- galaxy-user - lists.galaxyproject.org

Text Manipulation: Filter out duplicates (uniq) from an plain text file ?
by Roman Valls 07 May '11

07 May '11

Hey galaxy users, Thats a fairly good question from one of my colleagues. I've looked through the menus (mainly "Text Manipulation" and "Filter and Sort"(Select)), googled (on the mailing list archives too), but couldn't find an answer: How should I remove duplicates on plain text files without resorting to: "echo file|sort|uniq" before uploading the file/text. or Putting a regexp together to replace the duplicate occurences as in: http://www.regular-expressions.info/duplicatelines.html I'm pretty sure I'm missing some really basic stuff here... is this basic operation something supposed to be done outside galaxy perhaps ? Thanks in advance !

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Galaxy's recent problems
by Dave Clements 07 May '11

07 May '11

Hello all, Galaxy has been ill recently due to disk space on the server filling up. In the short term we are working on freeing up space. In the longer term we are working on adding a quota system to limit how much space any one user can take, and we've also ordered a lot more disk. In the mean time, *please take a look at your saved histories and datasets and delete anything you no longer need*. This will greatly help us get through the current rough patch. In the longer term, you can also consider setting up your own local Galaxy instance, or running Galaxy on the cloud. See: http://getgalaxy.org/ https://bitbucket.org/galaxy/galaxy-central/wiki/cloud Thanks for your patience while we work this out, Dave C and the Galaxy Team -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/

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Composite Datatypes Q.
by Todd Yilk 06 May '11

06 May '11

I have a program I'm trying to "galaxify" that emits a variable number of result files. I would like the output of my Galaxy tool to show up in Galaxy as an html file with links to the result files. So when you click on the eye, the html file should up in the middle pane ... sorry if I'm not describing this in an elegant way. Creating a composite datatype is the way to go in this situation, correct? I'm creating a class that inherits from Html. How do I get the result returned from my custom "generate_primary_file" function to show up as a tool's output ... if that's the right way to go about this? Thanks!

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Composite Datatypes Q.
by Todd Yilk 06 May '11

06 May '11

I have a program I'm trying to "galaxify" that emits a variable number of result files. I would like the output of my Galaxy tool to show up in Galaxy as an html file with links to the result files. So when you click on the eye, the html file should up in the middle pane ... sorry if I'm not describing this in an elegant way. Creating a composite datatype is the way to go in this situation, correct? I'm creating a class that inherits from Html. How do I get the result returned from my custom "generate_primary_file" function to show up as a tool's output ... if that's the right way to go about this? Thanks!

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Indel work flow questions
by Mike Dufault 04 May '11

04 May '11

Hi All, I have a question about the NGS: Indel analysis and SNP Calling. Assuming I have loaded my paired end reads, groomed, and got all the way through to alignment with BWA my question the becomes does the analysis for indel analysis and SNP analysis split in the work flow? For SNP analysis, It seems that I need to filter on SAM, convert SAM-to-BAM, etc... For Indel, It seem that I should use the BWA output that is in SAM format for indel analysis. Are these two above statments correct? I also have a question regarding the input for indel analysis. Should I use the BWA output directly (which is in SAM format) or should I first "filter on SAM" and use that output (which is also in SAM format). I have tried the indel analysis using both filtered and unfilterd and I get very similar results. It seems to me that should use the "filtered on SAM" output where I can indicate that the reads are paired=Yes, proper pairs=yes, unmapped=NO. Any thought, insight, etc. Thanks if advance, Mike

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RNA seq analysis
by puvan001＠umn.edu 04 May '11

04 May '11

I am new to Galaxy and I am not sure whether these topics were discussed earlier. I followed the steps up to cufflinks and I did not have any problems. Thanks for the RNA seq tutorial. My questions are 1. How do I know the number of reads mapped against the reference genome used after Top Hat mapping 2. I am aware that Cuffdiff is used to find the differences in expression. How do I combine replicates (3) of different treatments ? SP

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quality stat.
by Robin Mjelle 04 May '11

04 May '11

Dear User, I am trying to use the tool "Compute quality statistics<http://main.g2.bx.psu.edu/tool_runner?tool_id=cshl_fastx_quality_statistics>" in galaxy on Ilumina single reads. The file is 2.3 Gb, fastq format. I have performed Quality format converter on the data set and the format is now qualillumina. Despite of this, galaxy don't recognize any dataset in the workflow to use as input into quality statistics. Any idea why my dataset is not accepted as input? Best, Robin

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change queue with sge
by Sylvain Thomas 03 May '11

03 May '11

Hi I currently use a galaxy server with cluster. This cluster uses SGE. I'd like to specify a queue other than the default. I have tried many combinaisons with drmaa:/// without success. The queue used is always the default one. Does anyone has solved this problem? Thanks, Sylvain -- Sylvain Thomas tel : +33 (0)5 61 28 54 27 INRA - Unité de BIA Génopôle - plateforme Bio-informatique Chemin de Borde-Rouge - AUZEVILLE BP 52627 - 31326 CASTANET-TOLOSAN CEDEX

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uploading files from remote server
by camelia botez 02 May '11

02 May '11

How can we upload files from remote server running galaxy and using big storage for data ? Thank you

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Only first 5000 reads are displayed in this tile
by Jeremy Chien 02 May '11

02 May '11

Hi During the visualization of my mRNAseq data, some area have red line indicating that only the first 5000 reads are displayed. Within this region, some area have many reads. Some area, where exons exist, I don't see any reads. How do I interpret the data? If there are no reads shown in the visualization, although there is a read line saying only the first 5000 reads are displayed, does the absence of reads corresponding to a particular exon means it is not expressed? Thanks, Jeremy

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