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cloud instance of galaxy
by Randall, Thomas (NIH/NIEHS) [C] 24 May '12

24 May '12

I have put up an instance of galaxy on the cloud and as a simple test am trying to retrieve hg19 sequences corresponding to a bed file using the Extract Genomic DNA tool. hg19 is supposed to be a "loaded, system installed build" yet I get an error message stating that "No sequences are available for hg19". A similar thing occurred with an mm9 request. What is being done wrong? Tom Thomas Randall, PhD Bioinformatics Scientist, Contractor Integrative Bioinformatics National Institute of Environmental Health Sciences P.O. Box 12233, Research Triangle Park, NC 27709 randallta2(a)niehs.nih.gov<mailto:randallta2@niehs.nih.gov> 919-541-2271

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Problem using Galaxy
by Seyed Mehdi Jazayeri 23 May '12

23 May '12

Dear Sir/Madam, I am a PhD student working on RNA-Seq as my dissertation. As a matter of fact I want to do analyses of gene expressions for the sequences that I have and for that I have tried to use Galaxy tools as it is one of the best platforms in order to do analysis for RNA-Seq as well as others. I did all about installation of Galaxy on my Mac OS 10.7 Lion but when I run the commands I do not get any result from running any type of commands. And when I do *run.sh *I will have nothing done. As a sample I send you the command I ran on my system as follow * * *iMac-de-Biologia:galaxy-dist LabBioMol$ ./run.sh* *Traceback (most recent call last):* * File "./scripts/paster.py", line 34, in <module>* * command.run()* * File "/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 84, in run* * invoke(command, command_name, options, args[1:])* * File "/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 123, in invoke* * exit_code = runner.run(args)* * File "/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 218, in run* * result = self.command()* * File "/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py", line 276, in command* * relative_to=base, global_conf=vars)* * File "/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py", line 313, in loadapp* * **kw)* * File "/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 204, in loadapp* * return loadobj(APP, uri, name=name, **kw)* * File "/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 224, in loadobj* * global_conf=global_conf)* * File "/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 248, in loadcontext* * global_conf=global_conf)* * File "/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 278, in _loadconfig* * return loader.get_context(object_type, name, global_conf)* * File "/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 413, in get_context* * section)* * File "/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 458, in _context_from_explicit* * value = import_string(found_expr)* * File "/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 18, in import_string* * return pkg_resources.EntryPoint.parse("x="+s).load(False)* * File "/Users/LabBioMol/galaxy-python/galaxy-dist/lib/pkg_resources.py", line 1954, in load* * entry = __import__(self.module_name, globals(),globals(), ['__name__']) * * File "/Users/LabBioMol/galaxy-python/galaxy-dist/lib/galaxy/web/__init__.py", line 5, in <module>* * from framework import expose, json, json_pretty, require_login, require_admin, url_for, error, form, FormBuilder, expose_api* * File "/Users/LabBioMol/galaxy-python/galaxy-dist/lib/galaxy/web/framework/__init__.py", line 31, in <module>* * from babel.support import Translations* * File "/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/Babel-0.9.4-py2.7.egg/babel/support.py", line 29, in <module>* * from babel.dates import format_date, format_datetime, format_time, LC_TIME* * File "/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/Babel-0.9.4-py2.7.egg/babel/dates.py", line 34, in <module>* * LC_TIME = default_locale('LC_TIME')* * File "/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/Babel-0.9.4-py2.7.egg/babel/core.py", line 642, in default_locale* * return '_'.join(filter(None, parse_locale(locale)))* * File "/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/Babel-0.9.4-py2.7.egg/babel/core.py", line 763, in parse_locale* * raise ValueError('expected only letters, got %r' % lang)* *ValueError: expected only letters, got 'utf-8'* *iMac-de-Biologia:galaxy-dist LabBioMol$ * Now I would appreciate if you could advise me what is the problem and how to solve it. Thanks for your attention in advance. Best regards SMJ -- SMJ Seyed Mehdi Jazayeri

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Maq consensus calling changes quality score of the read?
by Antony Jose 22 May '12

22 May '12

Hi, We used the generate pileup tool with consensus base calling option using Maq with default options. In the output, the quality scores of the bases were changed. For example if the input score of bases in the SAM file were 'IIJIH'. They were changed to '22321'. Is this a glitch or is this expected? Thank you. Antony

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Mapping paired end reads with Tophat
by 杨继文 22 May '12

22 May '12

Hi all, After mapping, I used IGV to have a look at the mapping. There are a lot of mapped reads without pair reads. Should I keep these reads? or Is this a problem for cufflinks analysis? What I tried is: 1. BAM to SAM 2. Filter SAM: set Read mapped in a proper pair to Yes. The result is that only 1/5 reads were left. Can anybody tell me if this operation is proper?? How do you normally optimize the mapping rerults from Tophat? Which considerations should I take into account? Looking forward to your reply. Jiwen

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(no subject)
by Estorninho, Megan 22 May '12

22 May '12

I have been unable to upload data files into Galaxy Main since Friday 18th May 2012. Today is my fourth day of attempting uploads. Refreshing and leaving the files to upload overnight does not work. Although Jennifer has stated the bug has been fixed at 5.30pm today I am still unable to upload data files. I thought I may be exceeding maximum file capacity but I am well below at only 1.8Gb.

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Examples of quality score boxplots for 5500xl data
by Faber, Pieter [BSD] - SRF 21 May '12

21 May '12

Dear All, I am planning to use GALAXY to draw quality score boxplots for 5500xl data and am interested in seeing examples of such boxplots from other users for good / intermediate / bad sequencing runs. Can anybody share? Thanks, Pieter W. Faber, PhD University of Chicago Genomics Core. Knapp Center for Biomedical Discovery (KCBD) 900 E. 57th Street, Room # 1230B Chicago, IL 60637 Phone: (773) 834-8420 Website: http://fgf.uchicago.edu/ This email is intended only for the use of the individual or entity to which it is addressed and may contain information that is privileged and confidential. If the reader of this email message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication is prohibited. If you have received this email in error, please notify the sender and destroy/delete all copies of the transmittal. Thank you.

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server problem
by Elaine Wong 21 May '12

21 May '12

Dear Galaxy-support, I could not use Galaxy nearly for 2 days, I think there is a problem with the server. If I 'intersect' data sets then it just turned to 'job is wating to run' and never moved on. I have already informed other people working in another city, and they also have the same server problem. I live in the Netherlands (I don't know if you need this info). Could you please give me some information about this problem and how long it will take? Thank you in advance. Kind regards, Elaine Wong

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"Job is waiting to run" forever
by Lee Silver 21 May '12

21 May '12

For the last two days, nearly every job submitted to Galaxy at "main.g2.bx.psu.eud" has been successfully added to the queue but stuck in the waiting to run mode. A few exceptions have gotten through quickly, but if not, they stay in limbo land. Emptying the cache made no difference. Any advice?

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long wait on jobs
by Antony Jose 21 May '12

21 May '12

Hi, I started a workflow yesterday (user name: antonymerlinjose(a)gmail.com) and it still hasn't gone past being queued to run. In fact, no jobs are running. Please advice. Thank you. Antony -- Antony M Jose, Dept. of Cell Biology & Molecular Genetics, University of Maryland, Rm 2116, Bioscience Research Building, College Park, MD - 20742.

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cuffmerge loses p_id
by Christopher M. Weber 21 May '12

21 May '12

Hello, Problem: Cuffmerge loses p_id from reference genome in merged gtf file on Galaxy online server resulting in blank cds cuffdiff files. DATA Input to Cuffmerge or Cuffcompare: Two fly cufflinks transcript assemblies created from bam files in Galaxy server using reference annotation and bias correction. Options: Use Reference Annotation: YES UCSC DM3 genes gtf (D. melanogaster) or ENSMBL 5.25 genes gtf Use Sequence Data: YES Result: tss_id found in cuffmerge but no p_id with either reference annotation file. Examples included below. Reference: 2L protein_coding stop_codon 8608 8610 . + 0 exon_number "2"; gene_id "FBgn0031208"; gene_name "CG11023"; p_id "P13746"; transcript_id "FBtr0300689"; transcript_name "CG11023-RB"; tss_id "TSS8369"; Cuffmerge: Cufflinks exon 8193 9484 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "2"; gene_name "CG11023"; oId "FBtr0300689"; nearest_ref "FBtr0300689"; class_code "="; tss_id "TSS1"; 2L Cufflinks exon 66721 67003 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "1"; gene_name "dbr"; oId "CUFF.1.1"; nearest_ref "FBtr0078100"; class_code "j"; tss_id "TSS2"; Help is much appreciated, Thanks!

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