- galaxy-dev - lists.galaxyproject.org

Best practices for a local install of Galaxy
by Paul St. Amand 18 Jun '13

18 Jun '13

On Jun 18, 2013, at 8:02 AM, galaxy-dev-request(a)lists.bx.psu.edu wrote: > I have Galaxy running on a small Mac workstation. I have made a specific > user, 'galaxy', for it. It is cleaner, but probably overkill for 1 person. > > Note also that you can install a daemon to start Galaxy automatically > when your computer starts: > https://bitbucket.org/galaxy/galaxy-central/src/d2d4b6ac2139f1623301990462a… > > I don't think I have ever waited long enough to see the end of the unit > tests. If some fail without any obvious reason (missing dependencies or > what not), you should probably raise this issue on the Galaxy mailing > list or bug tracker. > > Cheers, > > Florent Thanks for the startup tip Florent. That would be useful for those using Galaxy daily. So you think that running the install as the current non-root but ADMIN user works OK? What about the install folder? Must it be the home folder or is a subfolder OK as I have it (/Users/pst/Applications/)? My test output "run_functional_tests.html" is 5.1MB. I suppose that is too much to post on the list. I think that most of the errors are not due to dependencies. How do I get help with that? Paul

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Trying to configure external data source
by Daniel Gorelik 18 Jun '13

18 Jun '13

Hello folks, I am trying to configure an external data source and it is driving me crazy. I keep getting the error "The remote data source application has not sent back a URL parameter in the request." , even though it is. My xml file is: <?xml version="1.0"?> <tool name="My tool" id="s3t" tool_type="data_source"> <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> <inputs action="myurl/" check_values="true" method="get"> <display>Let's do this! $GALAXY_URL</display> <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=s3t" /> <param name="sendToGalaxy" type="hidden" value="1"/> </inputs> <request_param_translation> <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" /> <request_param galaxy_name="URL" remote_name="URL" missing="myurl/" /> </request_param_translation> <uihints minwidth="800"/> <outputs> <data name="output" format="txt" label="test" /> </outputs> <options sanitize="False" refresh="True"/> </tool> And in myurl file I have: <FORM ACTION="%s" METHOD=POST> <input type="submit"></input> <INPUT TYPE=HIDDEN NAME='URL' VALUE='myfile/'> </form> %s is the GALAXY_URL Any help, pointers, or philosophical advice would be greatly appreciated. Thank you, Daniel Gorelik

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setting parameters for uploading a file for a java program
by vijayalakshmi 18 Jun '13

18 Jun '13

Hi all, I have a tool written in java for which I want to upload a file as a parameter. I have trouble figuring out how to do it. I tried writing the xml file similar to 'tools/data-source/upload.xml' but it is not working. *correlation.xml* <tool id="correlation" name="Compute correlation" version="1.1.3"> <description> for the given BAM file </description> <action module="galaxy.tools.actions.upload" class="UploadToolAction"/> <command>java -jar Correlation.jar $input_bam_file $output</command> <inputs nginx_upload="true"> <param name="async_datasets" type="hidden" value="None"/> <upload_dataset name="input" title="Specify Files for Dataset" file_type_name="file_type" metadata_ref="files_metadata"> <param name="input_bam_file" type="file" size="30" label="File (Please avoid Windows format text file)" ajax-upload="true" help="TIP1: Due to browser limitations"> <validator type="expression" message="You will need to reselect the file you specified (%s)." substitute_value_in_message="True">not ( ( isinstance( value, unicode ) or isinstance( value, str ) ) and value != "" )</validator> </param> </upload_dataset> <param name="dbkey" type="genomebuild" label="Genome" /> <conditional name="files_metadata" title="Specify metadata" value_from="self:app.datatypes_registry.get_upload_metadata_params" value_ref="file_type" value_ref_in_group="False" /> </inputs> <outputs> <data name="output" format="txt" /> </outputs> </tool> I am not sure where I am making a mistake... Is the procedure to upload a file for java different from python? Thanks, VJ.

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Clone Galaxy from repository: mercurial from behind proxy?
by Sebastian Schaaf 18 Jun '13

18 Jun '13

Hi all, I'm currently trying to set up a galaxy-dist instance on a SLES server within an 'encapsulated' network (hospital environment; here all sensitive data is stored and handled). Within this network, clients are only capable of accessing the internet via HTTP/HTTPS and FTP, using a proxy - adress and port (8080) are the same for all three protocols. Mercurial (which I had to set up in advance) is accessible and more or less in default configuration (more on that down below). What I get after executing the command 'hg clone https://bitbucket.org/galaxy/galaxy-dist#stable' is "abort: error: _ssl.c:491: error:140700FC:SSL routines:SSL23_GET_SERVER_HELLO:unknown protocol" Google search indicates something more general, so outside the exclusive scope of Galaxy. On top, no connection to Galaxy was listed, also not in this mailing list's archive. Following some hints I just tried to set the proxy via a '.hgrc' file in the galaxy user home like this: --- [http_proxy] host = url:port [https_proxy] host = url:port --- (re-login after that) and also set the system variables '$http_proxy' and '$https_proxy'. Another approach described was to call 'hg --config http_proxy.host=url:port clone https://bitbucket.org/galaxy/galaxy-dist#stable' Nothing worked out. Does anyone experienced similar behaviour or has got some ideas how to solve this? Thanks in advance, Sebastian -- Sebastian Schaaf, M.Sc. Bioinformatics University of Munich

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Galaxy setup from cloudman shows no tools in the tool panel
by Marco Ocana 18 Jun '13

18 Jun '13

Hi, Just setup Galaxy using cloudman on AWS. I updated the version of Galaxy using the Admin Console (it shows revision 10066:d2d4b6ac2139<http://bitbucket.org/galaxy/galaxy-central/changesets/d2d4b6ac2139> ). I also did the additional tool installation described in the Galaxy log file by running the script: sh ./scripts/migrate_tools/0007_tools.sh install_dependencies FInally, I added the genomespace tools as described in: http://wiki.galaxyproject.org/GenomeSpace >From the cloudman admin console all systems appear as "Running" . However, when I go to the Galaxy main page, the "Tools" panel is completely empty. I tried restarting Galaxy from the cloudman console a couple of times. There are errors that show up in the Galaxy log, though none that could tell me precisely what I should do to get the tools to display. I have attached the Galaxy log file. Any help would be appreciated. Thanks Marco

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trimest tool cuts the begining of my seq names in the output fasta file
by Inbar Plaschke 18 Jun '13

18 Jun '13

Dear galaxy developers, When I use the EMBOSS tool: trimest<https://main.g2.bx.psu.edu/tool_runner?tool_id=toolshed.g2.bx.psu.edu/repos…>, Trim poly-A tails off EST sequences , within galaxy The sequences names in the fasta output file comes out without their beginning, for instance: >gi|259479195|dbj|AB491800.1|Brachionusplicatilisstt3mRNAforoligosaccharytransferaseSTT3subunithomolog,partialcds Will be shortened into: >AB491800.1|Brachionusplicatilisstt3mRNAforoligosaccharytransferaseSTT3subunithomolog,partialcds How can I keep the beginning of the sequence names? Am I doing something wrong? Many thanks for your help Inbar [Description: logo_50prcnt] Inbar Plaschkes Bioinformatics Core Facility National Institute for Biotechnology Ben-Gurion University of the Negev Beer-Sheva 84105, Israel Building 51, room 323 Email: inbarpl(a)bgu.ac.il<mailto:inbarpl@bgu.ac.il> Tel: +972-8-6428676 Fax: +972-8-6479035 Web: http://bioinfo.bgu.ac.il<http://bioinfo.bgu.ac.il/>

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Best practices for a local install of Galaxy for only 1 user on a Mac
by Paul St. Amand 18 Jun '13

18 Jun '13

I am trying to install Galaxy on a new iMac (i7, 32gb ram, OSX 10.8). Mostly the install worked and I can use my local install. However, about 25% of the functional tests failed for me. And about 4 of the unit tests failed for me. Also, I can't seem to install anything from the toolshed (logged in as Admin). Below is what I did to install. Can any Galaxy/Mac gurus out there please fix the errors in the below install list so that we can have a good idea of the best practices for installing Galaxy on a Mac running the latest version of OSX? Also, tips for installing all of the dependencies would be great too. Best practices for a local install of Galaxy for only 1 user on a Mac. For Galaxy on a Mac (OSX 10.8): To uninstall: delete galaxy-dist folder (should anything else be done??) To install Galaxy on a Mac (OSX 10.8): 1. Install Mercurial, download latest version from http://mercurial.selenic.com/mac/ and unzip and run installer. 2. Run the following in the terminal as a NON-root user (change "pst" to your user ID). (Is it better to create a "galaxy" user and install as user "galaxy"???) (Is it OK to use /Users/MacID/Applications as the install location, or is the home folder best??): % cd /Users/pst/Applications % hg clone https://bitbucket.org/galaxy/galaxy-dist/ % cd /Users/pst/Applications/galaxy-dist % hg update stable 3. After install, run this to start the server and create defaults, then Control-C to quit the server: % cd /Users/pst/Applications/galaxy-dist % sh run.sh % Ctrl-c in the terminal 4. Make the following changes to the universe_wsgi.ini file (found in /Users/pst/Applications/galaxy-dist/) using any text editor, save file as a UNIX text only file (TextWrangler works great for this) (What other changes should be made?). library_import_dir = /Users/pst/Documents/GalaxyDataFiles allow_library_path_paste = True admin_users = yourID(a)yourLocation.com allow_user_dataset_purge = True debug = False use_interactive = False cleanup_job = onsuccess 5. Set Up Visualizations: % cd /Users/pst/Applications/galaxy-dist % cp datatypes_conf.xml.sample datatypes_conf.xml 6. Get wigToBigWig and bedGraphToBigWig from (http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/) and copy the files to the /Users/pst/Applications/galaxy-dist/ folder. 7. Set both files to be executable: % chmod +x /Users/pst/Applications/galaxy-dist/bedGraphToBigWig % chmod +x /Users/pst/Applications/galaxy-dist/wigToBigWig 8. Test installation with: % cd /Users/pst/Applications/galaxy-dist % sh run_functional_tests.sh 9. Check test output. The above command will output an html file called "run_functional_tests.html" (found in /Users/pst/Applications/galaxy-dist/) which contains all of the details of the test, along with additional information for failed tests. 10. Other tests: % cd /Users/pst/Applications/galaxy-dist % sh run_unit_tests.sh 11. Check test output. The above command outputs an html file called "run_unit_tests.html" (found in /Users/pst/Applications/galaxy-dist/) which contains all of the details of the test, along with additional information for failed tests. 12. Install dependencies?? To start the local Galaxy server: % cd /Users/pst/Applications/galaxy-dist % sh run.sh To use the local Galaxy server, enter this URL in your web browser: http://localhost:8080 To stop the Galaxy server, just hit Ctrl-c in the terminal window from which Galaxy is running. To see if new releases are available: % cd /Users/pst/Applications/galaxy-dist % hg incoming If "no changes found" then you are up to date. If changes are found, then add new versions with: % hg pull -u To update local galaxy: % cd /Users/pst/Applications/galaxy-dist % hg update stable

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dynamically load and run R scripts
by Keilwagen, Jens 17 Jun '13

17 Jun '13

Hi guys, I was searching for a possiblity to dynamically load and run R scripts and I found http://dev.list.galaxyproject.org/dynamic-loading-of-tools-tt4138600.html I know that it might be a security issue, but we only have a local instance here. Optimally an R script can be loaded into the history. Subsequently, this script can be execute via "tool" that takes this script and some parameters and returns the result. Is anything like that out there? Could anyone give me a reference? Thanks a lot, Jens

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The requested URL /cgi-bin-root/hgTracks was not found on this server
by Rodolfo Aramayo 17 Jun '13

17 Jun '13

Hi, I starting getting this error since late galaxy update I get data from UCSC Main (local), but when I click "display at UCSC main" I get: Not Found The requested URL /cgi-bin-root/hgTracks was not found on this server. Please help Thanks --R

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invalid frame access with data source
by Brian Craft 17 Jun '13

17 Jun '13

When loading a data source in an iframe, the galaxy js is doing some sort of invalid probing of the frame, leading to this error: Blocked a frame with origin "http://pk:8080" from accessing a frame with origin "https://tcga1.kilokluster.ucsc.edu". pk:8080 is the galaxy frame. Here is the offending code: jQuery( function() { $("iframe#galaxy_main").load( function() { $(this).contents().find("form").each( function() { What is this? And is there some way to work around it? On chrome it doesn't appear to cause any problem, however on FF it causes the js to abort in both frames, preventing the data source callback. b.c.

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