October 2011 - galaxy-user - lists.galaxyproject.org

Q about 'Compute' tool
by Ian Donaldson 10 Oct '11

10 Oct '11

Hi, Can 'if' statements by used in 'Text manipulation' > 'Compute'? The reason is that i have a interval file of UCSC genes, i want to identify the TSS of each and make a new interval reflecting the TSS position for each gene. But because the TSS of a '-' stranded gene is actually the 'end' coord i want to be able to check the strand in the compute statement. Is this possible or is there an easier way to do this inside GALAXY? Thank you, Ian

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Cost
by Lizex Husselmann 10 Oct '11

10 Oct '11

Hi Just a general question. How much is the cost of using the cloud on amazon, it says "pay-as-you-use". Can somebody give me a figure? Lizex Disclaimer This message is confidential and may be covered by legal professional privilege. It must not be read, copied, disclosed or used in any other manner by any person other than the addressee(s). Unauthorised use, disclosure or copying is strictly prohibited and may be unlawful. The views expressed in this email are those of the sender, unless otherwise stated. If you have received this email in error, please contact ARC Service Desk immediately. (mailto:Servicedesk@arc.agric.za) To report incidents of fraud and / or corruption in the ARC use our Ethics Hotline by: Phone number : 0800 21 20 56 Fax number : 0800 200 796 Email address : fraud(a)kpmg.co.za For more information on the ARC Ethics Hotline, please visit our website at www.arc.agric.za.

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Problem uploading files to Cloudman Galaxy
by Kevin Williamson 09 Oct '11

09 Oct '11

Hello, I seem to be unable to upload .fna files (eg, ~19 Mb in size) to a Cloudman Galaxy instance on an Amazon EC2 cluster [AMI = galaxy-cloudman-2011-03-22 (ami-da58aab3)]. I know that I can interact w/ the instance since I'm able to create/save workflows and add them to the tools menu. However, when I attempt to upload data files (stored on the computer I'm working at), the upload seems to hang in the perpetually uploading state. The .fna files CAN be quickly uploaded to the Penn State Galaxy, so I know there's no issue w. the files themselves. Has anyone else encountered this issue, and if so, what did you do to work around it? Any ideas/tips would be greatly appreciated. Thank you in advance, kevin

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Subscribing to Job Status Events
by Oren Livne 06 Oct '11

06 Oct '11

Dear All, Does Galaxy provide a way for a client app to subscribe to job status change notifications? Best would be a web service that lists the currently running jobs (for the current user / all users) and their status. Thank you so much, Oren

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QUESTION
by dtrejo＠ira.cinvestav.mx 06 Oct '11

06 Oct '11

I WANT TO ALIGNMENT MILLIONS OF SEQUENCES FROM A sRNA LIBRARY WITH A SMALL GENOME (2600 BASES). HOW CAN I DO THIS ALIGNMENT IN GALAXY?. I HAVE TRIED WITH MULTIPLE ALIGNMENTS FROM TOOLS, BUT I CAN NOT SELECT BOTH FILES. THANKS FOR YOUR HELP DIANA TREJO -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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Possible to browse local filesystem
by alessandro albiero 06 Oct '11

06 Oct '11

Dear all, We are setting up a galaxy istance on our server (HPC Cluster with torque and PBS) for internal use. Our problem is that we manage only NGS data (SOLiD and Illumina Data) that are already stored on the server. When we connect to galaxy with our clients we are not able to browse the server file system. Having the possibility to browse the server filesystem would be the best solution for us!! We have look for this funtion but it seems it is not possible... Now, we tried to set up the user directory but adding new file and re-uploading the dir we found duplicated files (it seems that galaxy re-upload every time all the files ignoring if some are already present. This method is OK for us but how can we avoid the file duplications ? In a presentation found on web (blankenberg_pittsburg_2001), we saw that there is the possibility to automatically upload the sequenced reads on Galaxy (and let them available to all our user). Where can we find information for doing this ? All the best Alessandro -- ****************************** Alessandro Albiero Bioinformatics Lab CRIBI-Padua University Viale G. Colombo, 3 35121 Padova-Italy http://genomics.cribi.unipd.it http://genomics.cribi.unipd.it/index.php/User:Albiero Phone. +39. 049 827-6165 Fax. +39. 049 827-6159 ********************************

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Adding new tools in Galaxy
by Makis Ladoukakis 06 Oct '11

06 Oct '11

Dear Galaxy developers, Currently I am adding new tools to my galaxy instance as scripts written in Perl language. I was wandering if there is a way to add tools either as .bin or .exe format or if only scripts are supported. I couldn't find anything about it in the wiki or in the FAQ. Thank you, Makis Ladoukakis

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Re: [galaxy-user] How to count reads in 200bp windows and save the output per chromosome?
by Jennifer Jackson 06 Oct '11

06 Oct '11

Hello Di, Yes, the 200 bp windows should be for the reference genome, apologies if that was not clear. The idea is to create a simple text file of the chrom-start-stop (one line per chromosome), upload, convert to BED, then create windows. Or better and less manually, you can extract the "chromInfo" table from the UCSC Table Browser (since you are using mm9, sourced from UCSC), do a few text edits to format, and use that as the BED file to create windows. Once you have the 200 bp windows as the "target ranges" for the regional variation tool, compare your "query alignments" (BAM/SAM->Interval dataset) to get coverage. Group per window, per chrom, or however you wish with the tools I mentioned. If using "Group", the other data points are the numbers that can be graphed or manipulated. But that is just one suggestions, once you have the data in the right format (tabular), trying out different tools should be quick to do and tune/evaluate. Good luck with the project, Jen Galaxy team On 10/5/11 3:19 PM, Di Nguyen wrote: > Hi Jen, > > Why is that when I made 200bp windows using "gro-seq.bed" file (my data > file), it came up empty? Did I think about this the wrong way, my 200bp > window supposes to be my reference genome, in this case mm9? > > Secondly, when using regional variation, can I use a reference genome > such as mouse, and how do I created interval file for mm9, for example? > > Thank you, > > Di -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support

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How to count reads in 200bp windows and save the output per chromosome?
by Di Nguyen 05 Oct '11

05 Oct '11

Hi all, I recently have some Gro-seq data. What I want to do is this: 1. Workflow Counting how many reads per 200bp windows per chromosome. For this, my work flow is as followed: fasq -> fasq groomer -> bowtie -> BAM to SAM -> interval BED -> 200 bp windows regional variation -> feature 2. Questions: how do I sort and save per chromosome? For example, I would like to compare X chromosome versus autosomes or X versus chromosome 1? Please accept my appreciation, Di Nguyen, U of Washington, WA

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data libraries
by Hilary Morrison 05 Oct '11

05 Oct '11

How does one get admin privileges to make datasets available to multiple users? Or is that only available for local installations? ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Hilary G. Morrison, Ph.D. Senior Research Scientist Josephine Bay Paul Center Marine Biological Laboratory 7 MBL Street Woods Hole, MA 02543-1015 508-289-7339 508-457-4727 (fax) morrison(a)mbl.edu https://jbpc.mbl.edu/labs-morrison.html

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