May 2013 - galaxy-user - lists.galaxyproject.org

problem with registration
by Patel, Bella 31 May '13

31 May '13

Hi I have tried to register for Galaxy but apparantly a user with my email address already exists! Very strange as I have never registered for this software. Can you advise? Bella Patel

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tophat to cuffdiff without cufflinks
by Colaneri, Alejandro Cesar 31 May '13

31 May '13

Hi I comparing gen expression data (RNA-seq) in Arabidopsis. Different genotypes, different conditions. Since Arabidopsis is very well annotated I decided to do cuffdiff directly after tophat. However when building my workflow I found that the cuffdiff said a gtf file is necessary. Please see the picture in this email, under INPUT FORMAT. My question is if I can still compare my libraries in the way I designed below. [cid:FEC3DE9D-5361-483A-BEDD-E7160270E291] Dr. Alejandro Colaneri Departments of Biology University of North Carolina at Chapel Hill 310 Coker Hall, CB# 3280 120 South Road Chapel Hill, NC 27599-3280 Tel: 919-962-2273 fax: 919- 962-1625

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Making Public a Data Library Gives Internal Server Error
by Rodolfo Aramayo 30 May '13

30 May '13

Hi, As Admin, I uploaded a set of files from filesystems paths Uploading is successful but when I try to make the datasets public I get the following error: Internal Server Error Galaxy was unable to sucessfully complete your request <==By The Way...NOTE how sucessfully is misspelled!! URL: http://galaxy.tamu.edu/library_common/make_library_item_public?library_id=8… File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 128 in __call__ return self.handle_request( environ, start_response ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 184 in handle_request body = method( trans, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/library_common.py', line 1626 in make_library_item_public self._check_access( trans, cntrller, is_admin, ldda.library_dataset, current_user_roles, use_panels, library_id, show_deleted ) AttributeError: 'NoneType' object has no attribute 'library_dataset' Help will be appreciated Thanks --R

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"View details" of Tophat alignment
by Du, Jianguang 30 May '13

30 May '13

Hi All, After I finshed Tophat alignment for RNA-seq, I took look at the details of parameters by clicking the icon "View details", and I got the information as shown below: Input Parameter Value Note for rerun RNA-Seq FASTQ file 73: Filtered Groomed data1_rep2 Use a built in reference genome or own from your history indexed Select a reference genome /galaxy/data/mm9/bowtie_index/mm9 Is this library mate-paired? single TopHat settings to use full Library Type FR Unstranded Anchor length (at least 3) None Maximum number of mismatches that can appear in the anchor region of spliced alignment None The minimum intron length None The maximum intron length None Allow indel search No Maximum number of alignments to be allowed None Minimum intron length that may be found during split-segment (default) search None Maximum intron length that may be found during split-segment (default) search None Number of mismatches allowed in the initial read mapping None Number of mismatches allowed in each segment alignment for reads mapped independently None Minimum length of read segments None Use Own Junctions Yes Use Gene Annotation Model Yes Gene Model Annotations 1: mm9 genes.gtf Use Raw Junctions No Only look for supplied junctions No Use Closure Search No Use Coverage Search Yes Minimum intron length that may be found during coverage search None Maximum intron length that may be found during coverage search None Use Microexon Search No I am totally confused by so many "None"s. Then I checked the workflow I set and used for the TopHat alignment, the details are the same as above. However, the brief description just under the title of alignment output (. accepted hits) is as below: format: bam, database: mm9 Tophat for Illumina on data 1 and data 73: accepted_hits, TopHat v1.4.0 tophat -p 8 -a 8 -m 0 -i 70 -I 500000 -g 20 -G /galaxy/main_pool/pool1/files/004/425/dataset_4425972.dat --library-type fr-unstranded --no-novel-indels --coverage-search --min-cove Could you please tell me is there anything wrong (because so many "None" in the detail parameters)? Thanks. Jianguang DU

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sharing files and histories between different galaxy servers
by Colaneri, Alejandro Cesar 30 May '13

30 May '13

Hi, I have 40 fastq RNA-seq libraries uploaded in the galaxy mirror at UNC, however the tophat and cufflinks version in that server has not been updated for a while and I will like to use the main server at PSU. Do I have to upload the 40 files one by one again in the main galaxy or there any less painful way to share files and histories between different Galaxies? In addition, today I have been all day trying to connect with the main galaxy server (https://main.g2.bx.psu.edu/) and either do not responde or if the site is loaded then every time I try to submit a task it stop to respond Thank you Alejandro Dr. Alejandro Colaneri Departments of Biology University of North Carolina at Chapel Hill 310 Coker Hall, CB# 3280 120 South Road Chapel Hill, NC 27599-3280 Tel: 919-962-2273 fax: 919- 962-1625

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May 29th 2013 FTP login resolution
by Jennifer Jackson 29 May '13

29 May '13

Dear Galaxy Main Community, We apologize for recent FTP login issues, but are glad to report that a solution is now in place. *May 29th 2013 FTP login resolution* * *Issue*: FTP login failed for user accounts newly created or that had passwords updated during the time frame May 20th - May 29th. * *Solution*: Change your Galaxy password using the form on the Main <http://wiki.galaxyproject.org/Main> instance at http://usegalaxy.org o User -> Preferences -> Manage your information o On the "Manage User Information" form, change your password o Wait ~20 minutes for the server to update, then use FTP with the new credentials * *How to use FTP Upload <http://wiki.galaxyproject.org/FTPUpload>* * /Share notice/: http://bit.ly/ftpmay29 Thanks for using Galaxy, The Galaxy Team <http://wiki.galaxyproject.org/GalaxyTeam>

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concatenating files in galaxy
by Colaneri, Alejandro Cesar 29 May '13

29 May '13

Which is the right way to concatenate two files in galaxy? It is option 1 or 2? Or it is the same? Some times I can not do option 2, even in the same workflow, and I can not find why. Then, in the same work flow I have same files concatenated according to option one, and anthers according to option 2 and I do not know if it is a mistake. [cid:4EF49F9C-D91B-4009-BC9E-7474DDF9C995] Dr. Alejandro Colaneri Departments of Biology University of North Carolina at Chapel Hill 310 Coker Hall, CB# 3280 120 South Road Chapel Hill, NC 27599-3280 Tel: 919-962-2273 fax: 919- 962-1625

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Question on megablast databases
by Sun, Wenping [USA] 24 May '13

24 May '13

Dear galaxy members, I have a question on the databases used in megablast module from galaxy. There are four db options to blast against with - 1. htgs 28-Jan-2013 2. nt 28-Jan-2013 3. wgs 28-Jan-2013 4. phiX174 Is there any further information to guide which database would be appropriate to use? In addition, how to find the genome information contained in each database? Many thanks, Kathryn

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obsolete cuffdiff version in main.g2.bx.psu.edu
by Nikolay N. 24 May '13

24 May '13

Hi, I noticed that the version of cuffdiff used in main.g2.bx.psu.edu is really obsolete (0.0.5) whereas the most recent version is 2.1.1. Is there a chance that a more up-to-date version will be ever installed on the main galaxy instance? many thanks, Nikolay

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BWA errors
by Seattle Oneeechan 24 May '13

24 May '13

Hi, Two related issues: We tried to run BWA for Illumina on two groomed files (fastqsanger) and got the following error message. * * *24: Map with BWA for Illumina on data 6 and data 5: mapped reads* error An error occurred with this dataset: *BWA Version: 0.5.9-r16 The alignment failed. Error aligning sequence. [bwa_aln] 17bp reads: max_diff = 2 [bwa_aln] 38bp reads: max_diff = 3 [bwa_aln] 64bp reads: max_diff = 4 [bwa_aln] 93bp reads: max_diff = 5 [bwa_aln] 124bp reads: max_diff = 6 [bwa_aln]* We have done this many times before on the public server. However, this is a new local instance and we just uploaded the files for “hg19 indexed for bwa” (from the TopHat website) which put it into the pull down menu. Along those same lines. I thought that a .fa file put into history, could be used and would be indexed automatically in bowtie and bwa (maybe tophat as well, haven’t used that one yet). With bowtie, having the WholeGenomeFasta file from the UCSC seems to work, but not with bwa. Does anybody know if it should work with bwa as well? Any help is much appreciated. Thank you,

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