April 2012 - galaxy-user - lists.galaxyproject.org

Job waiting to RUN
by Ateeq ur Rehman 13 Apr '12

13 Apr '12

Dear Administrators Since yesterady my bowtie alignment is waiting to run, message is just, job waiting to run could you plesae see the problem Thank you Ateequr Rehman

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Alignment coordinates
by Erika Kruse 13 Apr '12

13 Apr '12

Hello, I imported a sequence alignment file from clustalw. How can I generate a list of the coordinates of the matching regions? Thank you. Erika

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History not accessible
by Luciano Cosme 13 Apr '12

13 Apr '12

Hi, After I uploaded a couple files yesterday, I hit the storage limit (250Gb), then I deleted 3 datasets from my history and now I can't see anything in that history. It still says that I am using 228Gb, but I can only access one history with ~98Gb. I try to use show deleted datasets and it still not showing. The history that I was using disappeared. When I use "saved datasets" I only see one history. I was logged as ento.purchase(a)gmail.com Thank you. Luciano

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find nothing but Workflows
by dongdong zhaoweiming 12 Apr '12

12 Apr '12

Hi, I have a problem with galaxy and galaxy test, I find nothing but Workflows All workflows, so what should I do? Thanks a lot! weimin zhao

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Galaxy logo: licence? (blog article project)
by Louise-Amélie Schmitt 11 Apr '12

11 Apr '12

Hello, I want to write an article on Galaxy on our bioinformatics blog ( http://bioinfo-fr.net/) so I would like to know what materials I can use and under which conditions. What is the licence of the pictures (logo etc.)? Can I use them? Is there anything particular you want me to mention? Thanks, L-A

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Megablast question
by shamsher jagat 11 Apr '12

11 Apr '12

Hi, I am using megablast and was wondering how can I get chromosome number and coordinates of its hits. Thanks Shamesher

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equicktandem search not yielding any results
by Harry Podschwit 10 Apr '12

10 Apr '12

Hello all, I am certainly new to using galaxy and I have already checked the message boards to get some assistance on this but was unsuccessful. Anyways, here is my problem, I have a a FASTA file of C. gigas partial sequences. I was trying to use Galaxy's equicktandem tool to identify micro satellites in the sequence. However, when I ran the tool it did not yield any results. This is strange because I could visually pick out where l thought the algorithm should have found a hit. Additionally, trimming my collection of sequences to a single sequence did not yield any hits. Moreover, I created a fake sequence with very obvious "microsatellites" and the algorithm appeared to work fine as it identified the repeats. While I suppose it is certainly possible that there may just not be any microsatellites in my sequence, I find it highly unlikely and suspect something else is going on. This seemed like such a simple tool yet I am having much difficulty in using it. I am simply uploading my FASTA file normally and then taking that file and using the tool. I am doing this all online through the galaxy website not a local instance and if you would like to see yourself the FASTA file can be downloaded at http://genefish.wikispaces.com/crassostreome and the FASTA file is cgigas_alpha_v0.3.2 (the collection of 272 sequences). Please help this has been excruciatingly frustrating for me and I suspect that a veteran Galaxy user may be able to see my error quickly. Best, Harry hpodschwit(a)gmail.com

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(no subject)
by Michael Sikes 10 Apr '12

10 Apr '12

Hi, I have hit a brick wall when trying to convert wig files from the GEO to bigwig files. Each time I try (and I have tried many times since October), I get the same error. For example, here is a downloaded wig file, that I assigned to the mouse mm8 genome, and the error I got when I tried to convert it to a bigwig file. The dataset came from Bing Ren's lab, and its GEO record is here: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM560344 The wig file was uploaded to Galaxy Dec. 8, 2011, and I assigned mm8 rather than mm9 based on the GEO record: 49: GSM560344_03112009_313D2AAXX_B7.wi ~960,000 lines format: wig, database: mm8 Info: uploaded wig file display at UCSC main The details for this upload are as follows: Tool: Upload File Name: GSM560344_03112009_313D2AAXX_B7.wi Created: Dec 08, 2011 Filesize: 12.1 Mb Dbkey: mm8 Format: wig Tool Version: Tool Standard Output: stdout Tool Standard Error: stderr Input Parameter Value File Format auto Genome Conditional (files_metadata) 32 Inheritance Chain GSM560344_03112009_313D2AAXX_B7.wi The wig-to-bigWig conversion on data 49 (using the wig to bigwig conversion tool in the convert formats toolbox) was run on March 21, 2012 and gave the following error: 77: Wig-to-bigWig on data 49 0 bytes An error occurred running this job:line 152351 of stdin: chromosome chr13 has 120614378 bases, but item ends at 120614600 line 298005 of stdin: chromosome chr17 has 95177420 bases, but item ends at 95177625 line 325066 of stdin: chromosome chr16 has 98252459 bases, but item ends at 9825252 The details for this operation are as follows: Tool: Wig-to-bigWig Name: Wig-to-bigWig on data 49 Created: Mar 21, 2012 Filesize: 0 bytes Dbkey: mm8 Format: bigwig Tool Version: Tool Standard Output: stdout Tool Standard Error: stderr Input Parameter Value Convert 49: GSM560344_03112009_313D2AAXX_B7.wi Conditional (settings) 1 Items to bundle in r-tree 256 Data points bundled at lowest level 1024 Clip chromosome positions True Do not use compression True Inheritance Chain Wig-to-bigWig on data 49 I gather that the chromosome ends are not being snipped off, even though I toggle this option on the galaxy conversion tool. And I know it's doing something, because if I toggle that option off, I get an error that includes "broken pipe" and simply aborts. I apologize for knowing so little about the bioinformatics involved here. And I'm sure I've overlooked something that is likely obvious to others and/or failed to provide some critical bit of info in this email. But any help would be greatly appreciated. Thanks, Mike

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permissions on folder created by Galaxy
by Guilhem Sempéré 10 Apr '12

10 Apr '12

Hi, I would like folders created by Galaxy under the location defined by the "file_path" parameter (which defaults to database/files) to be created with permissions 775 instead of 755. Is this possible? The reason for me asking this question is that I have developed an external tool (running under Tomcat) for feeding Galaxy libraries. And my tomcat user needs to be allowed to write to the mentioned folders. Any ideas? G.

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Tophat paired end read
by 杨继文 10 Apr '12

10 Apr '12

Hi all, I have paired end RNA-Seq reads ( Illumina Hiseq 2000) in seperate files. Before mapping, I need to trim the reads. My questions is : Do I have to join pair end reads before timming, and then split again for Tophat??? Lookiong forward to your answers. Thanks Jiwen

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