ucsc-bedgraphtobigwig installed but not working -bash: bedGraphToBigWig: command not found

Question

[enjolras]

I am trying to convert a bedgraph file to bigwig format through the method described here: Converstion of BED with scores into bigWig I had done this successfully many times on another computer, but today I had to install again everything. in order to install the bedgraphtobigwig tool, I installed Anaconda and followed the indications here presented: https://anaconda.org/bioconda/ucsc-bedgraphtobigwig. If I type conda list on my terminal I can see the package being present; nevertheless, if I then try to use the tool, only the following message is prompted: -bash: bedGraphToBigWig: command not found Has anyone incurred in this problem before? Any help is much appreciated!

[enjolras]

I also tried by installing the binaries as explained in UCSC website at example3: https://genome.ucsc.edu/goldenpath/help/bigWig.html#Ex3, but still with no success.

[e.rempel]

From the top of my head, try

ucsc

Followed by TAB button. It could be that the installed commands have “ucsc” prefix

[enjolras]

no, unfortunately, it is not present neither as bedGrapgToBigWig nor as ucsc-bedgraphtobigwig (even though the second one is listed among the conda packages)

[e.rempel]

This is really strange, I tried on my computer

conda install -c bioconda ucsc-bedgraphtobigwig

and it worked. It was installed in ~/miniconda3/bin and I could execute "bedGraphToBigWig". One thing you could try (sorry, maybe you have checked it already) whether the path to your conda is in the $PATH (echo $PATH).

[enjolras]

If I check the $PATH I obtain this: /Library/Frameworks/Python.framework/Versions/3.9/bin:/opt/anaconda3/condabin:/Library/Frameworks/Python.framework/Versions/3.6/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/opt/X11/bin:/Library/Apple/usr/bin though I am not so sure what to gather from this..

[e.rempel]

Interesting that your conda was apparently installed in /opt. One more thing: could you run

find / -name 'bedGraphToBigWig'

You will receive a lot of Operation not permitted but if bedGraphToBigWig is installed, we will see where it is. Then we have to adjust your $PATH.

[enjolras]

So, it was a lot of operation not permitted and permission denied as you said, but at the end also:

/opt/anaconda3/bin/bedGraphToBigWig

/opt/anaconda3/pkgs/ucsc-bedgraphtobigwig-377-h516baf0_1/bin/bedGraphToBigWig

btw thank you so much for all your help..!

Answer 1

[e.rempel]

So there are two possibilities:

• using absolute path to bedGraphToBigBig: /opt/anaconda3/bin/bedGraphToBigWig
• (better one) add /opt/anaconda3/bin to your PATH (look this link)