November 2007 - galaxy-user - lists.galaxyproject.org

Galaxy installation
by Gerard Schaafsma 27 Nov '07

27 Nov '07

Hi, I am a Bioinformatics student (MSc) at VU university Amsterdam, and currently working as a trainee at Leiden University Medical Center. I had a lot of trouble installing galaxy, but finally found out that I had an 'old' version of pysqlite: /usr/lib/python2.4/site-packages/pysqlite- 1.0.1.egg-info I downloaded a newer version somewhere: pysqlite-2.3.4.egg-info and installed it in the same directory, but that still didn't do the trick Then I removed the old 1.0.1 package (actually I renamed it), and then all things worked, but I don't think this is the proper way to do it. Does anyone have suggestions how to do this the right way? I installed this on a PC which runs under Linux/Ubuntu 7.10 operating system Regards, Gerard Schaafsma Amsterdam, The Netherlands

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cluster operation is still in test?
by xu_jianzhen 22 Nov '07

22 Nov '07

Hi,galaxy users, hi,everyone. I am a member of GIBH,Chinese Academy of Science. I found the Operate on Genomic Intervals :cluster operation is in test version but not in main version. So how well does it if i use it now? Regards, Xu Jianzhen GIBH,CAS

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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.--------------------------------------------------------

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