we have decided that Conda is the one that best fulfills our needs. The following are some of the crucial Conda features that led to this decision: * Installation of packages does not require root privileges (Installation at any location the Galaxy user has write access to) * Multiple versions of software can be installed in parallel * HPC-ready * Faster and more robust package installations through pre-compiled packages (no build environment complications) * Independent of programming language (R, Perl, Python, Julia, Java, pre-compiled binaries, and more) * Easy to write recipes (1 YAML description file + 1 Bash install script) * An active, large and growing community (with more and more software authors managing their own recipes) * Extensive documentation: Conda documentation (http://conda.pydata.org/docs/building/build.html) and Conda quick-start (http://conda.pydata.org/docs/get-started.html) Below we answer some common questions (collected by Lance Parsons): 1. How do I enable Conda dependency resolution for existing Galaxy installations? ------------------------------------------------------------------- Most Galaxy administrators have not set up a dependency resolvers configuration file (dependency_resolvers_conf.xml) which means they are using Galaxy’s default (dependency_resolvers_conf.xml.sample). Galaxy has enabled Conda dependency resolution by default since release 16.04 (if Conda was installed already), so many existing installations can use Conda dependencies. Having Conda enabled in dependency_resolvers_conf.xml means that Galaxy will look for dependencies using the Conda system when it attempts to run tools. If conda_auto_install is True, and a dependency is not found, Galaxy will attempt to install it using the configured Conda channels. A graphical user interface that allows administrators install Conda packages directly from Galaxy when tools are installed from the Tool Shed is available in the 16.07 release of Galaxy. 2. How do Conda dependencies work? Where do things get installed? ----------------------------------------------------------------- In contrast to the old dependency system, which was used exclusively by Galaxy, Conda is a pre-existing, independent project. With Conda it is possible for an admin to install packages without touching Galaxy at all – managing your dependencies independently from Galaxy. Galaxy can handle these dependencies for you, but admins are not required to use Galaxy for dependency management. There are a few new config options in the galaxy.ini file, but by default Galaxy will install Conda (the package manager) and the required packages in the <tool_dependency_dir>/_conda/ directory. In this directory, Galaxy will create an envs folder with all of the environments managed by Galaxy. Every environment contains a lib, bin, share, and include subdirectory, depending on the tool, and is sufficient to get a Galaxy tool up and running. Galaxy simply sources this folder via Conda and makes everything available before the tool is executed on your cluster. To summarize, there are four ways to manage Conda dependencies for use with Galaxy. For all of these options, Conda dependency management must be configured in the dependency_resolvers_conf.xml and the galaxy.ini file. a) Manual Install - Conda dependencies may be installed by administrators from the command line. Conda (and thus the conda environments) should be installed in the location specified by the conda_prefix path (defined in galaxy.ini and by default <tool_dependency_dir>/_conda/ directory). Galaxy will search these environments for required packages when tools are run. Conda environment names have to follow a specific naming pattern. As an example, to install samtools in version 0.1.19, the administrator can run the command: $ conda create --name __package__samtools(a)__version__0.1.19 samtools==0.1.19 --channel bioconda Tools that require samtools version 0.1.19 will then be able to find and use the installed conda package. b) Galaxy Admin Interface (>= 16.07) - Galaxy will install Conda tool dependencies when tools are installed from the Tool Shed if the option “When available, install externally managed dependencies (e.g. conda)? Beta” is checked. Admins may also view and manage Conda dependencies via the Admin interface. c) Automatically at tool run time - When a tool is run and a dependency is not found, Galaxy will attempt to install the dependency using Conda if conda_auto_install is activated in the configuration. d) Via the API, upon tool installation (>= 16.07) - The Galaxy community maintains an ansible role (https://github.com/galaxyproject/ansible-galaxy-tools) that uses BioBlend (https://github.com/galaxyproject/bioblend/) and the Galaxy API to install tools. 3. What is required to make use of this? Any specific packages, Galaxy revision, OS version, etc.? ------------------------------------------------------------------------ The minimum required version of Galaxy to use Conda is 16.01, however version 16.07 or greater is recommended. The 16.07 release of Galaxy has a nice graphical user interface to manage packages, but this is not required to have Conda dependencies managed and used by Galaxy. Conda packages should work on all compatible operating systems with glibc version (2.5) or newer (this includes Centos 5). We will most likely switch soon to glibc version 2.12 as minimum requirement (this includes CentOS 6). So all packages will run on all *nix operating systems newer than 2007. 4. How do I know what system is being used by a given tool? ----------------------------------------------------------- The Galaxy log will tell you which dependency resolution system is used to satisfy each tool dependency and you can specify priorities using the config/dependency_resolution_conf.xml file. If you put Conda on top, Galaxy will at first try to use Conda to resolve a tool dependency; if this does not work, the following dependency resolvers is used, as specified. See https://docs.galaxyproject.org/en/master/admin/dependency_resolvers.html for detailed documentation. Starting from galaxy release 16.07, you can see which dependency will be used (“resolved”) in the admin panel. 5. How do I go about specifying conda dependencies for a tool? All the docs still seem to recommend (or exclusively discuss) the tool_dependencies.xml method. ----------------------------------------------------------------------- The simple answer is: you don‘t need to do much to make Conda work for a tool. The <requirement> tag in the tool XML file is enough. The name and the version should correspond to a Conda package in the `default`, `r`, `bioconda` or `iuc` Conda channel (you can extend this list if you like in your galaxy.ini). If this is the case you are ready to go. Read more about Conda channels here: http://conda.pydata.org/docs/custom-channels.html and browse their packages on https://anaconda.org/ url followed by the channel name (e.g. https://anaconda.org/bioconda). We need to adjust the documentation about tool_dependencies.xml and deprecate them everywhere. 6. During tool installation what if there is no Conda package available for given requirement? What if the requirement is resolved in a different software than the original wrapper author meant to use? ------------------------------------------------------------------------ If there is no Conda package available during tool installation the tool will install successfully, and can be used if its dependencies are satisfied by another dependency system such as Tool Shed package recipes, Docker containers or modules. If there is a package of correct name and version it will be used. There is no equivalent of the “owner” concept used in Galaxy packages installed from the Tool Shed. 7. Where can I find a list of existing Conda packages that I can point to, so I don't have to reinvent the wheel for common dependencies? ----------------------------------------------------------------------- With Conda installed run: $ conda search <package_name> -c bioconda -c iuc This will search in all channels that are activated by default in Galaxy. If you find your package your are ready to go. If not please create (http://conda.pydata.org/docs/building/recipe.html#conda-recipe-files-overvi…) a Conda package and submit (https://bioconda.github.io/#step-4-join-the-team) it to BioConda (https://bioconda.github.io) or get in contact with the IUC (https://gitter.im/galaxy-iuc/iuc). 8. How can I create a new conda package for a dependency? ----------------------------------------------------------- Adding a package to the bioconda or iuc conda channels will make it available for Galaxy tools to use as a dependency. To learn how, get in touch with the awesome BioConda community. They have great documentation and assist with all development. You will also see a few of us at this project to get you started :) Don’t be scared! Conda recipes are really simple to write. Conda also offers you, so called `skeleton` generators, generating recipes from pypi, cran, cpan for you (mostly) automatically. 9. Is there a way to convert traditional Tool Shed package recipes that are not yet in a Conda channel? ------------------------------------------------------------------------ First, you do not need to do anything to your wrapper as long as the package name in the requirement tag is matches the name of correct Conda package. (You may want to mention in the README or a comment the Conda channel that contains the package). We have developed scripts for conversion of Tool Shed package recipes to Conda, but have not followed up and they are not ready for production. If you want to migrate some recipes from XML to Conda, we are happy to give you a hand. We are trying to get all new versions under Conda and leave the old versions as they are – simply because of time. 10. What is the recommendation for existing installations? Will I continue to maintain both systems or migrate to the new Conda system eventually? --------------------------------------------------------------------- Old tools will use the traditional installation system, this system will stay and will be supported to install old tools. This we promised to our community to guarantee sustainability and reproducibility. New tools from the IUC, may be Conda only. 11. If I have Conda enabled, what do I need to do to install tools using it? For example, how can I install the latest Trinity? And how will I know dependencies are installed? ------------------------------------------------------------------------- This depends on your galaxy.ini setting. Galaxy will install Conda for you if you have enabled conda_auto_init. If conda_auto_install is enabled, Galaxy will install Trinity via Conda when a Trinity job is launched and Trinity is not yet installed. With the latest 16.07 release you can see which dependencies are being used in the “Manage installed tools” section of the admin panel and you can select whether or not to install Conda packages or Tool Shed package recipes when you install new tools, even if conda_auto_install is disabled. More improvements to the UI will be coming with 16.10. To see if Galaxy has created a Trinity environment for you have a look at folder under <tool_dependency_dir>/_conda/envs/. 12. Can I mix traditional Galaxy packages and Conda packages? -------------------------------------------------------------- Yes, the way this works is that Galaxy goes through the list of requirements for a tool, and then determines for each requirement if it can be satisfied by any of the active resolver systems. The order in which resolvers are tried is listed in the dependency_resolvers_conf.xml file, and the default order is Tool Shed packages Packages manually installed by administrators Conda packages The first system that satisfies a requirement will be used. 13. What can I do if conda doesn’t work for me? ------------------------------------------------ There is currently a limitation in the way conda packages are being built. This limitation will be addressed shortly by the Conda community, however this requires all packages to be rebuilt. To work around this limitation, please make sure that the total length of the conda_prefix and job_working_directory path is less than 50 characters long. If this is your problem, you should see a warning similar to the following in your galaxy log files: ERROR: placeholder '/home/ray/r_3_3_1-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_pl' too short In rare cases conda may not have been properly installed by galaxy. A symptom for this is if there is no activate script in conda_prefix/bin. In that case you can delete the conda_prefix folder and restart galaxy, which will again attempt to install conda. If this does not solve your problem or you have any trouble following the instructions, please ask on the galaxy mailing list or the galaxy IRC channel. --- One last thing that is important to me: the entire Galaxy-Conda project is an amazing community effort - not only within the Galaxy community, but we team up with the Conda community as well, in particular with the BioConda folks. Thanks to Johannes Köster, Ryan Dale and the entire community around this package manager which have created around 1500 bioinformatics packages just in the last year. Thanks to John Chilton who has written the Galaxy Conda integration last December and is pushing tool development in Galaxy to a new level. Many thanks to Nicola Soranzo for his constant support and reviews in all mentioned projects, he is everywhere to help - you will see! Thanks also to Peter van Heusden, Marius van den Beek and Brad Langhorst – they have worked hard on Conda-Galaxy Integration to make it shine in 16.07. I want to thank Lance Parsons for his questions that inspired me to write this down and his constant support in making tools better in Galaxy – Lance I hope with Conda you will have less pain with dependencies in general! Last but not least I would like to thank the entire IUC and the over 50 IUC contributors that have migrated most of the IUC tools to Conda packages over the last 6 months. You all did a truly amazing work here – and I‘m sure it will benefit the tool development in Galaxy tremendously. Enjoy Galaxy + Conda, Björn, on behalf of the IUC P.S. As soon as you have a Conda package, we have a system for you to generate Docker containers out of it: https://github.com/mulled/mulled. These containers can than be used by Galaxy to resolve dependencies as well, if you prefer Docker containers over Conda packages.

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bug in fastqmcf
by Jochen Bick 01 Sep '16

01 Sep '16

Hi they migrated the code of e-utils to github. Download path is corrupted: https://expressionanalysis.github.io/ea-utils/ Cheers Jochen

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error on startup
by Cristel Thomas 01 Sep '16

01 Sep '16

Galaxy admins, One of you has probably seen the below error before, can someone explain? for background, we're running our instance on a AWS server (if that makes a difference) galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,545 Enabling 'sample_tracking' controller, class: SampleTracking galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,545 Enabling 'system' controller, class: System galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,546 Enabling 'workflows' controller, class: Workflows galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,546 Enabling 'users' controller, class: Users galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,547 Enabling 'jobs' controller, class: Jobs galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,547 Enabling 'root' controller, class: Report galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,547 Enabling 'home' controller, class: HomePage galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,548 Enabling 'httpexceptions' middleware galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,549 Enabling 'recursive' middleware galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,551 Enabling 'error' middleware galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,551 Enabling 'trans logger' middleware galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,552 Enabling 'x-forwarded-host' middleware Starting server in PID 14676. Traceback (most recent call last): File "./scripts/paster.py", line 26, in <module> serve.run() File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py", line 1061, in run invoke(command, command_name, options, args[1:]) File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py", line 1067, in invoke exit_code = runner.run(args) File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py", line 223, in run result = self.command() File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py", line 673, in command serve() File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py", line 650, in serve server(app) File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 234, in server_wrapper **context.local_conf) File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 94, in fix_call val = callable(*args, **kw) File "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 1361, in server_runner serve(wsgi_app, **kwargs) File "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 1310, in serve request_queue_size=request_queue_size) File "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 1153, in __init__ request_queue_size=request_queue_size) File "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 1132, in __init__ request_queue_size=request_queue_size) File "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 345, in __init__ HTTPServer.__init__(self, server_address, RequestHandlerClass) File "/usr/lib/python2.7/SocketServer.py", line 419, in __init__ self.server_bind() File "/usr/lib/python2.7/BaseHTTPServer.py", line 108, in server_bind SocketServer.TCPServer.server_bind(self) File "/usr/lib/python2.7/SocketServer.py", line 430, in server_bind self.socket.bind(self.server_address) File "/usr/lib/python2.7/socket.py", line 224, in meth return getattr(self._sock,name)(*args) socket.error: [Errno 99] Cannot assign requested address Removing PID file reports_webapp.pid Thanks, Cris

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Re: [galaxy-dev] Send repeat parameter to code file for multiple select list
by Katherine Beaulieu 01 Sep '16

01 Sep '16

On Thu, Sep 1, 2016 at 9:36 AM, Katherine Beaulieu < katherine.beaulieu014(a)gmail.com> wrote: > Hi Peter, > The code file tag is generally used in populating select lists. So > basically you have a function from a code file that is loaded before > runtime of the tool and you can dynamically load content based on that > function and you can pass it parameters from your tool but I'm wondering > how you would pass it the contents of a repeat parameter. > This is how the code file tag works: > https://wiki.galaxyproject.org/Admin/Tools/Custom%20Code > Thanks, > Katherine > > On Thu, Sep 1, 2016 at 8:23 AM, Peter Cock <p.j.a.cock(a)googlemail.com> > wrote: > >> I'm not quite sure what you mean by a "code file", but if you >> mean using the <configfile> tag, here's an example: >> >> https://github.com/peterjc/galaxy_mira/blob/master/tools/mir >> a4_0/mira4_de_novo.xml >> >> I am using a Cheetah syntax for loop to access each entry >> in a repeat parameter. >> >> Peter >> >> On Thu, Sep 1, 2016 at 12:58 PM, Katherine Beaulieu >> <katherine.beaulieu014(a)gmail.com> wrote: >> > Hello Galaxy Community, >> > I was wondering if anyone had ever come across a situation where they >> have >> > had to pass the contents of a repeat parameter to a code file in a >> Galaxy >> > tool config? Is there any way to do this? >> > Katherine >> > >> > ___________________________________________________________ >> > Please keep all replies on the list by using "reply all" >> > in your mail client. To manage your subscriptions to this >> > and other Galaxy lists, please use the interface at: >> > https://lists.galaxyproject.org/ >> > >> > To search Galaxy mailing lists use the unified search at: >> > http://galaxyproject.org/search/mailinglists/ >> > >

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Conda: confused dependencies with multiple R versions and rpy
by Steve Cassidy 01 Sep '16

01 Sep '16

Hi, trying to get my tools going, part 29. I have a Docker image with the latest Galaxy release, patched to fix the Conda install bug I found earlier, my tools are installed ok and I’ve added a few from the toolshed for good measure. One of my tools requires R 3.0.2 which is installed ok. I also installed scatterplot from the toolshed which requires R 2.11; that is also installed ok by conda. However, I get this message when trying to run scatterplot: Traceback (most recent call last): File "/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/scatterplot/d243056b22ed/scatterplot/scatterplot.py<http://toolshed.g2.bx.psu.edu/repos/devteam/scatterplot/d243056b22ed/scatte…>", line 5, in <module> from rpy import * File "/tool_deps/rpy/1.0.3/devteam/package_rpy_1_0_3/82170c94ca7c/lib/python/rpy.py", line 134, in <module> """ % RVERSION) RuntimeError: No module named _rpy3002 RPy module can not be imported. Please check if your rpy installation supports R 3.0.2. If you have multiple R versions installed, you may need to set RHOME before importing rpy. For example: >>> from rpy_options import set_options >>> set_options(RHOME='c:/progra~1/r/rw2011/') >>> from rpy import * So it seems that rpy is installed and is aware of one version of R but not the other, and the other is being found (perhaps because it’s the default install in the Docker image?) FYI my docker image recipe is here: https://github.com/Alveo/docker-galaxy-alveo and the image itself is here: https://hub.docker.com/r/stevecassidy/alveo-galaxy/ Any pointers to the way forward appreciated. Thanks, Steve — Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy

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galaxy-dev September 2016