- galaxy-user - lists.galaxyproject.org

Galaxy source repository change
by Nate Coraor 05 Aug '08

05 Aug '08

Hello, If you simply use the Galaxy Main or Test sites hosted at PSU, you can safely ignore this message. It pertains to people who've checked out their own copy of Galaxy for development or local use. Galaxy development has recently moved source control systems, from Subversion to Mercurial. This means that anyone using a local copy of Galaxy will need to make some changes to be able to download future updates. The preferred method of obtaining Galaxy source is through Mercurial directly (the 'hg' command): hg clone http://www.bx.psu.edu/hg/galaxy galaxy_dist Tarballs are also available via the zip/gz/bz2 links here: http://www.bx.psu.edu/hg And the repository is mirrored in Subversion here: svn co http://www.bx.psu.edu/svn/galaxy galaxy_dist Unfortunately, modifications to local copies of Galaxy will need to be transferred from your old checkout to the new checkout. Please let us know via <galaxy-bugs(a)bx.psu.edu> of any issues. Thanks, and thank you for using Galaxy. --nate

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Importing features from BioMart
by Alexandre Gattiker 04 Aug '08

04 Aug '08

Hello, I would like to import features from BioMart into galaxy. However the 'embedded' BioMart view yields an HTML table. How do I convert that to GFF or BED? Best regards -- -------------------------------------------------------- Alexandre Gattiker Bioinformatics & Biostatistics Core Facility EPFL School of Life Sciences / Faculté des Sciences de la vie FSV http://people.epfl.ch/Alexandre.Gattiker

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Synteny
by Claudio Casola 30 Jul '08

30 Jul '08

Hello, I found Galaxy extremely helpful in the past months and I have an issue that could again be solved using your wonderful platform. I am playing with a bunch of sequences (genome coordinates) from the human genomes that I obtained from some blast searches. I would like to see if these exact sequences are shared by (in synteny with) chimp, orang and macaque. I got MAF blocks from Galaxy and played with them, but I don't see an easy solution. It would be great if you have some suggestion about how to work with synteny using Galaxy, if possible. Thanks a lot! Claudio Casola Postdoctoral fellow, Hahn Lab Department of Biology 1001 East Third Street Bloomington, IN 47405-3700 Indiana University 812-856-7016 ccasola(a)indiana.edu

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Lift-Over update with orangutan assembly
by Claudio Casola 22 Jul '08

22 Jul '08

Hello, Is there any chance to have the orangutan assembly included in the Lift-Over menu any time soon? That would be great! Thanks, Claudio Casola Postdoctoral fellow, Hahn Lab Department of Biology 1001 East Third Street Bloomington, IN 47405-3700 Indiana University 812-856-7016 ccasola(a)indiana.edu

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Interfacing galaxy with a local copy of the UCSC genome browser
by Tim Yu 22 Jul '08

22 Jul '08

hi there, We've just set up a local instance of Galaxy to serve as a framework for adding custom tools. We also have a local server running a copy of the UCSC genome browser with our own data on it. Is there a way to configure Galaxy to interface with our in-house UCSC server, instead of (or in addition to) the central site? Is this, by the way, the approved place to direct such questions? I didn't see an email address for support on the main site or wiki. Thanks! Tim Yu

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How to get output from Galaxy
by i rezwan 02 Jul '08

02 Jul '08

Hi, I am a very new user at Galaxy. I have downloaded the Galaxy and am running it in my computer locally. Actually I am developing a script in python which I want to integrate with Galaxy on TEST basis. I can add the tool and run the program very well by following Galaxy tutorials. But the one problem that I am facing is, I don't know how to get an output from Galaxy. I will prefer to get the output in a text file locally mentioned by user (to make it a bit more user friendly). I have examined through the example .xml file and also seen the galaxy screencast, but still unable to generate an output file for my tool. I'm using browser: mozilla 3.0 and OS: ubunutu linux. Thanks in advance. Regards /Faisal -- Faisal Ibne Rezwan BioComputation Group, Rm # 1E114 Science and Technology Research Institute University of Hertfordshire College Lane Campus Hatfield, AL10 9AB UK Tel +44 (0)1707 286356

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Re: [galaxy-user] local sequence storage
by David Goodstein 24 Jun '08

24 Jun '08

We identified our local sequence file in tool-data/faseq.loc. However, that file never shows up as an option under the "database/ build" pulldown (when we "pencil" edit a dataset). What additional configuration is necessary to have our local files show up in the database/build pulldowns? regards, David Goodstein > UCB Center for Integrative Genomics > > On 24 Jun 2008, at 16:47, Rochak Neupane wrote: > >> ---------- Forwarded message ---------- >> From: Greg Von Kuster <ghv2(a)psu.edu> >> Date: Wed, Jun 18, 2008 at 1:06 PM >> Subject: Re: [galaxy-user] local sequence storage >> To: Rochak Neupane <rneupane(a)berkeley.edu> >> Cc: galaxy-user(a)bx.psu.edu >> >> >> Hello Rochak, >> >> Yes, this is certainly possible. The Galaxy distribution is >> configured to look in the ~/tool-data directory for files which point >> to your locally cached sequences. See the "tool_data_path" >> setting in >> the Galaxy config ( universe_wsgi.ini ). This directory contains >> sample ".loc.sample" files that are included in the distribution to >> provide information about how to point the ".loc" versions of the >> same >> files to your own locally cached sequences. The comments at the >> beginning of each of these files provides this information. >> >> Greg Von Kuster >> Galaxy Development Team >> >> >> Rochak Neupane wrote: >>> >>> Hello, >>> >>> I recently started using galaxy. I installed a local copy of >>> galaxy, and am wondering how I can add our own sequences so that >>> galaxy understands them when fetching. So instead of fetching >>> from PSU it'll look at a local source. Is this doable? If so, >>> how can I configure this? >>> >>> Thanks, >>> Rochak >>> _______________________________________________ >>> galaxy-user mailing list >>> galaxy-user(a)bx.psu.edu >>> http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user >>> >>> >>> >

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local sequence storage
by Rochak Neupane 18 Jun '08

18 Jun '08

Hello, I recently started using galaxy. I installed a local copy of galaxy, and am wondering how I can add our own sequences so that galaxy understands them when fetching. So instead of fetching from PSU it'll look at a local source. Is this doable? If so, how can I configure this? Thanks, Rochak

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TFBS search
by Anton Nekrutenko 13 Jun '08

13 Jun '08

Tony: We do not have a specific tool for clustering of TFBS. However, if you know good open source tools that can be used for that purpose we will consider integrating them into Galaxy framework. Thanks, anton > Hello, > > I am just starting to use galaxy, and I was wondering if there is a > simple way to search genome wide for clustering of custom > transcription > binding sites (preferentially with weight matrixes). All other > programs > (~10) I have used till so far have their limitations, either the > length > of the sequence they can handle is rather limited, they use only in > house transcription factor binding sites or they are not able to check > for evolutionary conservation. > > Thanks, > > Tony Anton Nekrutenko Asst. Professor Department of Biochemistry and Molecular Biology Center for Comparative Genomics and Bioinformatics Penn State University anton(a)bx.psu.edu http://nekrut.bx.psu.edu 814.865.4752

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Re: [galaxy-user] galaxy query
by Anton Nekrutenko 13 Jun '08

13 Jun '08

Gareth: Sorry for the delay. There are two way of dealing with this. I attached a link to a screencast that highlights the two approaches. In the first, you must upload datasets into galaxy and simply run the join tool. The second approach is to use a new galaxy tool called "Annotation profiler". It allows you to compare your set of genomic features against the entire UCSC database in a single pass (at this point it can only be used against hg18 annotations). Try it out and let us know if you have any further questions. The movie is here: http://screencast.g2.bx.psu.edu/SNPs_TFBS.mov anton On Jun 5, 2008, at 11:21 AM, Whiteley, Gareth wrote: > Hi Anton, > That's exactly what I'm trying to do. I'm also trying to intersect > the SNPs with the UCSC tracks - CpG islands, T-ScanS miRNA, PicTar > miRNA - and any other regulatory sequence data. > A step-by-step demo would be wonderful. > Kind Regards, > Gareth > > -----Original Message----- > From: Anton Nekrutenko [mailto:anton@bx.psu.edu] > Sent: 05 June 2008 15:58 > To: Whiteley, Gareth > Cc: galaxy-user(a)bx.psu.edu > Subject: Re: [galaxy-user] galaxy query > > Gareth: > > You can do all the intersects within Galaxy. If I understand > correctly you are trying to intersect conserved TFBPs with SNPs? > Right? > > Let me know and will send you a detailed step-by-step demo. > > anton > galaxy team > > On Jun 5, 2008, at 8:02 AM, Whiteley, Gareth wrote: > >> Hello, >> >> >> >> If I was to choose the following search criteria Group:all tracks, >> track:SNP, region: chr5:7922217-7954237, then click INTERSECT and >> choose Group:all tracks, track:TFBS conserved and select GTF output >> format. This example searches for any SNPs that are in the >> Transcription factor binding sites within the genomic region that >> codes for the MTRR gene, but the output does not tell me that the >> SNP rs6868871 is found in the TFBS V$58_01 914, I have to work that >> out for myself by then searching the whole table again but from a >> TFBS start point and intersecting with SNPs. >> >> >> >> I am trying to use galaxy to Join two Queries side by side on a >> specified field. I am trying to relate SNPs to the TFBS they are >> associated with. For example, SNP rs6868871 is found in TFBS V >> $58_01 914. However, i can not seem to get galaxy to work, i think >> this is because the SNP site is something like this ‘165878639 - >> 165878640’ and a TFBS site is something like this ‘165878630 - >> 165878641’ and although the positions overlap, galaxy can not tell >> that. Is this the case? Or do you know of how i can get around it? >> Regards,Gareth Whiteley >> >> >> Gareth Whiteley >> >> University of Liverpool >> >> Department of Pharmacology and Therapeutics >> >> The Sherrington Buildings >> >> Ashton Street >> >> Liverpool L69 7GE >> >> >> >> Tel: 0151 795 4224 >> >> E-mail: g.whiteley(a)liverpool.ac.uk >> >> >> >> _______________________________________________ >> galaxy-user mailing list >> galaxy-user(a)bx.psu.edu >> http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user > > Anton Nekrutenko > Asst. Professor > Department of Biochemistry and Molecular Biology > Center for Comparative Genomics and Bioinformatics > Penn State University > anton(a)bx.psu.edu > http://nekrut.bx.psu.edu > 814.865.4752 > > > > Anton Nekrutenko Asst. Professor Department of Biochemistry and Molecular Biology Center for Comparative Genomics and Bioinformatics Penn State University anton(a)bx.psu.edu http://nekrut.bx.psu.edu 814.865.4752

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