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Error running cufflinks on Galaxy
by David Robinson 06 Jul '11

06 Jul '11

Hello, When I attempt to run cufflinks based on .sam output from bowtie I get an error: An error occurred running this job: *cufflinks v1.0.1 cufflinks -q --no-update-check -I 300000 -F 0.050000 -j 0.050000 -p 8 -b /galaxy/data/hg19/sam_index/hg19.fa Error running cufflinks. [Errno 2] No such file or directory: 'transcripts.gtf' *What can I do to get around this problem and run cufflinks? My workflow is on http://main.g2.bx.psu.edu and can be found here (I ran it using a .fastq file): http://main.g2.bx.psu.edu/u/dgrtwo/w/cufflinks-workflow-imported-from-uploa… Thanks in advance for your help! -David ************************************************ David Robinson Graduate Student Lewis-Sigler Institute for Integrative Genomics Carl Icahn Laboratory Princeton University 646-620-6630 ************************************************

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random intervals from mouse genome
by Jèrôme Buard 06 Jul '11

06 Jul '11

Hi, I would like to generate a random intervals file by mimicking a bed file of interest from the mouse genome. Does someone know how to do that? NB: the "random intervals" tool from "Encode tools" does this but only for human genome. Thanks Jerome

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double login / deleting users
by Joseph Hargitai 05 Jul '11

05 Jul '11

Hi, 1, referencing old thread: http://gmod.827538.n3.nabble.com/Deleting-accounts-td867222.html is the delete functionality still status-quo? i.e - there is no delete other than the workaround? 2, switched from SQLlite to postgres and have this strange double login issue. Included image - need to login twice and logout twice. Double tab - joe

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Several errors from run.sh
by charlie 05 Jul '11

05 Jul '11

Hi all, I am upgrading to the most recent galaxy-dist 720455407d1c<https://bitbucket.org/galaxy/galaxy-dist/changeset/720455407d1c> . First time run.sh shows following errors as in attachment. It seems when I use 'manage_db.sh upgrade' it doesn't create necessary tables for these tools. Wonder if these are known issues? Thanks

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Fwd: uploading error
by Gordon, Assaf 05 Jul '11

05 Jul '11

Hello Rubina, I'm not familiar with Windows 7, so I'm forwarding your email to the galaxy public mailing list, where the Galaxy team can further help you with your fastq conversion. -gordon Begin forwarded message: From: <rdalvi01(a)students.poly.edu<mailto:rdalvi01@students.poly.edu>> Date: July 4, 2011 19:43:31 EDT To: <gordon(a)cshl.edu<mailto:gordon@cshl.edu>> Subject: RE: uploading error Hi Gordon, I followed the instructions you mentioned. I was able to upload the fastq file on the website. However I am getting error while converting the fastq file to fasta format. I use windows 7. Thank You. Rubina > Date: Mon, 20 Jun 2011 14:18:31 -0400 > From: <mailto:gordon@cshl.edu> gordon(a)cshl.edu<mailto:gordon@cshl.edu> > To: galaxy-user(a)bx.psu.edu<mailto:galaxy-user@bx.psu.edu>; <mailto:rdalvi01@students.poly.edu> rdalvi01(a)students.poly.edu<mailto:rdalvi01@students.poly.edu> > Subject: Fwd: uploading error > > Hello Rubina, > > I've forwarding your email to the galaxy public mailing list, where the Galaxy team can further help you with your upload. > > Generally speaking, uploading big FASTQ using the web interface is prone to errors. > The Galaxy team added a new upload method, using FTP, which is more reliable. > > Detailed instructions are available here: > <https://bitbucket.org/galaxy/galaxy-central/wiki/UploadViaFTP> https://bitbucket.org/galaxy/galaxy-central/wiki/UploadViaFTP > > Regards, > -gordon > > -------- Original Message -------- > Subject: uploading error > Date: Mon, 20 Jun 2011 18:10:57 +0000 > From: <rdalvi01(a)students.poly.edu<mailto:rdalvi01@students.poly.edu>> > To: <gordon(a)cshl.edu<mailto:gordon@cshl.edu>> > > > > Hi, > My name is Rubina. I am using Galaxy to convert fastq files to fasta format. > I tried to upload fastq file on the following link. > <http://main.g2.bx.psu.edu/> http://main.g2.bx.psu.edu/ > > However I am not able to upload. Its been a week, but it still shows uploading. > > Thank You, > Rubina

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blastn: NameError: name 'cmd' is not defined
by Sergei Ryazansky 02 Jul '11

02 Jul '11

Hello all, First of all I would like to thank you guys for developing and mainting this so useful tool as Galaxy! I have our own installation fo Galaxy (galaxy-dist version) with ncbi-blast-plus. Calling blastn results to the following error message: An error occurred running this job:*Traceback (most recent call last): File "/home/galaxy/galaxy-dist/tools/ncbi_blast_plus/hide_stderr.py", line 29, in <module> sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err)) NameError: name 'cmd' is not defined* * * Could you please explain, what this error can mean? The link to the shared history is* * http://dmbcserv.dyndns.org:8080/u/hogart/h/test-of-blast* * * * Thank you in advance!

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Question regarding quality filtering of 454 amplicons
by Jackie Lighten 01 Jul '11

01 Jul '11

Hi, I have a question for you guys regarding quality filtering. I have a data set of double MID tagged 454 amplicons, from which I wish to select high quality sequences above Q20. The 454 quality filtering system seems to work differently from that given for the Illumina sequencing i.e. 454 filtering takes high quality segments, while Illumina (FASTQ) can select high quality full reads based on certain parameters. OK, so I know that the total length of my amplicon, including primers and barcodes is around 260bp. If I then set the 454 quality filtering tool to extract contiguous high quality sequence of >260, it gives me back around 45% of my raw data as hitting this criterion i.e. All 260bp are above Q20. I don¹t necessarily need this high stringency as most bases may not be informative. But if I convert my 454 data to FASTQ format and then run the Illumina filtering system which also allows me to set the number of bases allowed to deviate from the Q20 criteria, I get back over 90% of my data (allowing 10bp to deviate from Q20). I then need to go ahead and convert back to 454 format. Can you tell me if this is OK? Will I loose /confuse information somewhere along these conversions? It seems that if I do this, my barcodes are removed, as amplicons do not sort properly when I parse them through my barcode filtering program. Does anyone know of a program to filter 454 data based on average sequence quality score, which doesn¹t involve Linux and the Roche off instrument program (I have no experience in Linux! ) Thanks! -- Jack Lighten, Ph.D. Candidate, Bentzen Lab, Room 6078, Department of Biology, Dalhousie University, Halifax, NS, B3H 4J1 Canada Office:(902) 494-1398 Email: Jackie.Lighten(a)Dal.Ca Profile: www.marinebiodiversity.ca/CHONe/Members/lightenj/profile/bio

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Yeast Genome Assembly
by Edward Turk 01 Jul '11

01 Jul '11

For yeast analysis I use the following assembly: S. cerevisiae June 2008 (SGD/sacCer2) (sacCer2). Recently a new yeast genome has appeared as an option in Galaxy: S. cerevisae str. S288C (Saccharomyces_cerevisiae_S288C_SGD2010). Is this an update to sacCer2? Where is it coming from? I don't see it at UCSC?

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Adding a reference genome
by Jeremy Coate 30 Jun '11

30 Jun '11

Greetings, My apologies for a what is a naive question, but I would like to map NGS reads to a genome that isn't currently in the list of reference geneomes (soybean, Glycine max). To the guys at Galaxy - can this be added to the list? Or can someone explain to a bioinformatics ignoramus how I would install it in my history? Thanks for your help. Sincerely, Jeremy Coate

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adding tools to cloud version
by Joseph Hargitai 30 Jun '11

30 Jun '11

Hi, just like universe..ini.cloud in bucket, is the assumption to edit this file in the bucket? ( How about the tool directory edits on the regular mount? Will they be wiped on a reboot? Again, do we have a doc somewhere about the cloud version's persistence issues as far as edits and data? best, joe

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