November 2009 - galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] [galaxy-bugs] /tmp directory
by juan perin 05 Feb '10

05 Feb '10

Thanks for the answer! I've copied this response to the dev list email instead, after realizing its probably best there. I'm also having some trouble getting our PBS system configured. I have pbs://hostname/ as my pbs parameter in the universe file, as well as everything else specified in the documentation. I'm getting no error in the interface, and the backend never actually gets the job. The error I see in the logs says: galaxy.jobs.runners.pbs ERROR 2009-10-30 13:40:27,762 Uncaught exception queueing job Traceback (most recent call last): File "/home/perin/galaxy-dist/lib/galaxy/jobs/runners/pbs.py", line 144, in run_next self.queue_job( obj ) File "/home/perin/galaxy-dist/lib/galaxy/jobs/runners/pbs.py", line 219, in queue_job script = pbs_symlink_template % (job_wrapper.galaxy_lib_dir, " ".join(job_wrapper.get_input_fnames() + output_fnames), self.app.config.pbs_stage_path, exec_dir, command_line) TypeError: sequence item 1: expected string, DatasetPath found I'm guessing this has something to do with my config parameters, and the queue its trying to submit to. the pbs://hostname/ value was used under the assumption that it would default to the 'default' queue on our cluster, so I'm wondering if I need to hard code those values into the connection string? I'm a little confused as to how the syntax translates to the actual required string. My guess is, for our values: pbs://variome.chop.edu/default Perhaps its related to the scrambling of the egg instead? I simply passed LIBTORQUE_DIR to the directory containing my libtorqure.so etc... ? Thanks in advance. Juan Perin On Fri, Oct 30, 2009 at 12:07 PM, Nate Coraor <nate(a)bx.psu.edu> wrote: > Juan Perin wrote: > > I'm hosting galaxy locally and am trying to figure out how to change the >> temporary upload location of files from the root / /tmp folder to something >> else. My /tmp partition is too small to handle large fastq files and this >> is causing me problems. I see where to change things in the universe file, >> but that's the final location, not the temporary space. >> > > Hi Juan, > > A quick solution is to set $TEMP in your shell environment. In the future, > we'll force uploads to honor new_file_path in universe_wsgi.ini. > > --nate >

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Slow Galaxy
by Dijk, F van 03 Dec '09

03 Dec '09

Hi, Today I downloaded the new Galaxy version which supports python 2.6. I installed it and it works fine so far. But I'm experiencing some problems with the speed of Galaxy compared to the version I was using before. I perform alignments with Bowtie and for some reason it takes a lot of time to go further with my workflows. I thought maybe it was due to Bowtie using only 4 threads, so I changed the --threads option in bowtie_wrapper.xml to 16 and performed the alignment again. When I take a look at my processes I see Bowtie using 16 cores, but afterwards it changes back to only using 4 cores while Galaxy (graphic webbrowser view) still indicates it is busy with the alignment. This takes more than 30 minutes, which it doesn't take with the older version. Do you know how this is possible? Are there more settings which should/could be changed to speed Galaxy up? I hope to hear from you soon. Sincerely, Freerk van Dijk De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.

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R not working on Snow Leopard
by Dean Snyder 03 Dec '09

03 Dec '09

The R modules (Rg Data, etc.) are not working on my local Galaxy install in Mac OS X Snow Leopard (their UI's don't even appear when clicking on the tool link): Mac OS X = 10.6.2 Galaxy = galaxy-82b63d47a0d8 R = 2.10.0 Python = 2.6 I believe the problem is with Rpy (I cannot get it to build, or install to a working state). Anybody running Galaxy with its R tools under Snow Leopard? Dean A. Snyder Senior Programmer/Analyst Center for Inherited Disease Research (CIDR) Johns Hopkins School of Medicine Bayview Research Campus 333 Cassell Dr, Triad Bldg, Suite 2000 Baltimore, MD 21224 www.cidr.jhmi.edu cell:717 668-3048 office:410-550-4629

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no reference genome listed for NGS bowtie or bwa
by Dean Snyder 01 Dec '09

01 Dec '09

The "Select a reference genome" popup in the NGS mapping section is empty for the Bowtie and BWA tools on my local Galaxy install (latest release). How can I populate it? Dean A. Snyder Senior Programmer/Analyst Center for Inherited Disease Research (CIDR) Johns Hopkins School of Medicine Bayview Research Campus 333 Cassell Dr, Triad Bldg, Suite 2000 Baltimore, MD 21224 www.cidr.jhmi.edu cell:717 668-3048 office:410-550-4629

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Some NGS tools not available on local Galaxy install
by Dean Snyder 30 Nov '09

30 Nov '09

Some of the NGS tools like fastx_quality_stats and fastq_quality_boxplot_graph.sh are not available on my local Galaxy install, while others, like the fastq groomer, are. An example error message is: "An error occurred running this job: /bin/sh: fastx_quality_stats: command not found" Two questions: 1) Why are these tools not available with the standard install while being listed in the tools list? 2) How do I go about installing them? Thanks, Dean A. Snyder Senior Programmer/Analyst Center for Inherited Disease Research (CIDR) Johns Hopkins School of Medicine Bayview Research Campus 333 Cassell Dr, Triad Bldg, Suite 2000 Baltimore, MD 21224 www.cidr.jhmi.edu cell:717 668-3048 office:410-550-4629

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Saving large files
by Dijk, F van 29 Nov '09

29 Nov '09

Hi, I use Galaxy to do Next-gen sequencing analysis. I do the alignment and such and after the alignment performed by Bowtie I want to save the files to my own harddisk, using the save option. The problem is I can't download large files (probably due to http which can't transfer files larger than 2 gb I think). Is there a way to work around this problem? I tried using the gzip options, but those options crashed Galaxy. I hope to hear from you soon. Sincerely, Freerk van Dijk De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.

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Re: [galaxy-dev] Request for showing output plots in galaxy frame
by James Taylor 26 Nov '09

26 Nov '09

PNG and JPG should already work fine as well. The only thing that may require some tweaking is to allow a choice between two output formats, but you can certainly do that using a post job hook to change what Galaxy thinks the datatype is. On Nov 26, 2009, at 11:26 AM, matthew.iyer(a)gmail.com wrote: > Would the system be able to handle PNG or JPG images too? I want to > integrate a plotting script using matplotlib and can easily follow > the examples that already exist. If I can add an option for the > user to select png or pdf output that would be ideal. > > That way the user can use PNG for just viewing the data without any > browser issues and PDF for downloading.

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Removing/Hiding shared workflows/histories
by Assaf Gordon 25 Nov '09

25 Nov '09

Hello, I've finally pulled the latest changes - kudos for the history search feature - I like it a lot. Now, as usual, some usability questions: 1. How do I remove or hide or delete workflows and histories other people shared with me ? Sounds like a silly question, but it's an aspect in *my* galaxy account over which I have absolutely no control. I found no way to remove a shared workflow except asking the person who shared it with me to stop sharing it. If somebody wanted to play a trick on me, he could share hundreds of histories with me and I'll have no control over it - making it hard for me to find the actual shared histories I'm looking for (this is of course an absurd scenario, but I'm trying to make a point). The real-world scenario is that I'm the go-to guy for galaxy in our little lab, and everybody who has a problem in his history or workflow shares it with me and ask me to take a look at it. After I'm done fixing it - I don't want to see it any more. Asking to user to "unshare" the history is technically OK, but I don't think that's the way it should work. If I don't want to see a history/workflow in my galaxy account, I should be able to do it myself, without asking it from other users. 2. consistency in the workflow management screen "Workflows shared by others" appear as a link (underlined) - clicking on the does the default (and expected) action of "run workflow". "Your workflows" (mine, that is) - are not links, although they do get a rounded-box-frame when hovered upon - clicking on them does nothing. One has to pin-point the tiny triangle to run/edit/etc on my workflow. If one clicks on "Workflows"->"All Workflows" from the tools menu, then all workflows appear as clickable-links. So it's only a tiny matter of consistency. Thanks, -gordon.

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Request for showing output plots in galaxy frame
by Matthew Iyer 25 Nov '09

25 Nov '09

Dear Galaxy team, My name is Matthew Iyer and I am a Bioinformatics PhD student at the University of Michigan. I am doing my thesis in Arul Chinnaiyan's cancer research lab and generally work with NGS data. I am interested in incorporating galaxy for displaying customized bar/scatter plots showing gene expression levels for many samples. I have downloaded and am successfully using a galaxy locally and I really love it. However, all of the graph display/plotting tools create images (PDF) for download. Of course, the option to download the images is important, but is it also possible to display these images in the main window? This feature would make a crucial difference for me and would create many users of galaxy in our lab. I am a python programmer myself and would be interested in contributing to this effort rather than developing this in a separate framework. I am sure that it is a simple modification to show an image in the main window. I look forward to working with you and using galaxy! Best, Matthew

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Writing functional test for galaxy tools
by Vipin Thankam Sreedharan 25 Nov '09

25 Nov '09

Dear Galaxy development team, I am working with Gunnar Raetsch's group in Tuebingen and now I am writing functional test for mGene modules in our galaxy instance. Here my tools will automatically create an output directory and write all output files into that. The tool will keep most of its output files behind the galaxy screen. User will be able to see a summary file for his/her experiment. So my question is simple. Whether do you have any system to perform a functional test for such kind of situations? I would like to hear from you. Many thanks, Vipin T S

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