question about executable binaries

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M. K. Raghuraman

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Apr 6, 2018, 1:49:10 PM4/6/18
to gen...@soe.ucsc.edu
Hi,

I am trying to use one of the executable binaries for Mac OS X from http://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/ (in particular, the bigwigtowig utility). However, every utility I try comes with a .dms file extension, and attempting to run the binary with no arguments just generates an error (“command not found”). I am issuing the command from within the directory containing the utility, so it’s not just a file path issue. What am I missing? Please help! I couldn’t find any solutions searching the web.

Thanks,
Raghu

*********************************
M. K. Raghuraman
Research Professor
University of Washington
Department of Genome Sciences Box 355065
Seattle WA 98195-5065

Phone +1 206 543 0334 (Office)
+1 206 543 9447 (Lab)
FAX +1 206 685 7301
email: ra...@u.washington.edu
*********************************

Hiram Clawson

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Apr 6, 2018, 2:09:00 PM4/6/18
to M. K. Raghuraman, gen...@soe.ucsc.edu
Good Morning Professor Raghuraman:

I'm not sure what you mean with the .dms file extension.
What procedure do you use to obtain the binary from
the URL address ?

After downloading the file, it should appear:

$ ls -og bigWigToWig
-rw-rw-rw- 1 923340 Apr 6 11:05 bigWigToWig

Then, set the execute bit on the binary:
$ chmod +x bigWigToWig
$ ls -og bigWigToWig
-rwxrwxrwx 1 923340 Apr 6 11:05 bigWigToWig

It should then run:
$ ./bigWigToWig
bigWigToWig - Convert bigWig to wig. This will keep more of the same structure of the
original wig than bigWigToBedGraph does, but still will break up large stepped sections
into smaller ones.
usage:
bigWigToWig in.bigWig out.wig
options:
-chrom=chr1 - if set restrict output to given chromosome
-start=N - if set, restrict output to only that over start
-end=N - if set, restict output to only that under end
-udcDir=/dir/to/cache - place to put cache for remote bigBed/bigWigs


These commands are run from the terminal application on the command line.

--Hiram
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