bedGraphtobigWig utility not executable

[Xu, Cindy]

Dear UCSC Genome Browser Team,

 

I recently downloaded the linux.x85_64 binary utility, bedGraphtoBigWig (http://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/bedGraphToBigWig).

 

However, this utility is not executable and when I peek into the file it appears as random characters rather than the expected script. See photo below.

 

Is the binary corrupted and if so, could you please update the file and/or send me the appropriate utility? Thanks!

 

Best,

Cindy

 

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[Gerardo Perez]

Hello Cindy,

Thank you for your interest in the UCSC Genome Browser and for your question regarding the bedGraphtoBigWig utility.

The link you shared is for the macOS. To download the Linux.x86_64 binary utility you can use the following link:
http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig

Once you download it, you need to change the system's permission to run the program. We have the following directions at the top of our utilities directory:

In order for your computer to run a freshly downloaded utility, you will need to update the file
system permissions to allow your operating system to run the program.
To make utilities usable, turn on its 'executable' bit:
$ chmod +x ./filePath
$ ./filePath/utility_name
See also: http://en.wikipedia.org/wiki/Chmod

I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

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[Xu, Cindy]

Dear Gerardo,

 

My mistake but the version I do have downloaded is the Linux.x86_64 binary utility.

 

I’ve also turned on the executable bit and added the utility to my bash profile but the command is either not found or it cannot be executed. See below for my command line prompts.

 

[cx026@eris1n3 test]$ bedGraphToBigWig

-bash: bedGraphToBigWig: command not found

[cx026@eris1n3 test]$ bash bedGraphToBigWig

bedGraphToBigWig: bedGraphToBigWig: cannot execute binary file

 

I am running the utility on a user account on a remote Linux cluster. Further advice is appreciated.

 

Best,

Cindy

 

From: Gerardo Perez <gpe...@ucsc.edu>
Date: Thursday, January 21, 2021 at 4:25 PM
To: "Xu, Cindy" <CX...@mgh.harvard.edu>
Cc: "gen...@soe.ucsc.edu" <gen...@soe.ucsc.edu>
Subject: Re: [genome] bedGraphtobigWig utility not executable

 

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[Gerardo Perez]

Hello Cindy,

Thank you for your follow up question regarding the bedGraphtoBigWig utility.

If the directory containing the bedGraphtoBigWig utility is not defined inside of your PATH variable, you will have to specify the location of the tool before your system can run the program. For example, if your current working directory contains the bedGraphtoBigWig utility, then you can execute the utility by running:

$ ./bedGraphToBigWig in.bedGraph chrom.sizes myBigWig.bw

If the bedGraphToBigWig utility is in a different directory then you will need to use the full path to the directory that contains bedGraphToBigWig.

A quick way to verify if the utility is defined in your PATH variable is to use the "which" command, i.e.,

$ which bedGraphToBigWig

Or print out the PATH variable:

$ echo $PATH

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly-accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genome Browser