bedGraphToBigWig : command not found

Question

[anatolybridge]

I have a problem with bedGraphToBigWig.

The code used to work, but today it started to output 'command not found' for no good reason.

I did

chmod +x ./filePath 
./filePath/utility_name

To be more precise, that's what i did exactly:

chmod +x /home/anatoly/Epigenetics/Internship/assignment/
/home/anatoly/Epigenetics/Internship/assignment/bedGraphToBigWig

and it printed the usage message, and then I tried running the code, but it didn't work:

    bedGraphToBigWig v 4 - Convert a bedGraph file to bigWig format.
usage:
   bedGraphToBigWig in.bedGraph chrom.sizes out.bw
where in.bedGraph is a four column file in the format:
      <chrom> <start> <end> <value>
and chrom.sizes is a two-column file/URL: <chromosome name=""> <size in="" bases="">
and out.bw is the output indexed big wig file.
If the assembly <db> is hosted by UCSC, chrom.sizes can be a URL like
  http://hgdownload.soe.ucsc.edu/goldenPath/<db>/bigZips/<db>.chrom.sizes
or you may use the script fetchChromSizes to download the chrom.sizes file.
If not hosted by UCSC, a chrom.sizes file can be generated by running
twoBitInfo on the assembly .2bit file.
The input bedGraph file must be sorted, use the unix sort command:
  sort -k1,1 -k2,2n unsorted.bedGraph > sorted.bedGraph
options:
   -blockSize=N - Number of items to bundle in r-tree.  Default 256
   -itemsPerSlot=N - Number of data points bundled at lowest level. Default 1024
   -unc - If set, do not use compression.

 

~/Epigenetics/Internship/assignment$ bedGraphToBigWig tl.bedgraph hg38.chrom.sizes tl.bw
bedGraphToBigWig: command not found

So, I take it I gave the right path to the utility because the usage message printed, yet the result was 'command not found' message.

[venu]

Try this

./bedGraphToBigWig tl.bedgraph hg38.chrom.sizes tl.bw

Also do this before trying above command,

chmod +x /home/anatoly/Epigenetics/Internship/assignment/*

Not sure your command chmods all contents of the directory.

[GenoMax]

If you wish to use bedGraphToBigWig without specifying full or relative paths then you need to ensure that the directory containing that executable is added to your $PATH by doing export PATH=$PATH:/full_path_to_executable.

[anatolybridge]

I've tried both './bedGraph...' and 'PATH=$PATH...' methods and they both worked like a charm, thank you! Though I run into 'access denied' when tried to execute the tool after adding the $PATH, but then managed to solve it by typing chmod +x ./bedGraphToBigWig

Overall, the problem is solved, thank you very much!

[Ram]

Are file and path 2 arguments to chmod or are you passing in a file_path? Similarly, does that change your second command?

Can you post the actual commands and error messages?

[anatolybridge]

I've edited the question to make it more clear.