Question: Data Files
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gravatar for Alastair Kerr
9.7 years ago by
Alastair Kerr30 wrote:
Hi, first a quick word of thanks to the galaxy devs: this is a great system thanks, we are using it to roll-out our own in-house tools/scripts. We are now in the about to gather the UCSC data files so that the rest of the tools (liftover, Fetch sequences/alignments etc) work. I am wondering whether there is an easy way of gathering this data? e.g. are there any wget /rsync scripts available or does each data source need to be added manually. thanks - Alastair -- Alastair Kerr, Ph.D., Bioinformatician, Wellcome Trust Centre for Cell Biology, 2.21, Michael Swann Building, Kings buildings, The University of Edinburgh, Edinburgh, EH9 3JR, UK Tel: 44-(0)131-650-7527 http://bifx1.bio.ed.ac.uk/ The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
galaxy • 661 views
ADD COMMENTlink modified 9.7 years ago by Nate Coraor3.2k • written 9.7 years ago by Alastair Kerr30
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gravatar for Nate Coraor
9.7 years ago by
Nate Coraor3.2k
United States
Nate Coraor3.2k wrote:
Hi Alastair, We don't really have an easy way to do this, as the data comes from a wide number of sources, made available via different methods. That said, I did write a perl script a few years ago to download sequences and alignments from UCSC. Note that it only downloads the axt's, and Galaxy now uses maf for pairwise alignments. http://www.bx.psu.edu/~nate/get_from_ucsc.pl --nate
ADD COMMENTlink written 9.7 years ago by Nate Coraor3.2k
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