- galaxy-dev - lists.galaxyproject.org

About pileups
by Ciara Ledero 02 May '12

02 May '12

Hi all, I am implementing a script in Galaxy that runs samtools' pileup command. Although it is running, I always get an empty file. I'm curious: what is the datatype of the output of a pileup/mpileup command? I think I might be having a problem with the output since the output data type might be incorrect. Thanks in advance for the help! Cheers, CL

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Full path through API display.py
by Carlos Borroto 02 May '12

02 May '12

Hi, Recently "Full Path" display was added as an option. I was wondering if this information could also be available when accessing a dataset information through the API. Thanks, Carlos

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Can someone help me spec out a new computer for using Galaxy? Need to spend money this week!
by Stephen Turner 02 May '12

02 May '12

The tl;dr short story - I've come across about $5,000 I can use to build a machine, and this money has to be spent by Friday. I'd like some help spec'ing out a machine that can be used as a small-scale production Galaxy server for internal use by a handful of folks. Would anyone be willing to talk with me tomorrow morning, Thursday May 3, and tell me about your experience setting up a Galaxy installation on a scale like this? With about $5k to spend, what kind of hardware should I prioritize? I'd also like to get a sense of how much admin time is required to keep things running smoothly, updated, backed up, etc. I've had a difficult time getting ITS to help me get Galaxy running on the university's cluster. This will hopefully be a proof of principal that people here want this - hopefully I can get enough people here using this small-scale installation that the university ITS realizes the demand and has more motivation to get things working on the cluster. Many thanks, Stephen ----------------------------------------- Stephen D. Turner, Ph.D. Bioinformatics Core Director University of Virginia School of Medicine bioinformatics.virginia.edu

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Re: [galaxy-dev] Toolshed initial upload errors
by Paul-Michael Agapow 02 May '12

02 May '12

And the saga continues. For those who came in late - I've installed a local toolshed, which allows me to create repositories, but every time I attempt to upload files, it errors out with "TypeError: array item must be char". Working off the latest Galaxy bleeding edge copy has failed to fix this. Things I've looked at: - Initial os was CentOS (4?), Mercurial 2.1.2, Python 2.6.4, with sqlite. Also tried with Ubuntu 10.04, Python 2.7. - The Mercurial and Python I used was is local to the account I was working in, so maybe the toolshed was getting confused with another version. Nope - there's no hg on the system. Galaxy seems to be calling the right Python (libraries) - This happens with plain text and binary files. I haven't attempted to upload an archive yet - Figured there could still be something peculiar to my environment, so installed Galaxy on a fresh server I had elsewhere (the Ubuntu one listed above). Nope - exactly the same error. - As there are some reported issues of Windows file names with Unicode under Mercurial, and I'm uploading from a Windows machine, I used a Mac to create a repo and add a file. Nope, same behaviour. - Further investigations reveal that the files appear to be in the repo (database/community_files). The error occurs in the middle of Mercurial, in manifest.py where it attempts to coerce a Unicode string into a character array. The Cistrome galaxy fork (https://bitbucket.org/cistrome/cistrome-harvard/src/e7e2fdd74496/lib/galaxy…) mentions occasional similar errors. - Wondered if it was specific to my db setup. Used Postgres instead, same behaviour. - The only changes I make to community_wsgi.ini are setting the host and port, setting the database details, and setting the admin user Frankly, I'm fresh out of inspiration. There must be something I'm consistently doing (or not doing). Any suggestions - or wild-ass guesses - where to look next? ---- Paul Agapow (paul-michael.agapow(a)hpa.org.uk) Bioinformatics, Health Protection Agency ----------------------------------------- ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk **************************************************************************

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Toolshed - 502 Bad Gateway error
by graham etherington (TSL) 02 May '12

02 May '12

Hi, The Galaxy Toolshed is giving a 502 Bad Gateway error. Is there a problem with it at the moment? If so, is it just a matter of restarting it or is there a likelihood of it being down for a while? Cheers, 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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Debugging upload via nginx
by Peter van Heusden 02 May '12

02 May '12

Hi there I've got nginx 1.0.5 in front of my Galaxy instance, and I'm trying to get uploads to work as per 'Receiving files using nginx' instructions on the Galaxy wiki. I've added the relevant config to my nginx setup (pastebin http://paste.ubuntu.com/961983/) and universe_wsgi.ini (pastebin http://paste.ubuntu.com/961985/) but it isn't working. How do I debug this? What should I be looking for in the log files? What seems to be happening is that the files are being uploaded - entries are created in database/tmp/upload_store with the contents of the relevant files - but Galaxy is not being informed that the upload is complete. Thanks, Peter

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Re: [galaxy-dev] Interested in speaking with other, institutions deploying Galaxy locally?
by Sarah Maman 02 May '12

02 May '12

Hello, This is a great idea. I'm interested. Thanks ! Sarah Maman ---------------------------------------------------------------------- Message: 1 Date: Fri, 27 Apr 2012 13:45:16 -0500 From: Ann Black-Ziegelbein <annblack(a)eng.uiowa.edu> To: galaxy-dev(a)lists.bx.psu.edu Subject: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally? Message-ID: <4F9AE93C.20907(a)eng.uiowa.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein

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Unable to set BAM Metadata
by Ciara Ledero 01 May '12

01 May '12

This is my code for running a samtools command internally, via Galaxy: open INP,"< $ARGV[0]" or die "Cannot open file: $!"; $file = "$ARGV[1]"; open OUT, "> $file" or die "Cannot open file: $!"; @out = `/home/applications/samtools-0.1.7a/samtools view -bS $ARGV[0] 2>&1`; print OUT @out; close INP; close OUT; The 2>&1 is used to redirect the STDERR to STDOUT. When I run this in the console, it gives a non-empty file. But when run it in Galaxy, Galaxy can no longer find the path. This error message is given to me. Traceback (most recent call last): File "/home/applications/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 126, in run_job job_wrapper.finish( stdout, stderr ) File "/home/applications/galaxy-dist/lib/galaxy/jobs/__init__.py", line 618, in finish dataset.set_meta( overwrite = False ) File "/home/applications/galaxy-dist/lib/galaxy/model/__init__.py", line 874, in set_meta return self.datatype.set_meta( self, **kwd ) File "/home/applications/galaxy-dist/lib/galaxy/datatypes/binary.py", line 179, in set_meta raise Exception, "Error Setting BAM Metadata: %s" % stderr Exception: Error Setting BAM Metadata: /bin/sh: samtools: command not found The weird thing is, when I remove the 2>&1 from the code and run it again in Galaxy, I am able to get this diagnostic message: [samopen] SAM header is present: 66338 sequences. This is the reason why I added the 2>&1 in the first place, so that this diagnostic message would be 'ignored' (since it is detected as an error). Now, if the other code (the one without 2>&1) is able to produce the aforementioned diagnostic message, then I assume that it is able to at least execute the samtools command internally. But when I add the 2>&1, galaxy can no longer find the command. Do I need to specify a path somewhere in the galaxy-dist? I apologize for the very long message. Thanks in advance, CL

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server error from history view while setting [debug=False]
by JIE CHEN 01 May '12

01 May '12

Dear all, When I check a new copy of galaxy source code(may 1st) and set [debug=False] in the universe_wsgi.ini, the history panel of the web UI can not be displayed properly. It says "server error". I did some searchings and find a thread http://gmod.827538.n3.nabble.com/Server-error-from-history-view-td1009053.h…. According to the thread, i think it is a problem long time ago. I don't know why it happens again. Anyone can tell me how to resolve the problem? I also tried the latest repository of galaxy-central. No luck either. Shall i just leave [debug=True] until the bug has been fixed. Thanks, Tyler

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Server error again from history view when setting [debug=False]
by JIE CHEN 01 May '12

01 May '12

Dear all, When I check a new copy of galaxy source code(may 1st) and set [debug=False] in the universe_wsgi.ini, the history panel of the web UI can not be displayed properly. It says "server error". I did some searchings and find a thread http://gmod.827538.n3.nabble.com/Server-error-from-history-view-td1009053.h…. According to the thread, i think it is a problem long time ago. I don't know why it happens again. Anyone can tell me how to resolve the problem? I also tried the latest repository of galaxy-central. No luck either. Shall i just leave [debug=True] until the bug has been fixed. Thanks, Tyler

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