April 2010 - galaxy-user - lists.galaxyproject.org

Python error when running Bowtie for Illumina
by Weng Khong Lim 01 Feb '11

01 Feb '11

Hi all, I'm new to next-gen sequencing, so please be gentle. I've just received a pair of Illumina FASTQ files from the sequencing facility and intend to map them to the hg19 reference genome. I first used the FASTQ Groomer utility to convert the reads into Sanger reads. However, when running Bowtie for Illumina on the resulting dataset under default settings, I received the following error: An error occurred running this job: *Error aligning sequence. requested number of bytes is more than a Python string can hold* * * Can someone help point out my mistake? My history is accessible at http://main.g2.bx.psu.edu/u/wengkhong_lim/h/chip-seq-pilot-batch Appreciate the help! Weng Khong, LIM Department of Genetics University of Cambridge E-mail: wkl24(a)cam.ac.uk Tel: +447503225832

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The uploaded file contains inappropriate content
by Erick Antezana 04 Jun '10

04 Jun '10

Hi, It seems there is a (serious) bug while "Adding datasets" via the "Upload directory of files" (with or without copying the data into Galaxy (3545:2590120aed68), i.e. (un)tick the 'No' box) if the files are in ZIP format. Actually the files get erased from the filesystem. In the "information" column, I get: Job error (click name for more info) Then, after clicking on the file name: Information about 2010.fastq.zip Message: Uploaded by: erick(a)mydomain.com Date uploaded: 2010-03-23 Build: ? Miscellaneous information: The uploaded file contains inappropriate content error We have no problems with adding unzipped files... thanks, Erick

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Server Error
by Rathi Thiagarajan 10 May '10

10 May '10

Hi there, Just to notify that there is currently a Server Error. Thursday 10pm (EDT) Cheers, Rathi

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Load Balancing
by Erick Antezana 06 May '10

06 May '10

Hi, where can I find some more info/docs about 'load balancing' in Galaxy? it seems that the right place is: http://bitbucket.org/galaxy/galaxy-central/wiki/Config/LoadBalancing as indicated in the universe_wsgi.ini (enable_job_running). cheers, Erick

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MACS input format
by Steve Taylor 05 May '10

05 May '10

Hi, What format does MACS take as input within Galaxy? Thanks, Steve

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import local files
by Ryan Golhar 30 Apr '10

30 Apr '10

Hi - I recently discovered Galaxy and am just getting started with it... I installed a local instance to test with NGS data. We have a lot of NGS datasets (both Solid and illumina) on a SAN available via NFS. Each user that has data has an account on the system in a directory tree such as: /ngsdata/user1 /ngsdata/user2 /ngsdata/project1 /ngsdata/project2 where user1 and user2 are distinct users with their own dataset, and project1, project2 contain datasets shared by multiple users. I want to import this data in Galaxy and I came across this thread in the mailing list (quoted below). I set up my Galaxy instance to see this NFS share...btw Galaxy is running as its own user on a virtual machine. The Galaxy user only has read access to this read and nothing else. When I went to import the files by specifying a local system path on the admin user interface, I got errors importing the data. I checked the paster.log file and I saw errors related to galaxy trying to change the permissions of the files to 0644. Does this mean all the files need to be owned by Galaxy? ------------------- Old thread: Hello Andreas, The best approach to handle this is to have a Galaxy administrator upload the files into a library, creating library datasets. Set the following config setting to point to the NFS accessible directory you use to contain the files: # Directories of files contained in the following directory can be uploaded to a library from the Admin view library_import_dir = /var/opt/galaxy/import You can set ACCESS permissions on the library to restrict access to specific users, or leave it public to allow anyone to access the library datasets. Users can import the library datasets into their own histories for analysis - doing this does not create another disk file, but simply a "pointer" to the library dataset's disk file. Greg Von Kuster Galaxy Development Team Andreas Kuntzagk wrote: > Hi, > > to reduce traffic when importing big dataset into our local galaxy we > would like to copy directly from the fileserver (which is accessible > from the galaxy server via NFS) into galaxy without moving through the > users desktop computer. > Is there already such a tool by chance? At a glance I could only find > import.py which imports only from a predefined set of files. > So if no such tool exist what would be the best starting point? > upload.py? > For security reasons I would restrict the import to a certain directory. > Anything else to keep in mind? > > regards, Andreas > _______________________________________________ > galaxy-user mailing list > galaxy-user at bx.psu.edu > http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user > >

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orthologus regions
by research pal 30 Apr '10

30 Apr '10

From: research pal <workinformatics(a)yahoo.com> Hi, I have a bed file for the chimp genome and I want to download the same region for the human genome. Do you have a tool in Galaxy which can help me for these orthologus regions. warm regards, Amit.

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universe_wsgi.ini -- "true" case sensitivity?
by Erick Antezana 30 Apr '10

30 Apr '10

Hi, some options in the file 'universe_wsgi.ini' are written 'true' (e.g. *use_new_layout = true*) and others 'True' (e.g. *static_enabled = True*). I was wondering whether using any of them is fine? cheers, Erick

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apache_xsendfile = true
by Erick Antezana 30 Apr '10

30 Apr '10

Hi, is there a way to test that the option apache_xsendfile = true is doing its job? (a log file message or so)? thanks, Erick

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Error uploading large files
by Linda Barnum 30 Apr '10

30 Apr '10

Hello, I am using a local install of galaxy for processing Illumina data. However, for large (about 3 GB) files, it gives an error and while it appears as if the upload is progressing, nothing happens. File "/home/lin/public_html/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg/webob/__init__.py", line 818, in str_POST keep_blank_values=True) File "/usr/lib64/python2.6/cgi.py", line 508, in __init__ self.read_multi(environ, keep_blank_values, strict_parsing) File "/usr/lib64/python2.6/cgi.py", line 635, in read_multi headers = rfc822.Message(self.fp) File "/usr/lib64/python2.6/rfc822.py", line 108, in __init__ self.readheaders() File "/usr/lib64/python2.6/rfc822.py", line 155, in readheaders line = self.fp.readline() File "/usr/lib/python2.6/site-packages/paste/httpserver.py", line 476, in readline data = self.file.readline(max_read) File "/usr/lib64/python2.6/socket.py", line 379, in readline bline = buf.readline(size) OverflowError: signed integer is greater than maximum ---------------------------------------- 127.0.0.1 - - [13/Apr/2010:12:14:00 +0600] "GET /history HTTP/1.1" 200 - " http://localhost:8080/tool_runner/upload_async_message" "Mozilla/5.0 (X11; U; Linux x86_64; en-US) AppleWebKit/533.2 (KHTML, like Gecko) Chrome/5.0.342.7 Safari/533.2" What could be going wrong? Thanks. Lin

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