How to add MUSCLE to my search path in Win7 and run demo("pca") successfully?

[Cheng]

I put muscle.exe into my folder and added E:\OneDrive\UCL\PhD\Experiment\Bio3D\MUSCLE\ into the Path by following here.

However, when calling demo("pca") in R, the muscle still could not be found. So how to properly install muscle?

This link seems only for the using, not installing on Windows

After running demo("pca"):

[Cheng]

It works now, simply close the RStudia and restart it again!

[Cheng]

update the RStudio by closing and opening it again!

[Barry Grant]

Thanks for posting and I am glad you were able to get it working. However, we probably should try to make this procedure easier for users in the future and ultimately not require the external muscle call. This is a good reminder!

[Cheng]

Thank you Grant! Hope it can be easier for us in the future!

[Matthew Watson]

Can I suggest that you certainly do make changes that ultimately no longer require the external call to MUSCLE (currently the instructions for installing MUSCLE as a windows user are not comprehensive or clear (how does one add to the path environment from within the R Studio console?),

[Matthew Watson]

Can I ask for clear instructions on ‘adding muscle to the path’ is it possible from within the Rstudio GUI? I placed the muscle.exe application file in the same folder as the RStudio.exe application, I added the file location to both the path and the python path in the environment variables settings, I tried restarting RStudio and bio3d then I tried rebooting the PC…none of these steps resulted in muscle being found when it was required by the PCA demo it continues to return the following error.

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Error in seqaln(s, id = files, ...) :
You do not have muscle installed/working locally on your machine.
We can attempt to use the EBI webserver if you provide an email address (required by the EBI).
Please note that the EBI states (see their Terms of Use):
'Using fake e-mail address may result in your jobs being killed and your IP, Organisation or entire domain being black-listed.'
In addition: Warning messages:
1: In get.pdb(ids, path = tmp.dir) :
C:\Users\fbsmaw\AppData\Local\Temp\Rtmp8AVJiR/1cdk.pdb exists. Skipping download
2: In get.pdb(ids, path = tmp.dir) :
C:\Users\fbsmaw\AppData\Local\Temp\Rtmp8AVJiR/3agm.pdb exists. Skipping download
3: In get.pdb(ids, path = tmp.dir) :
C:\Users\fbsmaw\AppData\Local\Temp\Rtmp8AVJiR/1cmk.pdb exists. Skipping download
4: In get.pdb(ids, path = tmp.dir) :
C:\Users\fbsmaw\AppData\Local\Temp\Rtmp8AVJiR/3dnd.pdb exists. Skipping download
5: In get.pdb(ids, path = tmp.dir) :
C:\Users\fbsmaw\AppData\Local\Temp\Rtmp8AVJiR/1q8w.pdb exists. Skipping download
6: In system(paste(exefile, ver), ignore.stderr = TRUE, ignore.stdout = TRUE) :
'muscle' not found

[Xinqiu Yao]

Bio3D supports alternative ways to do sequence alignment, not just calling external MUSCLE program. Read the manual carefully by ?seqaln.

For example, you can use the EBI web service through bio3d interface. If you are using the developmental version, it also supports msa function from Bioconductor (To use it, simply put exefile='msa').

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If you don’t set PATH, the muscle program should be put under your working directory, not where Rstudio is located.

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Setting environmental PATH is not via Rstudio. It is the operating system staff. Just simply Google and you will get tons of answers: https://www.java.com/en/download/help/path.xml

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[Matthew Watson]

I marry for the tone of my previous comments. Indeed I had not read carefully enough. Once I changed the initial name of the muscle program to simply 'muscle' it worked.

Thanks for your response and the great program!