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Bug in history when using Admin account ??
by Neil.Burdett＠csiro.au 17 May '13

17 May '13

Hi, I believe I have found a bug? Or maybe I'm not using Galaxy correctly? These are the steps I used: * Downloaded the latest version of Galaxy * Created a user me(a)me.com<mailto:me@me.com> * Uploaded several files * Logged out * Create a user you(a)you.com<mailto:you@you.com> * Uploaded several files * Logged out and then logged in as an Admin user (specified in universe_wsgi.ini file) * Uploaded a file. Now when I log into me(a)me.com<mailto:me@me.com> or you(a)you.com<mailto:you@you.com> the history shows only the uploaded file that I uploaded as an Admin. Even logging in as Admin and using the "impersonate" feature doesn't allow me to view the history of me(a)me.com<mailto:me@me.com> or you(a)you.com<mailto:you@you.com>. The files still exist as I can see them in database/files/000 Is this a bug? Or are Admins not supposed to upload files? Also I tried: * Deleted the above galaxy-dist * Downloaded the latest version of Galaxy * Created a user me(a)me.com<mailto:me@me.com> * Uploaded several files * Logged out * Create a user you(a)you.com<mailto:you@you.com> * Uploaded several files * Logged out and then logged in as an Admin user (specified in universe_wsgi.ini file) * Didn't upload a file * Logged out of Admin Now when I log into me(a)me.com<mailto:me@me.com> or you(a)you.com<mailto:you@you.com> the history is empty. This can't be correct is it? Neil

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Resizing galaxy cloudman /mnt/galaxyData partition
by Iry Witham 16 May '13

16 May '13

Hi Team, I urgently need to resize the data partition on my galaxy cloudman instance without loosing anything. I notice that there a gui on the cloudman admin page that will allow me to increase it to 1000GB. If I use that will it restart all of the processes? I need to maintain this as a functional instance since it needs to be available for use tomorrow at 8:00 AM and I do not have the time to rebuild it. The gui says it will create a snapshot. The following is what it says: "Expand Disk Space Through this form you may increase the disk space available to Galaxy. All of the cluster services (but not the cluster) WILL BE STOPPED until the new disk is ready, at which point they will all be restarted. This may result in Galaxy jobs that are currently running to fail. Note that the new disk size must be larger than the current disk size. During this process, a snapshot of your data volume will be created, which can optionally be left in your account. If you decide to leave the snapshot for reference, you may also provide a brief note that will later be visible in the snapshot's description. New Disk Size (minimum 100GB, maximum 1000GB): OK Note (optional): or delete the created snapshot after filesystem resizing? If checked, the created snapshot will not be kept" What is the likelihood that this will be successful? Has anyone utilized it? Is there another way to resize the /mnt/galaxyData/ and /mnt/galaxyIndices partitions that will allow me to do what I need to? Thanks, Iry Witham The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

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Recall: [External] Re: [galaxy-user] Question on galaxy data visualization
by Sun, Wenping [USA] 16 May '13

16 May '13

Sun, Wenping [USA] would like to recall the message, "[External] Re: [galaxy-user] Question on galaxy data visualization".

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Recall: [External] Re: [galaxy-user] Question on galaxy data visualization
by Sun, Wenping [USA] 16 May '13

16 May '13

Sun, Wenping [USA] would like to recall the message, "[External] Re: [galaxy-user] Question on galaxy data visualization".

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Re: [galaxy-dev] [External] Re: [galaxy-user] Question on galaxy data visualization
by Sun, Wenping [USA] 16 May '13

16 May '13

Jen, Thank you for the information. I am using galaxy cloud to try the trickster for one of the processed chipseq analysis. However, there is no visualization for the bed file created from galaxy. Meantime, I am having problem to get back to galaxy now. Here is the error message as below -- The proxy could not connect to the destination in time. URL: http://ec2-107-20-10-72.compute-1.amazonaws.com/cloud I have tried to re-launch the cloud instance, as well as directly access the DNS from aws, and keep getting the same error. Is this the bug? Please help to fix this since I have data there. Thanks! Kathryn From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Monday, May 13, 2013 6:18 PM To: Sun, Wenping [USA] Cc: galaxy-user(a)lists.bx.psu.edu Subject: [External] Re: [galaxy-user] Question on galaxy data visualization Hello Kathryn, Trackster is the primary data visualization tool and can be accessed by clicking on the mini graph icon within a dataset: [cid:image001.png@01CE5244.3D2016D0] or by going to "Visualization" in the upper menu bar and starting a new track browser. http://wiki.galaxyproject.org/Learn#Visualization If you are interested, for certain datasets, the icon will also offer other options: Circster and/or Scatterplot. The tool group "Graph/Display Data" has graphing tools and tools that prepare data to be visualized. The tool group "Motif Tools" has a sequence logo generator, and the groups " NGS: QC and manipulation" and " BEDTools" have more graphing tools. Hopefully this helps, Jen Galaxy team On 5/13/13 11:08 AM, Sun, Wenping [USA] wrote: Dear galaxy group, I have question on the data visualization from output of galaxy pipeline. Is there any ideogram tool inside of galaxy? Regards, Kathryn ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev 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/ -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

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Can't delete empty folder via Tool Shed web interface
by Peter Cock 16 May '13

16 May '13

Hi all, Due to some hickups with tar balls, I've been left with an unwanted empty folder: http://testtoolshed.g2.bx.psu.edu/view/peterjc/venn_list/51fe47a5a803 Trying to delete the folder has no effect - "No changes to repository " - is this a minor bug, or deliberate? [image: Inline image 1] Thanks, Peter

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memdump
by Nikos Sidiropoulos 16 May '13

16 May '13

Hi everybody Has anybody used the "profile memory usage" feature, and if so, what are the benefits and the compromises of it? I'm trying to find documentation about it, without any luck. Thanks Nikos

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Testing with <repeat> parameters
by Peter Cock 16 May '13

16 May '13

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

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rpy2 Core Tools
by John Chilton 16 May '13

16 May '13

I had promised these to someone on a bitbucket issue years ago and I said I would send them to Dannon and Nate on IRC today, so I am just going to spam these out far and wide. These are the MSI versions of many of the core tools that have been rewritten to target rpy2 instead of rpy . Caveat emptor, these were never meant for external consumption. It looks like the ones we never got to include: rgenetics/rgQC.py, regVariation/rcve.py, ngs_simulation/ngs_simulation.py, metag_tools/short_reads_figure_high_quality_length.py, and taxonomy/poisson2test.py. -John

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History page not opening
by sridhar srinivasan 16 May '13

16 May '13

Hi after installing galaxy, i could'nt see the history page in right end of galaxy web. it shows """ Content Encoding Error The page you are trying to view cannot be shown because it uses an invalid or unsupported form of compression. * Please contact the website owners to inform them of this problem. """ Please help me to solve the issue.. sridhar

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