May 2012 - galaxy-dev - lists.galaxyproject.org

Help for using Galaxy for PCA
by Kinshuk Nayak 04 May '12

04 May '12

Sir, I would like to use PCA for a set of FASTA formatted 1400 sequences (in a single file).I have stored all fasta formatted sequences in a text file. If there is any problem for it, you can help me in doing the corresponding analysis using R. I am herewith giving a weblink for R, which uses the frozen database for correspondence analysis for three organisms(Leishamnia major, Trypanosoma brucei and Trypanosoma cruzi) .Instead, I want to use my above dataset (sequences) of a organisms for same purpose. For this R code needs to be edited and I do not know how to do that.Could you please help me either way for this analysis work. Weblink: http://pbil.univ-lyon1.fr/datasets/charif04/ Thanking you Kinshuk Chandra Nayak Institute of Life Sciences Department of Biotechnology, Bhubaneswar-751023, India

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Migrating Workflows and Other Data to New Galaxy Instance
by Robert Chase 04 May '12

04 May '12

Hello, We are going to migrate to a new instance of the galaxy server. Our current instance contains a number of workflows and other data that we would like to have available on the new server. Is there a way to backup the workflows and then reload them on the new server? Regards, -Robert Paul Chase Channing Lab

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Best way to allow users to configure a display application url for a toolshed tool
by Ira Cooke 04 May '12

04 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 04 May '12

04 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 04 May '12

04 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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