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

Running jobs as real user and extra_file_path
by Louise-Amélie Schmitt 28 Apr '17

28 Apr '17

Hi everyone, I just wanted to ask how the extra_file_path is handled in case of job running as the real user since the file_path is only writable by the galaxy user. Any clue? Thanks, L-A

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Issue when using xsendfile with galaxy release_16.07
by SAPET, Frederic 28 Feb '17

28 Feb '17

Hello I'm trying the latest Galaxy (git status gives me : # On branch release_16.07) I've set the xsend option in galaxy.ini (in order to run Galaxy behind a web server proxy, and apply all methods described here : https://wiki.galaxyproject.org/Admin/Config/ApacheProxy) apache_xsendfile = True HTML, gff3,tabular files are just fine but the preview of some other files (txt, csv) is broken on the interface. When I want to preview a txt file : Not Found The requested URL /datasets/fd1df6a9052810d5/display/ was not found on this server. And apache says : [Thu Aug 18 15:33:48 2016] [error] [client 192.168.29.12] (13)Permission denied: xsendfile: cannot open file: /softs/bioinfo/galaxy-prod/database/files/000/dataset_19.dat, referer: http: But it looks like this is not really a problem related to access. Indeed, from the same file, I switch it from txt to tabular (edit attributes), the preview works. Are you able to reproduce the behavior ? The same problem occurs on release_16.01. It's fine with the release v15.05 which is my production server right now. Fred

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display at UCSC does not work
by Hans-Rudolf Hotz 24 Jan '17

24 Jan '17

Hi I am trying to set up the possibility to display data sets with the UCSC genome browser for our new galaxy installation. After clicking on "display at UCSC main", I get the UCSC genome browser, opening in the right assembly, and at the correct location, but I get the following Error: Warning/Error(s): redirected to non-http(s): /login?redirect=%2Froot%2Fdisplay_as In galaxy.ini, I did uncomment the line: display_servers = hgw1.cse.ucsc.edu,hgw2.cse.ucsc.edu,hgw3.cse. ... We use the 'new' authentication method to connect to our LDAP server, with the following changes in galaxy.ini: require_login = True auth_config_file = config/auth_conf.xml Connection from UCSC to our galaxy server is working, since I can display the data, when I switch to require_login = False it works, independent of whether I am logged in or not. Is there a way to get it to work, even if I have "require_login = True"? Thank you very much for your help Regards, Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland

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Python script can't can't import BioPython modules in Galaxy 16.01
by Makis Ladoukakis 17 Jan '17

17 Jan '17

Hello everyone, I've recently upgraded to Galaxy 16.01 and i have some issues with a python wrapper from a tool. When I run it via Galaxy I get the following error: Traceback (most recent call last): File "/home/galaxy_user/galaxy/tools/myTools/know_parser/know_parser.py", line 12, in <module> from Bio import SeqIO ImportError: No module named Bio However when I click on the "view details" icon to copy the command from the tool and run it on my command line the tool works perfectly. In addition this issue occurs while I already have installed BioPython. When I type Python and write "from Bio import SeqIO" I get no error. Can this be an issue related to the virtual environment that is initialized each time Galaxy starts? Thank you in advance, Makis Ladoukakis

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Python ValueError: too many values to unpack
by Matthias De Smet 18 Oct '16

18 Oct '16

Hi all, I’m trying to develop a tool that lets you select a file on the server. I’m using the dynamic_options setting to let Galaxy render a dropdown list of available file. However, when I try to test the tool in its current form, I get the following error: <pre> galaxy.web.framework.decorators ERROR 2016-01-26 13:08:35,649 Uncaught exception in exposed API method: Traceback (most recent call last): File "lib/galaxy/web/framework/decorators.py", line 260, in decorator rval = func( self, trans, *args, **kwargs) File "lib/galaxy/webapps/galaxy/api/tools.py", line 98, in build return tool.to_json(trans, kwd.get('inputs', kwd)) File "lib/galaxy/tools/__init__.py", line 2602, in to_json populate_state(trans, self.inputs, state_inputs, state_errors, params.__dict__) File "lib/galaxy/tools/__init__.py", line 2471, in populate_state state[input.name] = input.get_initial_value(trans, context, history=history) File "lib/galaxy/tools/parameters/basic.py", line 984, in get_initial_value value = [ optval for _, optval, selected in options if selected ] ValueError: too many values to unpack </pre> My tool xml looks like this: <pre> <tool id="archivetolibrary" name="Copy files" version="0.1.0"> <description>from the archive to a data library</description> <code file="list_files.py"/> <command interpreter="bash"> test.sh > $log </command> <inputs> <param name="archive_source" type="select" display="radio" label="Choose source archive"> <options from_file="archives.loc"> <column name="name" index="0"/> <column name="value" index="1"/> </options> </param> <param name="query" type="text" label="Search for files"/> <param name="selected_file" type="select" label="Choose your file" dynamic_options="list_files(archive_source,query)"/> </inputs> <outputs> <data name="log" format="txt" label="${tool.name} on ${on_string}"></data> </outputs> <tests> <test> </test> </tests> <help> This tool copies data from and archive folder to your history. Keep in mind this folder MUST be readable by Galaxy in order for this tool to work. </help> </tool> </pre> and the script called in the “code” tag looks like this <pre> def list_files(dir,query): listing=[] for fname in listdir(dir): fullpath = path.join(dir, fname) #only select datafiles, not md5 checksums if path.isfile(fullpath) and not fullpath.endswith(".md5"): listing.append( fname ) return listing </pre> This script should return a list with filenames that should be displayed in the dropdown list. I’m tracking Galaxy release 15.10, running on a Ubuntu 14.04.3 server Thanks for your help! Matthias

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Storing data in the user session
by Steve Cassidy 17 Oct '16

17 Oct '16

Hi again, I’m looking for the right way to store some user credentials in the galaxy session so that tools can work on behalf of the user with our repository. Currently users have an API key and they need to upload it as a data item to that is then passed to each tool that needs it as input. This doesn’t seem like the right solution since the API key becomes part of the history and so would be shared if the history were shared. What would be better would be a way of storing the API key in the user session and then being able to pass that into a tool. I note that there are a few user session variables available in the tool xml file: __user__, __user_email__, __user_name__ and __user_id__. There is also a user preferences page where they can fill out a few details. However, I can’t see a mechanism to extend this in any way and have extra properties in the preferences pane that would then be available to tools via the template file. I can see that the standard practice for the data sources on usegalaxy.org<http://usegalaxy.org> is to send the user off to a repository website to find data that is then posted back to the galaxy server. This isn’t appropriate for us since the interaction with the repository is not just for downloading a single dataset - tools will query the repository, download various kinds of data and possibly upload new data, so we need to store user credentials in some way. Is there already a good way to achieve this or is this an enhancement to Galaxy? Thanks, Steve — Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy

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Galaxy Admin Training: November 7-11, Salt Lake City
by Dave Clements 15 Oct '16

15 Oct '16

Hello all, *Early registration <https://wiki.galaxyproject.org/Events/AdminTraining2016/Registration> for Galaxy Admin Training 2016 <https://wiki.galaxyproject.org/Events/AdminTraining2016> ends in one week, on Monday, September 19.* Galaxy Admin Training 2016 <https://wiki.galaxyproject.org/Events/AdminTraining2016> is a weeklong event offering basic and advanced sessions. It will be held in Salt Lake City, Utah, November 7-11, 2016, the week before Supercomputing 16 (SC16) <http://sc16.supercomputing.org/> meets in Salt Lake. These workshops are aimed at admins from organizations and labs that are installing, upgrading, or prototyping Galaxy instances. *Basics Session: November 7-8* <https://wiki.galaxyproject.org/Events/AdminTraining2016/BasicsSession> This two day basics session <https://wiki.galaxyproject.org/Events/AdminTraining2016/BasicsSession> will introduce participants to what you need to know to get a Galaxy server up and running on a standalone server. You'll also learn how to extend your Galaxy with your own tools and tools from the community, and how to define reference data in your server. *Advanced Session: November 9-11* <https://wiki.galaxyproject.org/Events/AdminTraining2016/AdvancedSession> The three day advanced session <https://wiki.galaxyproject.org/Events/AdminTraining2016/AdvancedSession> will build on topics covered in the basics section <https://wiki.galaxyproject.org/Events/AdminTraining2016/BasicsSession>. This session both extends those topics, such as tool definition, and adds new ones, such as working with compute clusters and heterogeneous resources. The goal of the advanced workshop is to enable Galaxy administrators to create robust, high-performance Galaxy instances that take full advantage of available tools and compute and storage resources. Galaxy Admin Training 2016 is hosted by the University of Utah Center for High Performance Computing (CHPC) <http://www.chpc.utah.edu/>, the USTAR Center for Genetic Discovery (UCGD) <http://ucgd.genetics.utah.edu/>, Department of Biomedical Informatics <http://medicine.utah.edu/dbmi/> and the Clinical & Translational Science Biomedical Informatics Core (CCTS BMIC) <http://medicine.utah.edu/ccts/bmic/> at the University of Utah <http://utah.edu/>. We hope to see you in Salt Lake! The Galaxy Team <https://wiki.galaxyproject.org/GalaxyTeam> PS: Please share this flier <https://wiki.galaxyproject.org/Events/AdminTraining2016/Publicity> with any individuals or groups who might be interested in this event. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Modifying Values in the Database
by Katherine Beaulieu 04 Oct '16

04 Oct '16

Hello Everyone, I am trying to create a query to modify a value from a table in the galaxy database, but don't quite know what this language is that is being used to modify the database. The only command I know of are sa_session.add and sa_session.flush. Any help would be really appreciated! Katherine

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Workflow ID, Galaxy Instance URL, API Key in Galaxy Tool Config
by Katherine Beaulieu 30 Sep '16

30 Sep '16

Hi everyone, We are trying to obtain the three things in the tile of this post to enable a tool to use the bioblend api and get the .ga file so that any user can go back into our system, get the workflow associated with the end file, get the input parameters which are tags associated with the end file, and rerun that workflow if necessary. So simply put I am asking if there is a way to access a galaxy instance through the bioblend api from within a tool's config xml file. I have asked about getting the .ga file beforehand but still have not solved this problem so if anyone has any experience with this please let me know. Cheers, Katherine

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Galaxy Feature Request: Input naming deficiencies
by Ziphozakhe Mashologu 30 Sep '16

30 Sep '16

Hi All In using Galaxy, I would like to be able to keep track of the input dataset name down the analysis chain. This is a similar if not the same issue raised by Eric in https://github.com/galaxyproject/galaxy/issues/2752, to which he proposes in the context of a workflow that, "the rename dataset action should support usage of all the dataset names from Input Dataset elements, rather than just input files to the particular tool." Please see the issue for more details. There are other similar issues raise scattered all over regarding the same issue: Enhancements: 1. Ability to name datasets using the element identifier: https://github.com/galaxyproject/galaxy/issues/2006 2. Ability to define the collection name in a workflow: https://github.com/galaxyproject/galaxy/issues/2398 3. Name datasets according to both collection name and element identifier: https://github.com/galaxyproject/galaxy/issues/2140, https://github.com/galaxyproject/galaxy/issues/2023 Bug Fixes: 1. Renaming using the input from paired dataset collections: https://github.com/galaxyproject/galaxy/issues/1675, https://github.com/galaxyproject/galaxy/issues/1686 I have created a github issue regarding the above, in effort to try and consolidate all these related above issues. https://github.com/galaxyproject/galaxy/issues/2980 Can we use the above issue to discuss the best approach on these issues, point out work being done on the area and perhaps define clear milestones for each? Galaxy Devs please provide me some guidance to best tackle this. (particularly of tracking the input dataset names along the analysis chain). Thanks, Zipho

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