- galaxy-user - lists.galaxyproject.org

make publish histories only available to specific users
by mark.rose＠syngenta.com 13 Nov '13

13 Nov '13

Hello I am wondering whether it is possible to publish histories so that only certain users can see them. Histories that are published, rather than shared, appear to be more searchable. Thanks Mark This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.

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Re: [galaxy-user] Botryllus genome
by Enis Afgan 12 Nov '13

12 Nov '13

Hi Katie, For genomes that are not available on Galaxy Main (or general questions you might have about Galaxy), it's best to send an email to the galaxy-user mailing list (CC'd now). You can subscribe to the mailing list here http://lists.bx.psu.edu/listinfo/galaxy-user As far as the particular genome you're asking about, until it is to get added, you can upload it under your own account by following these instructions: http://wiki.galaxyproject.org/Support#Custom_reference_genome Hope this helps, Enis On Sat, Nov 9, 2013 at 1:37 AM, Katie Marshall <kmarshall(a)zoology.ubc.ca>wrote: > Hi, > > I'm sorry to bother you, but I'm not entirely certain who to contact. I'm > starting up a project looking at gene transcription in Botryllus schlosseri > (a tunicate) that was recently genome-sequenced. I would love to have this > genome available through Galaxy, and currently under mapping tools it says > to "contact Galaxy Team" if my organism isn't listed. There's no link, so > if you could please pass me along to the appropriate person, that would be > fantastic. > > The NCBI listing for B. schlosseri is here: http://www.ncbi.nlm.nih.gov/ > bioproject/PRJNA205369 > > Cheers and thanks, > Katie > > -- > Dr. Katie Marshall > Postdoctoral Fellow > Department of Zoology > University of British Columbia > Room 138, Biodiversity Research Centre > 6270 University Blvd > Vancouver, BC > >

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Tophat2 (version 0.6)
by Roberta Galletti 09 Nov '13

09 Nov '13

Is there any chance to have the Arabidopsis genome put in the sliding menu of the Tophat2 (version 0.6)? Thank you Roberta Galletti

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How to lower disc usage in order to resume workflow
by Chris Farnet 09 Nov '13

09 Nov '13

Hello, Re: https://usegalaxy.org/u/cmfarnet/h/pf2-34-map-1-r1-only I am a new user, and I uploaded WGS data to perform the published "CloudMap Hawaiian Variant mapping with WGS" workflow (History link above). I received the notice: "You are over your disk quota. Tool execution is on hold until your disk usage drops below your allocated quota." Can you please let me know how I can reduce my disc usage so the the job can continue? Thanks so much for your help! Chris Farnet Dept. of Biology McGill University

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multiple output tool in workflow
by Jun Fan 09 Nov '13

09 Nov '13

Hi all, I am trying to creating a workflow from history. One of the tool used generates multiple outputs in the format of gff3, fasta and sam. Gff3 will be visualized in IGV and the fasta file is doing further BLAST analysis. Now the problem is that the automatically generated workflow does not connect the having-multiple-output tool and the BLAST tool. I failed even I tried to connect these two tools in the workflow by hand. I am guessing this is due to only the main output type (gff3) is recognized in the workflow. How could I solve this problem? Best regards and have a nice weekend! Jun

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Quality report
by Benjamin Osei-agyeman 08 Nov '13

08 Nov '13

Hi, After obtaining a quality report in galaxy I found out that there is a difference between the mean and median at each cycle. How can this difference be reduced using galaxy? Thanks in advance Benjy

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How do I import protein coding genes location from UCSC?
by Himanshu Sharma 08 Nov '13

08 Nov '13

I have to import into Galaxy annotations of coding genes from the UCSC genome browser and then use the "Operate on genomic intervals" set of tools to remove transcripts that overlap with coding genes from my gtf file . How should I go about doing it?. Thanks, Himanshu

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Galaxy Pages - importing/downloading embedded data.
by Mohammad Heydarian 08 Nov '13

08 Nov '13

Hi All, Hope things are groovy. I am in the process of setting up a Galaxy page on the main server to host our NGS data. I am embedding the various datasets and they are showing up and viewable, but there is no way to import (or download) the data. Am I correct, or is the import button hidden on my screen? Would publishing the Page enable import of the data? Many thanks in advance, we are looking forward to utilizing Galaxy Pages and making our data accessible. Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 402 Biophysics Baltimore, MD 21205

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conditional statement in compute tool
by Leontovich, Alexey A., Ph.D. 08 Nov '13

08 Nov '13

Hello! I have the same question as Ido Tamir had about a year ago: Dec 07, 2012; 9:53am [Ido Tamir] <http://user.list.galaxyproject.org/template/NamlServlet.jtp?macro=user_node…> Ido Tamir<http://user.list.galaxyproject.org/template/NamlServlet.jtp?macro=user_node…> conditional in Compute tool Hi, is it possible to do a conditional in the compute tool? something like: "a" if c1 == 4 else "b" or if c1 == 4 "a" else "b" or c1 == 4 ? "a" else "b" thank you very much, ido Thank you very much, Alex

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Bowtie raw input
by Jonathan Glass 08 Nov '13

08 Nov '13

Hi There Im trying to map RNA-seq data to a reference genome in Galaxy (Main instance) using both Bowtie 1 and Bowtie 2. Im currently using publicly available data (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28755) which is not available in FASTQ format - only the raw sequences with the read count. Is there a way to set the input data for bowtie to raw, as is possible using the terminal? Or is there a way to convert a raw sequence to FASTQ (not sure if this would work, but it might be possible if I assigned accession numbers to each sequence and made all the quality scores identical)? Thanks very much Jonathan Glass Disclaimer - University of Cape Town This e-mail is subject to the UCT ICT policies and e-mail disclaimer published on our website at http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 650 9111. If this e-mail is not related to the business of UCT it is sent by the sender in the sender's individual capacity.

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