- galaxy-user - lists.galaxyproject.org

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 09 Apr '12

09 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 09 Apr '12

09 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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Question about megablast
by shamsher jagat 09 Apr '12

09 Apr '12

I have a question about megablast, I want to megablast my seq: the databases mentioned include (against target databases): htgs27 nt27 wgs 09 phiX174 How can I find details about these databases and which one is human or mouse or may be best for my case. Thanks Vasu

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inconsistency with query results at different time periods
by Jennifer Jackson 09 Apr '12

09 Apr '12

Hello Andigoni, To confirm, the data is being extracted using "Get Data -> UCSC Main" using the Table browser for the hg16 reference genome? If so, I can let you know that the reference genome itself remains the same through time. However, annotation tracks may or may not be updated. Genbank track update frequencies are incremental daily additions and add/remove/change at full releases. From your numbers, it seem like the data is coming from RefSeq Genes. This track was last updated on "2012-04-07". This can be seem at UCSC when browsing the track's description page, the last line of the top section: "Data last updated:". The dates for the corresponding files on their downloads server will also reflect updates (server updated weekly). Unfortunately, there isn't a straightforward way to get back to your prior data unless you have it saved. If you have the exact date of your original data pull, you may be able to reconstruct part of it by mining GenBank directly, but this would be non-trivial and involve your own methods/tools outside of Galaxy. Hopefully this helps to explain the data content. If you have comments or questions about how tracks are processed at UCSC (including this question, they may have a creative solution), their team can be reached at: http://genome.ucsc.edu/contacts.html Going forward, please use our mailing list for questions. Thank you! Jen Galaxy team > ---------- Forwarded message ---------- > From: *andigoni* <andigoni(a)med.auth.gr <mailto:andigoni@med.auth.gr>> > Date: Sun, Apr 8, 2012 at 7:06 PM > Subject: Re: [galaxy-user] inconsistency with query results at different time periods > > Dear Galaxy Gury, > > I would like to ask you a simple question about the human genome > assembly updates. Few months ago I extracted all the introns in bed > format of chromosomes 6,20 and 22 using the hg16 assembly. The total > number of records was 32.050. > > Could you please explain why today the same query results in 32.837 > introns? hg16 isn't a stable release? And how can I go back to the > 32.050 introns in order to process them further? > > > Thank you very much in advance, > Andigoni > > > Andigoni Malousi > Post-doc in Bioinformatics > Aristotle University of Thessaloniki

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MarkupSafe cannot be fetched
by Sarah Maman 06 Apr '12

06 Apr '12

Hi Nate, When I operate on Genomic Intervals → Get Flanks. The user interface for the tool will appear in the center panel. Make sure the dataset 2: UCSC Main... is selected and set Length of Flanking region to 1000 to create intervals 1000bp upstream of each gene. I have this error : Tool execution generated the following error message: WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched The tool produced the following additional output: Skipped 2 invalid lines starting with #40094L "chr5_h2_hap1 281 935 NM_022909 0 + 281 377 0 1 654, 0," Location: Upstream, Region: whole, Flank-length: 1000, Offset: 0 Epilog : job finished at ven avr 6 13:59:08 CEST 2012 Moreover, when I Map with BWA for Illumina ( genome ref and fastq fatsqsanger format ), I have this error : Tool execution generated the following error message: entree dans bwa wapperThe alignment failed. Error aligning sequence. /bin/sh: bwa: command not found WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched The tool produced the following additional output: entree dans bwa for illumina Could not determine BWA version Epilog : job finished at ven avr 6 14:04:13 CEST 2012 Could you please help me ? Thanks in advance, Sarah Maman

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