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Best way to allow users to configure a display application url for a toolshed tool
by Ira Cooke 03 May '12

03 May '12

Dear All, Our toolshed tools include a custom display application. Although the display application is open source ( https://bitbucket.org/Andrew_Brock/proteomics-visualise ) we do not yet have a public server for it. Actually, at present it isn't possible to have the application work properly if it is running on a completely separate server because it needs access to galaxy's database/files directory (I'll leave that for another question). For now I just need to be able to provide a way for administrators of a local galaxy to configure the url to this display application. At the moment we have it hard coded .. like this; <url target_frame="galaxy_main">http://${galaxy_url.qp}:8500/init_local?file=${encoded_filename.qp}&type=mzml</url> Using the galaxy_url (because we are on the same server) .. and hard coding the port. What would be the best way to allow local admins to configure this? Thanks Ira

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Are uploads already indexed and/or sorted?
by Ciara Ledero 03 May '12

03 May '12

Hi all, Do the uploaded files in Galaxy get indexed or sorted already? Cheers, CL

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Empty file generation
by Ciara Ledero 03 May '12

03 May '12

This is my code for running samtools pileup: open INP,"< $ARGV[0]" or die "Cannot open file! $!"; open INP2, "< $ARGV[1]" or die "Cannot open file! $!"; open OUT,"> $ARGV[2]" or die "Cannot open file! $!"; open SCRIPT,"samtools pileup -cv -f $ARGV[0] $ARGV[1] 2>/dev/null | "; while(<SCRIPT>) { print OUT $_; } close INP; close INP2; close OUT; close SCRIPT; In the console, it works perfectly. But when run in Galaxy, it gives me an empty file. I don't think it has something to do with the files that I am using as input, for I just uploaded the ones that I used in the console test-run. Any idea why this might be happening? Cheers, CL

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Purging deleted dataset
by Sahar Al Seesi 03 May '12

03 May '12

Hi, We have been working with a relatively old distribution that does not have the purge datasets feature in the history menu. We just pulled a new galaxy distribution, and I was trying to test this feature. I tried many scenarios and I always get "0 datasets have been deleted permanently" and the used disk space that appears at the top right of the screen does not change. I read the documentation on dependencies and when a dataset gets purged. So, I created a new history, and uploaded a file from my local machine. As a result, I could see that my used disk space increased. Then I deleted this item from my history and selected purge deleted datasets, but I got the same thing as described above. I also selected Delete history Permanently, but the disk space did not go down. What am I missing? Thanks, Sahar Al Seesi Postdoctoral Fellow Computer Science and Engineering University of Connecticut

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Problems saving a cloned workflow
by Liisa Koski 03 May '12

03 May '12

Hello, I cloned a workflow on my local Galaxy installation, renamed it, made some edits and pressed save. It has been saving now for about 3 hours. It only has 12 steps. Any suggestions? Thanks in advance, Liisa

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Keep header and output BAM options for "NGS: SAM Tools/Filter SAM" tool
by Carlos Borroto 03 May '12

03 May '12

Hi, I regularly use "NGS: SAM Tools/Filter SAM" tool. Filtering after mapping with BWA is a required step. I feel my current approach to reintroduce the header after filtering is very wasteful. Wouldn't be great if this tool had an option to keep the header? This sounds simple enough. In fact looking at the logic in the python script: for line in infile: line = line.rstrip( '\r\n' ) if line and not line.startswith( '#' ) and not line.startswith( '@' ) : fields = line.split( '\t' ) flags = int( fields[flag_col] ) valid_line = True for index, opt_bool in used_indices: if bool(flags & 0x0001 << index) != opt_bool: valid_line = False break if valid_line: print line It seems like it could be done by adding at most a couple of lines. Also, most of the time after filtering what you really want is a sorted BAM file. Most tools dealing with SAM/BAM files in Galaxy already have the option to output a sorted BAM file. I think it would be nice if "Filter SAM" followed the same path. Are these enhances in the radar? Would you take a pull request implementing them? Best, Carlos

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Can't upload Cuffmerge files to Galaxy Cloudman
by Mohammad Heydarian 03 May '12

03 May '12

Hello, I can not upload Cuffmerge files to Galaxy Cloudman. I can load other .gtf files just fine, but not the "merged transcripts.gtf" file from Cuffmerge. This is the first time this has happened. After I upload my "merged transcripts.gtf" file (via ftp) I can not move the file to the history pane. Upon asking Galaxy Cloudman to move the file from the ftp queue to the history pane, I get the error: "No data was entered in the upload form, please go back and choose data to upload" Even if I try to zip the file to fool Galaxy Cloudman the file still won't load. This may be unrelated, but I have never been able to download Cuffdiff out put files from Galaxy Cloudman directly, I always have to export my history to a file and then rename the files after download. Any help would be great! Cheers, Mo Heydarian

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Bug - uploading html file
by liram_vardi＠agilent.com 03 May '12

03 May '12

Hi, I would like to report about some uploading problem on Galaxy. When I tried to upload a html file which contains a href link, Galaxy failed with the following error message: "The uploaded file contains inappropriate HTML content". Anyway, I found a post about a similar issue and as a result I was able to "walk around" this problem. The solution is simple: I first compressed the file and then I successfully uploaded it to Galaxy. Hope this will be helpful for someone, Liram

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Galaxy Admin - Browsing any user's histories?
by Peter Cock 03 May '12

03 May '12

Hi all, Is it possible for a Galaxy Admin to browse any user's history? Sadly the "Admin" page on the wiki is still rather lean: http://wiki.g2.bx.psu.edu/Admin/Interface For instance, I've monitored a large Galaxy job on our cluster, and now that it has finished I'd like to see the results (in this case, the error messages) - without having to first ask the user to share their history with me. Is that possible via the normal Galaxy Admin pages? Alternatively, is this something I could do via the impersonation option? i.e. enable allow_user_impersonation in universe_wsgi.ini Thanks, Peter

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How to customize Galaxy web interface?
by Pascal Maugeri 03 May '12

03 May '12

Hi, I m running my own Galaxy instance and I would like to do some simple customization of the web interface such as adding my logos in the header frame, changing background colors, etc. I am having a look to static/ folders but I can't see clearly where the header frame is defined. Could you please tell me if there is any tutorial for doing so? Any starting point? Or which folder/file(s) corresponds to the web interface in the distribution? Best Regards, Pascal

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