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Galaxy Local Admin user
by Chadi Abdul Kader El Farran 16 Jul '13

16 Jul '13

Dear Madam/Sir, I have installed Galaxy Local in our system. I registered as a user. However when I try to give admin status to some users, I am unable despite following the steps mentioned in the help. "To give a user Galaxy admin privileges, add their Galaxy login ( email ) to the list in the following config setting in the Galaxy configuration file universe_wsgi.ini. # this should be a comma-separated list of valid Galaxy users admin_users = user1@bx.psu.edu,user2@bx.psu.edu" I have done what is mentioned above and the universe_wsgi.ini is edited accordingly. Still when I log on to Galaxy Local I don't see the admin tab. Can you kindly help me. With warmest regards Chadi EL Farran (Post Graduate Student) Dr. Jonathan Yuin-Han Loh's Laboratory #08-01, Institute of Molecular and Cell Biology (IMCB) 61 Biopolis Drive, Proteos Singapore 138673 Contact No: +65-91944793 E-mail: chadi(a)nus.edu.sg

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provide group(s) association as a tool parameter
by Christian Hundsrucker 16 Jul '13

16 Jul '13

Hi there! Is there an easy way to pass a users group associations to a tool as a parameter. Maybe similar to pass user information via the reserved variable "$__user_email__" ?! I tried "$__app__.model.UserGroupAssociation.group" however I end up with a mapper-object and are kind of stuck here... Thnx, Christian

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Re: [galaxy-dev] Testing with <repeat> parameters
by Joachim Jacob | VIB | 16 Jul '13

16 Jul '13

Oops, I was replying via theGalaxy Development List Archive <http://dev.list.galaxyproject.org/> interface, strange it has put the reply off list... So no functional test for my tool ( despite my enthousiasm :-) ), since the repeat tags must be provided in the test. Thanks, Joachim. Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 07/16/2013 01:46 PM, Peter Cock wrote: > Off list? > > They don't work yet, bar the simplest case of 0 or 1 repeats using a > single parameter perhaps. > > Peter > > > On Tuesday, July 16, 2013, wrote: > > Hi Peter, > > I was wondering if you have details on how to include tests for > repeat tag sets? > > Cheers, > Joachim > > <quote author='Peter Cock'> > Hello all, > > Should unit tests with repeat parameters work? If so, how do I give > each repeat group in the XML for the <test>? > > Sample tool here: > http://testtoolshed.g2.bx.psu.edu/view/peterjc/venn_list > > <inputs> > <param name="main_lab" size="30" type="text" value="Venn Diagram" > label="Plot title"/> > <conditional name="universe"> > <param name="type_select" type="select" label="Implicit or > explicit full ID list?"> > <option value="explicit">Explicit</option> > <option value="implicit">Implicit (use union of sets > below)</option> > </param> > <when value="explicit"> > <param name="main" type="data" > format="tabular,fasta,fastq,sff" > label="Full dataset (with all identifiers)" > help="Tabular file (uses column one), FASTA, > FASTQ or SFF file."/> > </when> > <when value="implicit"/> > </conditional> > <repeat name="sets" min="1" max="3" title="Sets"> > <param name="set" type="data" format="tabular,fasta,fastq,sff" > label="Members of set" > help="Tabular file (uses column one), FASTA, > FASTQ or SFF file."/> > <param name="lab" size="30" type="text" value="Group" > label="Caption for set"/> > </repeat> > </inputs> > > The first test attempts to use the repeat "set"/"lab" once - guessing > at how to give repeat parameters in a test: > > <test> > <param name="type_select" value="explicit"/> > <param name="main" value="venn_list.tabular" ftype="tabular"/> > <param name="main_lab" value="Some Proteins"/> > <param name="set" value="rhodopsin_proteins.fasta"/> > <param name="lab" value="Rhodopsins"/> > <output name="PDF" file="venn_list1.pdf" ftype="pdf"/> > </test> > > $ ./run_functional_tests.sh -id venn_list > ... > python /mnt/galaxy/galaxy-central/tools/plotting/venn_list.py > /mnt/galaxy/galaxy-central/database/files/000/dataset_1.dat tabular > "Some Proteins" > /mnt/galaxy/galaxy-central/database/files/000/dataset_2.dat fasta > "Rhodopsins" > /mnt/galaxy/galaxy-central/database/files/000/dataset_2.dat > fasta "Group" > /mnt/galaxy/galaxy-central/database/files/000/dataset_3.dat > ... > > This seems to have resulted in two <repeat> entries, and so fails. > What I was expecting was: > > python /mnt/galaxy/galaxy-central/tools/plotting/venn_list.py > /mnt/galaxy/galaxy-central/database/files/000/dataset_1.dat tabular > "Some Proteins" > /mnt/galaxy/galaxy-central/database/files/000/dataset_2.dat fasta > "Rhodopsins" > /mnt/galaxy/galaxy-central/database/files/000/dataset_3.dat > > Thanks, > > Peter > ___________________________________________________________ > 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/ > > </quote> > Quoted from: > http://dev.list.galaxyproject.org/Testing-with-repeat-parameters-tp4659840.… > > > _____________________________________ > Sent from http://dev.list.galaxyproject.org >

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Re: [galaxy-dev] Strange behaviour with galaxy history
by Ambrose Andongabo (RRes-Roth) 16 Jul '13

16 Jul '13

Many thanks for the observation. This will come handy next time I hit the same rock. I hope not so soon. Ambrose -----Original Message----- From: Groot, Philip de [mailto:philip.degroot@wur.nl] Sent: 16 July 2013 12:03 To: Carl Eberhard Cc: galaxy-dev(a)lists.bx.psu.edu; Ambrose Andongabo (RRes-Roth) Subject: RE: Strange behaviour with galaxy history Hi Carl, Thank you for your quite extensive answer! I finally managed to find the line in universe_wsgi.ini that caused the problem. The moment I UNCOMMENT the following line: #log_actions = True I no longer can see the histories. The moment I comment this line again everything works fine. Anyway, this exercise resulted in a clean and updated universe_wsgi.ini file and the problem is solved now! Thank you for your help! Regards, Dr. Philip de Groot Ph.D. Bioinformatics Researcher Wageningen University / TIFN Nutrigenomics Consortium Nutrition, Metabolism & Genomics Group Division of Human Nutrition PO Box 8129, 6700 EV Wageningen Visiting Address: Erfelijkheidsleer: De Valk, Building 304 Dreijenweg 2, 6703 HA Wageningen Room: 0052a T: +31-317-485786 F: +31-317-483342 E-mail: Philip.deGroot(a)wur.nl<mailto:Philip.deGroot@wur.nl> Internet: http://www.nutrigenomicsconsortium.nl http://humannutrition.wur.nl/ https://madmax.bioinformatics.nl/ ________________________________ From: Carl Eberhard [carlfeberhard(a)gmail.com] Sent: 11 July 2013 16:34 To: Groot, Philip de Cc: galaxy-dev(a)lists.bx.psu.edu; Ambrose.Andongabo(a)rothamsted.ac.uk Subject: Re: Strange behaviour with galaxy history Hello, Phillip I haven't been able to replicate this yet (https://trello.com/c/LdLlJDo9) Do you see any errors in your log near or after "GET /history/list HTTP/1.1"? Shane Sturrock worked around this problem by updating his universe_wsgi.ini file (if I understand his procedure): 1. Make a backup of your universe_wsgi.ini file (for example, copy it to your home directory) 2. Rename the universe_wsgi.ini file in your galaxy installation something like 'universe_wsgi.ini.saved' 3. Rename the most recent universe_wsgi.ini.sample file (that came with the latest update) to universe_wsgi.ini. 4. Copy any custom settings for your server from your older universe_wsgi.ini.saved file to the newer universe_wsgi.ini file 5. Start Galaxy That seemed to work for Shane. Ambrose re-installed and reconnected his database. Neither is a solution to the original cause, but you may want to try them while we investigate. Thanks, Carl On Thu, Jul 11, 2013 at 5:48 AM, Groot, Philip de <philip.degroot(a)wur.nl<mailto:philip.degroot@wur.nl>> wrote: Hi, First of all, I apologize for interrupting into this discussion, but I have exactly the same problem and did not find a solution yet. And no: prefix and cookies are set properly in our particular setting (as "/")! This is not the cause... I think that the problem occurred with the May Galaxy update, but it was unnoticed for a while. Problem is that the histories of all users are not listed when being asked for it within Galaxy. Only the current history is present for every user. In addition, when I login using another computer, a different history is being depicted (which suggest a cookie issue but I just cannot find it). Copying the current history works but the copy is not listed either. In the postgres database, the histories are properly listed. If I type in the proper history name in Galaxy, I even get the stored history back! So this all works, but users cannot see their histories. The java console does not reveal any problem. prefix and cookie are set properly (I think). So I don't know. Does anyone have any clue on how to tackle this issue? I am happy to provide more information if needed! Thanks! Dr. Philip de Groot Ph.D. Bioinformatics Researcher Wageningen University / TIFN Nutrigenomics Consortium Nutrition, Metabolism & Genomics Group Division of Human Nutrition PO Box 8129, 6700 EV Wageningen Visiting Address: Erfelijkheidsleer: De Valk, Building 304 Dreijenweg 2, 6703 HA Wageningen Room: 0052a T: +31-317-485786<tel:%2B31-317-485786> F: +31-317-483342<tel:%2B31-317-483342> E-mail: Philip.deGroot(a)wur.nl<mailto:Philip.deGroot@wur.nl><mailto:Philip.deGroot@wur.nl<mailto:Philip.deGroot@wur.nl>> Internet: http://www.nutrigenomicsconsortium.nl<http://www.nutrigenomicsconsortium.nl/> http://humannutrition.wur.nl/ https://madmax.bioinformatics.nl/ -- This message has been scanned for viruses and dangerous content by MailScanner, and we believe but do not warrant that this e-mail and any attachments thereto do not contain any viruses. However, you are fully responsible for performing any virus scanning. -- This message has been scanned for viruses and dangerous content by MailScanner, and we believe but do not warrant that this e-mail and any attachments thereto do not contain any viruses. However, you are fully responsible for performing any virus scanning.

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GALAXY LOCAL INSTALLATION: Remove history
by Rafael Hernández 15 Jul '13

15 Jul '13

Hi Galaxy devs, I've installed Galaxy in local and I see that in spite of the users remove their histories using the "Delete history" option, the used space is not free. As I understand reading the Galaxy documentation, after deleting the history, the history is marked as "Deleted" but files are not removed. After 60 days, Galaxy automatically remove them. > > 1. If you delete a specific history using the **Options** link at the > top of the history panel, that history and all of its associated datasets > will be removed from disk 60 days after you deleted the history. > 2. Those specific history items ( datasets ) that you delete from one > of your histories by clicking the "X" icon in the history item will be > removed from disk after 60 days, but unless you manually delete your > history, you will still be able to view the history itself ( only the > dataset that you deleted from your history will be removed from disk ). > > I suppose this should be the default behavior too for local installations. but I did not configure anything about that and I need to confirm this is true because the used space becomes bigger each day! Is there any way to change this periodicity to less days? Thank you and regards, Rafa Hernández de Diego Genomics of Gene Expression Lab. Bioinformatics and Genomics Department Prince Felipe Research Centre (CIPF) C/ Eduardo Primo Yúfera 3 46012 Valencia, Spain

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Galaxy Server Questions
by Jennifer Jackson 15 Jul '13

15 Jul '13

Hi Zain, The minimum requirements for Galaxy are pretty much any recent model computer. A basic install will load and run within a very short amount of time, following the instructions at: http://getgalaxy.org Advanced tools come from the Tool Shed. These are installed separately. No programming is needed, but some very basic unix skills are required, as they would be for ongoing server maintenance. The Tool Shed is one of the best documented parts of Galaxy, so you should be able to find all the answers here, or this is the right list to use for questions about local installs (galaxy-dev(a)bx.psu.edu) http://wiki.galaxyproject.org/Tool%20Shed However, running a production instance that is intended to run compute intensive tools (such as Tophat2), and where you have some throughput goals, will require more substantial resources. This is always a difficult question to answer since so much depends on the tools used and the data volume. But in general, minimum requirements are about around the same as what those underlying tools would require on their own, if run line-command. So for Tophat or Tophat2, and really the entire Tuxedo RNA-seq tool package, you might be able to get by on 8G memory and 2 or 4 cores. But, it will probably be slow and if you are running replicates through Cuffdiff at the end, you might run out of memory if the files are large and the genome is large (such as human). And if you are are hosting a web Galaxy at the same time with visualizations and such, well, this is why systems are often set up with clusters. With all of these will be competing for the same resources, going low can work, but this will be something that will have to be managed/tested, and it will change through time as tools upgrade. You could test this out by setting up a cloud instance with the hardware you plan to use, loading some of your data, and running your workflow to see how this benchmarks. Have users on the instance while you are doing this - to judge performance. Cloud installations come with many of the advanced tools and data indexes already installed/configured, so this would be less investment than buying the hardware first and finding out later it was not not enough. http://usegalaxy.org/cloud And of course Slipstream Galaxy is an option. The whole intention here is to make a complete package with tools & data already configured, in a system that has enough compute capability to do the work, for scientists/labs who do not want to deal with administrative tasks or work in the cloud (for whatever reason). http://bioteam.net/slipstream/galaxy-edition/ Good luck with your decision! Other are welcomed to comment about how they have set up their system. Jen Galaxy team On 7/15/13 7:14 AM, Zain A Alvi wrote: > Hi Jen, > > I hope this reaches you well. I have a small question in regards to > setting up a galaxy server. My mentors and I are looking into buying a > server for doing NGS analysis through the use of Galaxy. We saw that > slipstream's specifications for hardware to be the following: > > CPU: 2x Intel Xeon Processor E5-2690, 8 core (16 cores total) > RAM Memory: 12x 32GB RDIMM (384 GB) with option to upgrade it to 512 GB > Storage (Hard Drive space): 7x 3TB SAS 6 Gbps (16 TB usable) with 1 x > 100GB Solid State Disk > Power: Dual Pedundant Power Supplies > Network: Dual Gigabit Network Adapter > > We are wondering what can be the minimum server hardware > specifications that Galaxy be run on. > > Our second question is if we install Galaxy on the server, do all the > tools currently available on Galaxy come pre-installed on it or do we > have to program (Via Perl and Python) and install each of those tool > sets ourselves. If we have to install those tools ourselves, is there > a guide that we can do so? Lastly, how can we upgrade the tool sets > such as Tophat 1.44 to Tophat 2 on this server. I was wondering about > the last question as Tophat 1.44 is available on the main Galaxy > server whereas Tophat 2 is available on the test Galaxy server. > > Sorry for so many questions. Thank you again for all the great help. > > Sincerely, > > Zain -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

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Error Uploading Directory of Files
by Nicholas Kline 15 Jul '13

15 Jul '13

Hi, Our lab recently installed a local version of Galaxy on a mid-2012 Mac Pro computer. We can access the Galaxy server and sign in as an administrator. Today we tried creating a Data Library, adding a dataset to it, and uploading a directory of files. We followed the Galaxy documentation at http://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles?act… to setup this feature: - Admin > Data Library > Add datasets > Upload directory of files - file format was set to auto-detect - and we chose the option to link to files instead of copying them Galaxy confirmed that the files were successfully uploaded. However, in the data library, under the Message column, is a message in red saying "Job error (click name for more info)". Clicking on one of the uploaded files displays a page with this information: Date uploaded: 2013-06-28 File size: 7.5 GB Data type: auto Build: sacCer2 Miscellaneous information: Traceback (most recent call last): File "/Users/administrator/galaxy-dist/tools/data_source/upload.py", line 386, in __main__() File "/Users/administrator/galaxy-dist/tools/data_source/upload.py", line 357, in __main__ output_paths = Job Standard Error Traceback (most recent call last): File "/Users/administrator/galaxy-dist/tools/data_source/upload.py", line 386, in __main__() File "/Users/administrator/galaxy-dist/tools/data_source/upload.py", line 357, in __main__ output_paths = parse_outputs( sys.argv[4:] ) File "/Users/administrator/galaxy-dist/tools/data_source/upload.py", line 64, in parse_outputs id, files_path, path = arg.split( ':', 2 ) ValueError: need more than 1 value to unpack error Database/Build: sacCer2 Number of data lines: None Disk file: /Volumes/G-SPEED Q/data/Person 2012 project/DCP2 mef.fastq Questions: 1. Should we be concerned about this error? 2. If so, what is the right way to fix it? 3. If not, how do we remove the red error message next to each file: "Job error (click name for more info)" ? Thank you

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[GSoC2013] Week 4 Accomplishments and Week 5 Plans
by Saket Choudhary 15 Jul '13

15 Jul '13

Hi All, Week 4 blog post : http://galaxy-gsoc2013.blogspot.com/2013/07/week-4-accomplishments-and-week… Do drop in your comments , if any. Thanks Saket

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No samtools build after building index through Data Manager.
by graham etherington (TSL) 15 Jul '13

15 Jul '13

Hi, I've tried using the Data Manager (Admin > Data > Manage local data (beta)) to install builds for BWA and Samtools on my local Galaxy instance. Previous to using the Data Manager, I used to add the build to tool-data/shared/ucsc/builds.txt, create the .fai indexes (for samtools) from the command line, add them to tool-data/sam_fa_indices.loc and restart Galaxy (obviously doing a similar thing for BWA and adding the build to bwa_index.loc). I thought I'd try using the Data Manager to add builds for BWA and Samtools. The BWA builds work fine (I can map to the build), but when I try to use SAM-to-BAM I get the error "Sequences are not currently available for the specified build." Using the Data Manager creates the directory tool-data/n_sylvestris/ which contains the sub-dirs 'seq', 'bwa_index' and 'sam_index'. 'seq' contains a symlink to the n_sylvestris.fa sequence. 'sam_index' and 'bwa_index' both contains the sub-directory 'n_sylvestris', which contains a symlink to the symlink for n_sylvestris.fa in 'seq' along with their respective n_sylvestris.fa.xxx index files. OK - all goodŠ In tool-data/testtoolshed.g2.bx.psu.edu/repos/blankenberg/ there are three subdirectories: data_manager_bwa_index_builder, data_manager_sam_fa_index_builder and data_manager_fetch_genome_all_fasta All three directories contain all_fasta.loc, tool_data_table_conf.xml, tool_data_table_conf.xml.sample and (for sam and bam dirs) their pertinent index.loc file. The data_manager_fetch_genome_all_fasta/all_fasta.loc file contains the path to the fasta symlinks. The all_fasta.loc files in the sam and bwa data_manager_index_builder directories don't contain any uncommented lines. The index.loc files in the sam and bwa data_manager_index_builder directories point to: tool-data/n_sylvestris/bwa_index/n_sylvestris/n_sylvestris.fa tool-data/n_sylvestris/sam_index/n_sylvestris/n_sylvestris.fa As BWA runs fine, it's obviously reading the bwa_index.loc file from the directory: tool-data/testtoolshed.g2.bx.psu.edu/repos/blankenberg/data_manager_bwa_ind ex_builder/fe6508204acc/bwa_index.loc ...but it's not reading the samtools indexes at: tool-data/testtoolshed.g2.bx.psu.edu/repos/blankenberg/data_manager_sam_fa_ index_builder/926e50397b83/sam_fa_indices.loc For Galaxy to find the sam indexes, I have to go to the tool-data/sam_fa_indices.loc file and manually insert into it the contents of: tool-data/testtoolshed.g2.bx.psu.edu/repos/blankenberg/data_manager_sam_fa_ index_builder/926e50397b83/sam_fa_indices.loc So, I guess my question is: other than inserting the genome builds into builds.txt, should I be doing any other configuration to get Data Manager to write and configure Galaxy to read it's newly created builds. I find it strange that the BWA builds work OK, but the Samtools ones don't. I've done a few greps for mentions of .loc files in Galaxy and the only difference between the bwa and sam .loc files is that there is a file tool-data/tool_data_table_conf.xml (plus a .sample version) which contains:  <tables>  <table name="sam_fa_indexes" comment_char="#"> <columns>line_type, value, path</columns> <file path="tool-data/sam_fa_indices.loc" /> </table> </tables> Could Galaxy be reading this file and ignoring the one in tool-data/testtoolshed.g2.bx.psu.edu/repos/blankenberg/ ?? Best wishes, Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601

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Help with "Send output to Galaxy" function
by Huayan Gao 15 Jul '13

15 Jul '13

Hi, I am trying to connect my local database/webpages to my local galaxy server. But I have a hard to implement "send output to galaxy" function. Right now I have a sending page to send a form to galaxy and it looks like everything goes well. From the variable json_params(data_source.py), I can see that all parameters have been received by galaxy. But the problem is that how I get my parameters from my getfile.php file(This is used in the Galaxy_URL too, the callback function)? I tried to print out $_POST, $_GET, $_REQUEST, nothing shows up. I did see some output from $_Server. I am using php. Please help! Best, Huayan

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