- galaxy-user - lists.galaxyproject.org

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by Meabh Beatty 08 Aug '13

08 Aug '13

I am new to Galaxy and am using it for analysis of BLAST results and phylogeny. I have uploaded a file with contig names, the BLAST GI number, and the total read count for each contig. When I use Galaxy to 'Summarize taxonomy' and 'Draw phylogeny', I have lost the total read counts. Eg. In the results of these it tells me how many contigs belong to Fungi or Metazoa, whereas each contig actually has a different number of reads. Is there any way to reflect this in Galaxy? I hope this makes sense!

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Downloading Output File thru FileZilla
by Mark Edward Fabreag 08 Aug '13

08 Aug '13

Good day. I just want to inquire if there is a way to download output through FileZilla. Thank you very much.

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Database of c_briggsae_WS230 for SnpEff
by Fabrice BESNARD 07 Aug '13

07 Aug '13

Hi, Using SnpEff in the Galaxy main server, I need the Caenorhabditis briggsae genome as a reference, which is not an option in the genome list given by the tool as implemented in Galaxy right now. In the doc of SnpEff, it is said that this database is available (c_briggsae_WS230, down-load link here : http://sourceforge.net/projects/snpeff/files/databases/v3_3/) However, the version of SnpEff in Galaxy is 1.0. It is said in the SnpEff docs that the database version should match the SnpEff version (http://snpeff.sourceforge.net/download.html) I found that the first release of a C. briggsae database dates back to the version 2.1 of SnpEff (See here: http://sourceforge.net/projects/snpeff/files/databases/v2_1/) Would it be to possible to up-date the list of databases of SnpEff in the main server, to include the C. briggsae WS230? If versions are not compatible, would it be possible to update SnpEff to a more recent version? If this is not possible right now (I must confess I don't know how much work this upddate would require), I guess the best and quickest alternative option would be to install a SnpEff locally. Do you think it's worth trying this, knowing that I don't feel very comfortable with informatics (In other words, is the installation easy) ? many thanks in advance for your comments and advices, -- Fabrice Besnard Institute of Biology of the Ecole Normale Supérieure (IBENS) 46 rue d'Ulm, 75230 Paris cedex 05, France 8th floor. Office: Room 802. Lab: Room 817. mail: fbesnard(a)biologie.ens.fr Tel: +33-1-44-32-39-44

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jobrunner upload file
by Jasper Jan Koehorst 07 Aug '13

07 Aug '13

Hello, I have a very simple jobrunner script that allows only 1 job to be run as this galaxy is used for one thing in particular which consumes almost all resources. To do this I set the following: <plugins> <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="1"/> </plugins> This works, but is it possible to create a second worker that is only allowed to be used for uploading files? So people can upload their data already and only enter the queue for the big analysis? Otherwise if they turn their computer off in the evening the upload is gone...

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FTP problem
by Karen Schwarzberg 07 Aug '13

07 Aug '13

Hello, I am using the Galaxy server and I am trying to upload files. I do not see the FTP option even when logged in. Please advise. Best regards, Karen

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History & Visualization list empty
by Benjamin Schuster-Boeckler 07 Aug '13

07 Aug '13

Hi there, I've set up a local galaxy installation that so far is working very nicely. However one little issue that I'm having is that the "Saved Visualizations" and "Saved Histories" lists are empty, even though I have multiple histories and multiple visualizations. In fact, when I choose to visualize a dataset in Trackster and select "View in saved visualization", I DO see the list of existing visualizations. Pictures attached. The identical problem appears with Histories. Any idea what the problem might be? I tried in Chrome and Safari, I logged out and back in, I restarted the server, but nothing fixed the issue... Thanks in advance for the help, Ben -- Benjamin Schuster-Böckler Leadership Fellow for Bioinformatics Ludwig Institute for Cancer Research University of Oxford Old Road Campus Research Building Oxford OX3 7DQ United Kingdom [cid:CD86F63E-0203-45D3-8802-328573CCB3B1][cid:BECC9A41-D145-4D11-A38A-485DAAB3997E]

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after 'trim sequences', 'map w/Bowtie' job has been waiting for days to run
by Theresa Stueve 06 Aug '13

06 Aug '13

Greetings, I am using Galaxy Main; On 8/1/2013, and after 'trimming sequences' on my 'FASTQ groomed' data, I attempted to align my (single-end) 'trimmed sequences' output data to 'hg19 Canonical male' with 'Map with Bowtie for Illumina' It is now 8/3/2013, and the 'Map with Bowtie for Illumina' job has been 'waiting to run' >+48hrs. I have 're-newed' the history several times, but have not deleted or re-run the original job for fear of losing my place in the queue. To check if 'canonical male' was the problem, I queued a second alignment to be 'mapped w/bowtie for Illumina' against hg19 (no sex); this job has also not run after being queued mor than 24 hours ago. Can you tell me if the delay is because I've done something incorrectly or if there's some action I can take to speed things? your help is deeply and sincerely appreciated https://main.g2.bx.psu.edu/u/theresa-stueve/h/1stunsupctcfupload-1 -- (Theresa) Ryan Stueve Department of Preventive Medicine Ite Laird-Offringa Lab NTT 6420

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slow Galaxy server
by Politz, Samuel M. 06 Aug '13

06 Aug '13

This is a followup to my previous post on this topic. The exact message (in red) that I see after a long delay in running a tool is "An error occurred while getting updates from the server. Please contact a Galaxy administrator if the problem persists." I have seen this message twice while waiting for two unrelated tools to run. There is no green'bug' icon so I could not report this to an administrator. Another main server user reported this error message to the user mailing list as well. The response to their post was to wait a few minutes. Well, in this case I have been waiting overnight. Best regards, Sam Politz

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very slow server
by Politz, Samuel M. 06 Aug '13

06 Aug '13

Hello, for the last week or so the main Galaxy server has not completed any of my jobs. These were jobs that were successfully queued, but I deleted them after 48 hours passed without completion. I started a job last night (BEDtools BedGraph of genome coverage on a BAM file). This morning I got an error message, something to the effect that my account was having difficulty receiving updates from the Galaxy server. I am not sure this latest message had anything to do with the previous delays, but the current job is still queued up. Over the past month or two, the Galaxy server has been slow to complete jobs at times, but never more than a few hours, or at most, overnight. I wonder if the current problem is a symptom of increased use of the server, or if something is wrong with my particular usage. Either way, it is currently preventing me from getting any analysis done on the server. Best regards, Sam Politz

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after 'trim sequences', 'map w/Bowtie' job has been waiting for hours
by Theresa Stueve 06 Aug '13

06 Aug '13

Greetings, I am using Galaxy Main On 8/1/2013, and after 'trimming sequences' on my 'FASTQ groomed' data, I attempted to align my (single-end) 'trimmed sequences' output data to 'hg19 Canonical male' with 'Map with Bowtie for Illumina' It is now 8/2/2013, and the 'Map with Bowtie for Illumina' job has been 'waiting to run' all night, over night. I have 're-newed' the history several times, but have not deleted or re-run the job for fear of losing my place in the queue. Can you tell me if the delay is because I've done something incorrectly? https://main.g2.bx.psu.edu/u/theresa-stueve/h/1stunsupctcfupload -- (Theresa) Ryan Stueve Department of Preventive Medicine USC

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