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

Can I create sub workflows in Galaxy?
by Sonali Amonkar 16 Jan '11

16 Jan '11

Hi, Am a newbie to Galaxy and was looking for some basic answers about Galaxy's offerings till date: 1. Is there any way that I can plug in a small work flow inside another work flow (sub work flow) in Galaxy? 2. Is there any step wise process documented somewhere to install Galaxy on Windows? 3. Does Galaxy have any commercial support offered? 4. Which languages can the Galaxy tools be built in? (Java, C, C++, etc) ? 5. Does Galaxy have any monitoring tools to keep a check on the process and the statistics at run time? Answers to any questions above will be greatly appreciated. Thank you, Sonali Amonkar DISCLAIMER ========== This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails.

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"group"
by Keith E. Giles 14 Jan '11

14 Jan '11

Everytime I try to run the "group" function, under the "join subtract group" menu, I get an error. the application never even loads. any ideas why?

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cancel
by Eberhard Schneider 14 Jan '11

14 Jan '11

Please cancel my name from the user list. Thanks. * * Dr. Eberhard Schneider Kurze Straße 17 65451 Kelsterbach am Main Tel. (privat): +49 / 6107/ 968670 Labor: +49 / 9131 / 3188793 mobil: + 49 / 173 / 1573761

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Ordering Workflow Inputs on Run?
by Jesse Erdmann 13 Jan '11

13 Jan '11

Hi, I have a workflow that requires a large number of files that happen to come in pair but are processed by different tools. One tool allows the user to specify inputs 1...N and produce a single output. The other tool takes a single input and produces a single output. In the simplest example say we have two pairs, the workflow looks something like: Set1.TypeA \ TypeA.Output Set2.TypeA / Set1.TypeB - Set1.TypeB.Output Set2.TypeB - Set2.TypeB.Output However when the user runs the workflow the inputs are requested in random order. While the inputs are labelled this can be confusing. It would be nice to be able to order the inputs for the workflow to always be something like: Set1.TypeA Set1.TypeB Set2.TypeA Set2.TypeB I searched the mailing lists and saw a request for something like this in 2008, but as far as I can tell nothing has ever been implemented. Is there a solution I am missing or do I need to implement a wrapper tool that would do this as opposed to using a workflow? Thanks! -- Jesse Erdmann Bioinformatics Analyst Masonic Cancer Center University of Minnesota jerdmann(a)umn.edu 612-626-3123 jesse(a)jesseerdmann.com Twitter: http://twitter.com/jesseerdmann

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Re: [galaxy-user] [Genome] Problems with MAF blocks from Galaxy
by James Taylor 12 Jan '11

12 Jan '11

Excerpts from ele.gatti(a)tiscali.it's message of Wed Jan 12 15:19:36 +0000 2011: > I have a problem with MAF blocks using Galaxy. Hi Elena, I'm copying the galaxy-user list since this is a Galaxy related question. > 1) the starting position of the MAF block extracted from Galaxy is > shifted of one position downstream; If you enter a region into the position box in the genome browser, it will interpret it as one-based. However, when working with bed files in Galaxy (and the genome browser) the intervals are zero-based. This is likely the problem. > 2) the number of species displayed is not 28 in both Maf (from Galaxy) > and Genome Browser. This is entirely expected. If the alignment procedure does not identify putatively orthologous sequence in the other species, no sequence will be shown in the MAF output for that species. There are several reasons this could happen, including: no significant pairwise local alignment found by lastz, or a signifigant alignment found, but eliminated by the chaining/netting procedure. > 3) the alignment seems to be different (for example, species that have > aligned sequences in the Genome Browser, are not in the MAF block > retrieve from Galaxy). Can you point out an example of this? In particular, are you sure you are using the same original alignments in Galaxy and the Genome Browser? Thanks, James -- James Taylor, Assistant Professor, Biology / Computer Science, Emory University

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Re: [galaxy-user] Converting pileup files to wig/bigwig
by Nick Schurch 12 Jan '11

12 Jan '11

HI, I can't find any mention of a program called 'wiggles' in the source code distribution of bowtie 0.12.7, or out install of 0.12.3. Could someone point me to the location of the program in the bowtie file structure, or failing that a website for it? -- Cheers, Nick Schurch Data Analysis Group (The Barton Group), School of Life Sciences, University of Dundee, Dow St, Dundee, DD1 5EH, Scotland, UK Tel: +44 1382 388707 Fax: +44 1382 345 893

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Can I plug in Java code tools in Galaxy?
by Sonali Amonkar 12 Jan '11

12 Jan '11

Hi, (Am new to Galaxy) I am analyzing the Galaxy tool to find out the feasibility of plugging in existing Java tools, along with some Galaxy in-built tools, to implement a simple work flow. Is this possible? If yes is there a guide/tutorial of how I can do it? Thank you, Sonali Amonkar DISCLAIMER ========== This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails.

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Scatter and gather workflow
by Sonali Amonkar 12 Jan '11

12 Jan '11

Hi, Am a complete newbie, at investigating Galaxy. I found my question(Scatter-Gather data) in the mailing list about 10 months ago, but did not see any action on it hence asking again. I want to create a sub work flow where, 1. I scatter/split a file into little files, 2. Find the occurrence of each sequence in the little files, within a huge reference file and recreate the little files with the index positions appended against each sequence, as to where they appeared in the huge file. 3. Gather back the little files into a whole big file. Can you tell me if it is possible to do this in Galaxy? If yes, are there any existing/in-built tools that I can use to do the same? Thank you, Sonali Amonkar DISCLAIMER ========== This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails.

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Galaxy does not startup on machine with no Internet access
by Sonali Amonkar 12 Jan '11

12 Jan '11

Hi, I'm trying to install and run galaxy-dist-8729d2e29b02 on a Linux RHEL 5.5 box. This machine has no direct access to the Internet. I followed the steps listed on the page https://bitbucket.org/galaxy/galaxy-central/wiki/Config/Eggs to download the eggs offline and placed them in the correct location. Now when I try to run Galaxy (sh run.sh), it appears to be stuck trying to contact http://128.118.200.71 - this was seen through netstat. [workflow@vm-ps4121 galaxy-dist]$ netstat -antp | grep tcp (Not all processes could be identified, non-owned process info will not be shown, you would have to be root to see it all.) tcp 0 1 10.88.176.157:44233 128.118.200.71:80 SYN_SENT 5796/python Why does galaxy try to connect to this server when all the eggs are already updated? My questions are: 1. Can galaxy-dist-8729d2e29b02 can be run on a box with no Internet access? 2. How does one enable this no-Internet-available setting in galaxy-dist-8729d2e29b02? Thank you for your time. Regards, Sonali Amonkar DISCLAIMER ========== This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails.

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Converting pileup files to wig/bigwig
by Swathi Ashok Kumar 12 Jan '11

12 Jan '11

Hi, I was wondering if you have a tool that converts pileup files to variable step wigs so I can view coverage on UCSC. At present I have a rnaseq data mapped using bowtie. I've converted them to bam and generated pileups. thanks -- Swathi A. Kumar Interdepartmental Program in Genetics Center for Comparative Genomics Huck Institute of Life Science email : sak980(a)psu.edu tel : +1 814 441 8120

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