- galaxy-user - lists.galaxyproject.org

How does Galaxy Obtain Transcription Regulation Region?
by Edward WIJAYA 21 Nov '07

21 Nov '07

Dear all, In Galaxy website http://main.g2.bx.psu.edu/, especially under: Get Encode Data -> Transcription Regulation I would like to know the procedure of Galaxy of obtaining the region of all the transcription regulation. For example the entry: AFFX_Brg1_HL60_seqsp (20060206) We are aware that it comes from ENCODE, but not sure the exact procedure of obtaining it. Is it from Chip-CHIP? Or something else? There seem to be no documentation on this. -- Edward ------------ Institute For Infocomm Research - Disclaimer -------------This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you.--------------------------------------------------------

1 0

help about using sixpack and get orf (Genomic assignment)
by ZHENHAI ZHANG 12 Sep '07

12 Sep '07

Dear all, So sorry to bother you if you are not interested! I'm doing my genomic assignment whichi is trying to find the ORF of 10,000-bp E. coli genome segment. The thing is, I can not find the graphic out put. Several out formats have been tried including FASTA, CODATA, but all of them only renderred me the txt format result. Anybody knows which format is the ORF in graphic view? Thanks a lot! Zhenhai

1 0

ACD2XML
by Marc Logghe 13 Aug '07

13 Aug '07

Hi, (not sure whether this should go to the user or the dev list, so please forgive if I have chosen the wrong one ;-) First I had some trouble getting galaxy to work. It all had to do with the proper configuration of python. But google found a thread on the galaxy mailing list; this did the trick (somebody might find it useful): ./configure --enable-unicode=ucs4 I have 2 questions: 1) is there a script to convert EMBOSS' ACD format to galaxy XML ? It is just a matter of 'write-once-use-many-times'. If a tool is described in ACD you can easily wrap it into a webservice using SOAPLAB, or into a galaxy app, or ... 2) how can you run galaxy with apache ? Thanks and regards, Marc

1 0

Licensing terms?
by Michael Pheasant 23 Jul '07

23 Jul '07

Just wondering what the licensing terms were, couldnt find them anywhere. Cheers Mike __________________________________ Michael Pheasant, PhD Bioinformatics Research Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4067 Australia P: +61-7-3346-2080 M: +61-405-679-541 http://www.imb.uq.edu.au

1 0

request for the platypus genome database
by Iris Vargas Jentzsch 18 Jul '07

18 Jul '07

Dear Galaxy team, I would really appreciate if you could make the Platypus (Ornithorhynchus anatinus v5.0.1)database available among the genome options in the Galaxy portal. I need to do some genomic interval operations in databases for this genome, and I can't use this tool if the genome is not specified. Thank you, Iris ====================================== Iris M. Vargas Jentzsch School of Biological Sciences University of Canterbury Private Bag 4800 Christchurch - New Zealand phone: +64 (0) 3 364 2987 ext 7048

2 1

Install problem: SQLite DBAPI not found
by Ross Lazarus 22 May '07

22 May '07

Thomas, this problem bit me too and you'll probably get half a dozen identical responses :) - you need to use a Python2.4 compiled with the '--enable-unicode=ucs4' flag - see the # 15 in http://g2.trac.bx.psu.edu/wiki/FAQ As I understand it, this isn't a problem for Mac users but will affect most linux distributions using the system python, so FWIW, I think this is going to annoy enough potential developers to be worth some effort to solve. Unfortunately, aside from a separate release with all-ucs2-compatible eggs for linux, I'm not sure there's an obvious solution.... > Message: 7 > Date: Fri, 16 Feb 2007 15:49:40 +0100 > From: Thomas Junier <Thomas.Junier(a)medecine.unige.ch> > Subject: [galaxy-user] Install problem: SQLite DBAPI not found > To: galaxy-user(a)bx.psu.edu > Message-ID: <200702161549.40705.thomas.junier(a)medecine.unige.ch> > Content-Type: text/plain; charset=us-ascii > > > Hi folks, > > First of all, I'm not sure if this is the right list to post to, so my > apologies if it isn't. > > I'm trying to install Galaxy on my machine, according to the instructions at > http://g2.trac.bx.psu.edu/wiki/HowToInstall. > > Everything works fine until I try to do: > > $ sh run.sh > > at which point I get a Python traceback in which the last call raises the > following error: > File > "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.3.3-py2.4.egg/sqlalchemy/engine/strategies.py", > line 52, in create > sqlalchemy.exceptions.InvalidRequestError: Cant get DBAPI module for dialect > '<sqlalchemy.databases.sqlite.SQLiteDialect object at 0x2a983a6fd0>' -- Ross Lazarus MBBS MPH, Director of Bioinformatics Channing Laboratory, 181 Longwood Ave., Boston MA 02115, USA. Voice: +617 525 2730 Fax: +617 525 0958

1 0

[Fwd: Re: [Genome] Chimp assembly 2 pairwise alignments]
by Daniel Gaffney 09 May '07

09 May '07

Hi there, further to the query below, I'm trying to follow the steps outlined in the email below to send the 28way genome alignment to galaxy. I'm currently waiting on this job to complete on galaxy - as mentioned below, it does take some time, but can anybody give me an idea of how long this might take (its already been running for a while)? Is it likely to be minutes/hours/days? Cheers Dan -------- Original Message -------- Subject: Re: [Genome] Chimp assembly 2 pairwise alignments Date: Mon, 07 May 2007 16:00:42 -0700 From: Archana Thakkapallayil <archanat(a)soe.ucsc.edu> Reply-To: archanat(a)soe.ucsc.edu To: Daniel Gaffney <daniel.gaffney(a)mcgill.ca> CC: genome(a)soe.ucsc.edu References: <463F58BC.8050306(a)mcgill.ca> Hello Dan, Here is the response from one of our engineers: I think that the easiest way to do this is using Galaxy 2. This method will involve using the pairwise alignments extracted from the multiz multiple alignment (from the Conservation track). This is a best in genome alignment with the best aligning region for chimp aligned to each region of the human genome. This means that there is less information than in the chain track which contains all alignments (passing certain criteria) of the chimp genome to each region of the human genome. If this is ok, then you can use Galaxy by going to: http://test.g2.bx.psu.edu/ You will need to use the test version of Galaxy because this has the option of using our genome-test server. There are only panTro1 alignments in the 17-way alignment on hg18, but there are panTro2 alignments in the 28-way on hg18. Be aware that this our test server and that some of the data here (including the 28-way alignment) has not gone through our rigorous quality assurance checks. Here are the instructions to follow: 1) Go to http://test.g2.bx.psu.edu/ 2) Click on "Get Data" in the pane at the left side. 3) Click on "UCSC Test table browser" link in the expanded list. 4) In the middle an interface will appear that looks like the Table Browser. You can then select the Human Mar 2006 (hg18) assembly. Select Comparative Genomics as the group, 28-way Cons as the track and "multiz28wayAnno" as the table. Make sure that genome is selected as the region. Then select MAF as the output type. 5) Check the box that says "Send output to Galaxy". Press "get output" button and the "Send query to Galaxy" button. (Up to this point can also be done in the Table Browser on genome-test). Getting the MAF output seems to be rather slow. 6) Then from the "Get Data" menu, select "Upload File" and you can paste in or upload a file of the regions for which you want alignments (position or BED format is fine). 7) Then click on the "Fetch Sequences and Alignments" in the left pane. >From the expanded list, select "Extract MAF blocks". First select the genomic intervals (query 2) and then press "Next Step" and select the MAF format output (query 1). The result is the multiple alignments for the regions defined by the user. 8) To limit this to only the pairwise alignment between human and chimp, select the "Maf Limit to Species" from the left pane and choose hg18 and panTro2. If you have questions about using Galaxy, you can contact their help desk: galaxy-user(a)bx.psu.edu If you would rather use the human/chimp chain or net alignments to get alignments for specific regions of the human genome, then we can walk you through using several of the programs that we have available for command line use in order to extract human/chimp pairwise alignments from this data. I hope this information is helpful to you. Let us know if you have further questions. Regards, Archana UCSC genome Bioinformatics Group Daniel Gaffney wrote: > Hi there, > I have ~ 1500 small regions in the human genome, for which I would like > to get the human-chimp > pairwise alignment for the latest chimp assembly. However, I'm having a > little trouble in figuring out the best > way to do this - can this be done locally? Or is there a batch > submission tool that I can retrieve all alignments > from UCSC directly - I've tried the table browser, but I can't seem to > get the specific region I want (i.e. if i select the chimp chain > track, and retrieve sequence, I get the the alignment of that entire > region, not just the region corresponding to the coordinates I've > entered). Any ideas? > Cheers > Dan > > -- ================================================================ Daniel Gaffney McGill University and Genome Quebec Innovation Centre 740 ave Dr Penfield Rm 7208 Montreal (Quebec) H3A 1A4 http://dutch.cap.ed.ac.uk/ Tel: +1 514 398 3311 ext: 04592 Fax: +1 514 398 1790 ================================================================

2 1

PHYLIP fdrawgram
by Ying Zhang 05 Apr '07

05 Apr '07

Hi, there, I tried this fdrawgram several times recently. I must say that is a "slow" tool. For a 45 species tree, it took more than 10 minutes to generate the png file. I found a better tool online at http://cgi-www.daimi.au.dk/cgi-chili/ phyfi/go . The cons are: 1. first, 2. colorful, 3. multi-format (jpg, png, etc) for download. So if we replace the old PHYLIP drawing program with this new one, that will be much better. Best, Ying

1 0

My solution Fwd: A problem in main.g2.bx.psu.edu
by Ying Zhang 03 Apr '07

03 Apr '07

I solved this problem by clearing my "cookies" and "cache". In this case, "reloading" didn't work. Begin forwarded message: > From: Ying Zhang <yuz111(a)psu.edu> > Date: April 3, 2007 12:01:03 PM EDT > To: galaxy-bugs(a)bx.psu.edu > Cc: Anton Nekrutenko <anton(a)bx.psu.edu> > Subject: A problem in main.g2.bx.psu.edu > > Hi, there, > > I am not sure whether this is a problem in test.Galaxy. > > Today, I opened galaxy main and a UCSC window browser at the same > time. You can see the screen shot for the two browser tabs sitting > together. And in UCSC Browser I searched for a Known Gene -- Zfpm1. > > > Then, I went back to Galaxy to "get data" from UCSC Main table > browser, if u r careful enough you can see the "click" (dotted-line > square). But the middle frame came out not to be the table browser > but the page I opened in the independent browser. > > So seems Galaxy doesn't work well if you open an independent UCSC > browser at the same time. > > > Best, > Ying >

1 0

Announcing New Galaxy tool
by yizhang＠bx.psu.edu 01 Mar '07

01 Mar '07

Dear Galaxy Users, We are pleased to announce the new direct link to the UCSC Table Browser is available in the Get Data section. The Galaxy Development Team

1 0