Hi, I have a local Galaxy instance. (http://bioanalysis.otago.ac.nz/ galaxy) A problem I'm having is when I try to extract a multiple alignment I get an error, "The MAF source specified (28_WAY_MULTIZ_hg18) appears to be invalid.," The background is that I have downloaded the alignment from http://hgdownload.cse.ucsc.edu/goldenPath and modified the maf_index.loc file according to the commented example. I'm new to python but I did have a look in the debugger and it seems to be missing an index file. The parameters it has loaded from maf_index.loc appear to be as expected. I'm guessing with more looking at the code it will become clear that a script to produce these indexes from mafs needs to be run. Or should these indexes be being built on the fly? Maybe someone can save me a load more digging? Thanks if you can! Cheers, Stewart -- Stewart Stevens Software Developer - Integrated Genomics University of Otago Department of Biochemistry Tel: +64(0)3 479 7863 Fax: +64(0)3 479 7866
Hi Stewart, You are correct in that you need to create indexes for the MAF files. A script to create indexes is included in the bx-python package (named maf_build_index.py in the scripts directory of this package), which is distributed as an egg with Galaxy. Dan
Hi,
I have a local Galaxy instance. (http://bioanalysis.otago.ac.nz/ galaxy) A problem I'm having is when I try to extract a multiple alignment I get an error, "The MAF source specified (28_WAY_MULTIZ_hg18) appears to be invalid.,"
The background is that I have downloaded the alignment from http://hgdownload.cse.ucsc.edu/goldenPath and modified the maf_index.loc file according to the commented example.
I'm new to python but I did have a look in the debugger and it seems to be missing an index file. The parameters it has loaded from maf_index.loc appear to be as expected. I'm guessing with more looking at the code it will become clear that a script to produce these indexes from mafs needs to be run. Or should these indexes be being built on the fly? Maybe someone can save me a load more digging? Thanks if you can!
Cheers,
Stewart
--
Stewart Stevens Software Developer - Integrated Genomics
University of Otago Department of Biochemistry Tel: +64(0)3 479 7863 Fax: +64(0)3 479 7866
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Stewart Stevens