September 2012 - galaxy-user - lists.galaxyproject.org

Help with Summary Statistics
by D. A. Cowart 23 May '14

23 May '14

Hello, I am attempting to use Galaxy to calculate the mean sequence read length and identify the range of read lengths for my 454 data. The data has already been organized and sorted by species. The format of the data is as follows: >HD4AU5D01BHBCQCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC >HD4AU5D01A093MCTCTGTCGCTCTGTCTCTCTTCTCTCTCTCTCTCTCT etc...for each species I have attempted to use the "Summary Statistics" button, however it appears to only be for numerical data and not sequence data. Is this tool/task available via Galaxy? Thank you, Dominique Cowart User name: dac330

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from Galaxy to Megan
by Judith van Bleijswijk 10 Oct '12

10 Oct '12

Dear Galaxy users that also use Megan, I hope you can help me combining Galaxy with Megan4. I followed the Galaxy metagenome workflow (author aun1) on shotgun DNA 454 sequences of two samples that I would like to compare. The results are two nice trees and tables with the lowest taxonomic ranks for the two samples. Besides the taxonomy I am also interested in the functions and I would like to use Megan4 (with SEED and KEGG classification) for this purpose. I tried to import a Galaxy file (.tabular) with c1 =high quality segment name and c2-c13 =blasthit results and a Galaxy fasta file with the high quality segment names and sequences. This does not work and I receive the message parsing failed, no reads found. I am interested to know how you solved this issue and which files in the Galaxy metagenome workflow you use to import into Megan4. Or maybe there is other software that you use to compare suits of functional genes in your metagenome datasets? Regards, Judith van Bleijswijk

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Why doesn't bowtie in galaxy accepting colorspace reads directly?
by Praveen Raj Somarajan 10 Oct '12

10 Oct '12

Hi All, I'm wondering why the Bowtie version in (even latest) Galaxy does NOT support .csfasta/.qual input files directly, though it is mentioned under "Map with Bowtie for SOLiD". This is the case of "BWA for SOLiD" as well. One would expect direct support on colorspace files. Do you have any plans of implementing this?I see this would be a great support to SOLiD users. Look forward to your comments Thanks, Raj ________________________________ This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment. The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system. OCIMUMBIO SOLUTIONS (P) LTD

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GeneTrack server error
by Doo Yang 04 Oct '12

04 Oct '12

Hi, I can't connect the GeneTrack server. This is the error message. I tried this a couple times in different days but keeps failing. Firefox can't establish a connection to the server at genetrack.g2.bx.psu.edu. Thank you,

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FTP Upload Error
by Amanda Jones 01 Oct '12

01 Oct '12

I'm having trouble uploading via FTP to my Galaxy account. I've been receiving the following error message: 503 Sorry, the maximum number of clients(3) for this user are already connected. I've ensured that I'm only using a single connection to upload. Any clue what's going on? I still have available space in my Galaxy account for the upload and I've previously uploaded similarly sized files with no problems.

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igenome error
by Paul Brady 01 Oct '12

01 Oct '12

I try to download the human hg19 from igenomes in galaxy. I use 'shared data' > 'data libraries' > 'igenomes' > select hg19, but this persistently downloads the mm9 mouse genome not the human genome. Any suggestions? Paul Brady Afdeling CME-UZ, O&N I Herestraat 49 - bus 602, 3000 Leuven, Belgium. Tel: +32 16 345902 e-mail: Paul.Brady(a)med.kuleuven.be

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Errors during database migration after updating galaxy
by Joel Rosenberg 01 Oct '12

01 Oct '12

My cloud galaxy cluster can't boot up after attempting a bitbucket update due to a 502 HTTP error when trying to update the DB. Here's the log: /mnt/galaxyTools/galaxy-central/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1: RuntimeWarning: __builtin__.file size changed, may indicate binary incompatibility from csamtools import * python path is: /mnt/galaxyTools/galaxy-central/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/boto-2.5.2-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/Fabric-1.4.2-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/ssh-1.7.14-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Whoosh-0.3.18-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/amqplib-0.6.1-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/pexpect-2.4-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Babel-0.9.4-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/Mako-0.4.1-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/WebHelpers-0.2-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/wchartype-0.1-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/docutils-0.7-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/WebOb-0.8.5-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Routes-1.12.3-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Paste-1.6-py2.6.egg, /mnt/galaxyTools/galaxy-central/lib, /usr/lib/python2.6/, /usr/lib/python2.6/plat-linux2, /usr/lib/python2.6/lib-tk, /usr/lib/python2.6/lib-old, /usr/lib/python2.6/lib-dynload galaxy.tool_shed.tool_shed_registry DEBUG 2012-09-30 21:13:18,317 Loading references to tool sheds from tool_sheds_conf.xml galaxy.tool_shed.tool_shed_registry DEBUG 2012-09-30 21:13:18,317 Loaded reference to tool shed: Galaxy main tool shed galaxy.tool_shed.tool_shed_registry DEBUG 2012-09-30 21:13:18,318 Loaded reference to tool shed: Galaxy test tool shed galaxy.model.migrate.check DEBUG 2012-09-30 21:13:18,344 psycopg2 egg successfully loaded for postgres dialect galaxy.model.migrate.check INFO 2012-09-30 21:13:18,610 At database version 107 galaxy.tool_shed.migrate.check DEBUG 2012-09-30 21:13:18,620 psycopg2 egg successfully loaded for postgres dialect Traceback (most recent call last): File "/mnt/galaxyTools/galaxy-central/lib/galaxy/webapps/galaxy/buildapp.py", line 36, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/app.py", line 47, in __init__ verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tool_shed/migrate/check.py", line 54, in verify_tools missing_tool_configs_dict = check_for_missing_tools( app, tool_panel_configs, latest_tool_migration_script_number ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tool_shed/migrate/common.py", line 33, in check_for_missing_tools response = urllib2.urlopen( url ) File "/usr/lib/python2.6/urllib2.py", line 126, in urlopen return _opener.open(url, data, timeout) File "/usr/lib/python2.6/urllib2.py", line 397, in open response = meth(req, response) File "/usr/lib/python2.6/urllib2.py", line 510, in http_response 'http', request, response, code, msg, hdrs) File "/usr/lib/python2.6/urllib2.py", line 435, in error return self._call_chain(*args) File "/usr/lib/python2.6/urllib2.py", line 369, in _call_chain result = func(*args) File "/usr/lib/python2.6/urllib2.py", line 518, in http_error_default raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) HTTPError: HTTP Error 502: Bad Gateway Removing PID file paster.pid

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server down?
by DEDRICK＠pitt.edu 28 Sep '12

28 Sep '12

I am using Galaxy main and my jobs aren't running. They are still grey colored, indicating that they haven't started. I used Galaxy main yesterday just fine. Is something wrong with the server? I tried re-running the jobs, still no progress. -- Rebekah Dedrick, Ph.D. University of Pittsburgh Hatfull Laboratory 376 Crawford Hall 4249 Fifth Avenue Pittsburgh, PA 15260

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Training
by Ryan Peters 28 Sep '12

28 Sep '12

To whom it may concern, Can you tell me about how I can schedule a training for Galaxy and any Galaxy trainings that are coming up in the East Coast which I can attend. I would be willing to travel. Thanks

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FreeBayes repeated error
by Dalgard, Clifton 27 Sep '12

27 Sep '12

Dear Team and Galaxy Users, I have been running FreeBayes on BAM output generated from pooled sequencing of 30 haploid yeast genomes with a total of 90 million reads. I am observing an inconsistent but repeated error using FreeBayes which states: An error occurred running this job:*terminate called after throwing an instance of 'std::out_of_range' what(): vector<bool>::_M_range_check Aborted* * * Interestingly, I can view partial output of the tool run and after running the tool repeated with the same data and parameters, I have noticed that the partial output has different lengths (and thus suggests it is not data dependent). Is there any insight to why FreeBayes won't complete? Thank you, Clifton

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