troubles with installation

[Ben Read]

Hi There,

 

I am having some issues with the installation process of Bali-Phy (version 3.5.0). I am using a windows machine and have successfully managed to install the software and add it to my path.

 

Inputting the command:

$ bali-phy --version

Gives me the following output:

VERSION: 3.5  [HEAD -> master, tag: 3.5.0 commit 6e653866b]  (Mar 02 2020 16:05:53)

BUILD: Mar  2 2020 17:55:56

ARCH: windows x86_64

COMPILER: gcc 9.2.0 x86_64

 

The next section of the installation guide (2.7) says to test the process using the following:

bali-phy ~/Applications/bali-phy-3.5/share/doc/bali-phy/examples/sequences/5S-rRNA/25.fasta --iter=150

% bali-phy ~/Applications/bali-phy-3.5/share/doc/bali-phy/examples/sequences/5S-rRNA/25.fasta --iter=150

% bp-analyze 25-1 25-2

However, when I try this I receive the following:

$  bali-phy ~/Applications/bali-phy-3.5/share/doc/bali-phy/examples/sequences/5S-rRNA/25.fasta --iter=150

Created directory '25-5/' for output files.

Created directory '25-5/' for output files.

bali-phy: Error! Failed to read from alignment-file '/home/br33/Applications/bali-ph

y-3.5/share/doc/bali-phy/examples/sequences/5S-rRNA/25.fasta': file does not exist.

 

When I investigate the directories in the “~/Applications/bali-phy-3.5.0/share/doc/bali-phy/examples/sequences/5S-rRNA” directory the “25.fasta” file is present, so I am a little confused (although I should say this is my first experience using any kind of command line program so I could be doing something silly!). Is there anything I am missing/Do you have any advice on what I can do to fix this?

 

Kind Regards,

Ben Read

[Benjamin Redelings]

Hi Ben,

Thanks for letting me know about this.  I think the problem is hard to spot by eye, but the manual has "3.5" whereas the actual files have "3.5.0".  So the commands from the manual didn't work - drat.

I updated the manual so it should say "3.5.0" instead of "3.5", so hopefully the commands should work now as written.

-BenRI

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[bobbyr...@gmail.com]

Hi Ben, Apologies for the delay in my response.

Changing the command to "3.5.0" made no effect on the output message (error: file does not exist). It does, however, create the directories "25-1" etc. So BAli-Phy is trying to do something but cannot read the file.

I have attempted to copy the file, paste it in a different directory and attempt the code from a different path, but it still says the file does not exist, so the confusion continues! Do you have any further suggestions?

Kind regards,

Ben Read

[Benjamin Redelings]

Hi Ben,

OK, I was able to reproduce the problem.  On windows, you have to make a local copy of the file first:

 $ cp ~/Applications/bali-phy-3.5.0/share/doc/bali-phy/examples/sequences/5S-rRNA/25.fasta .
 $ bali-phy 25.fasta --iter=150

This is because the "bali-phy" program wants windows-style filenames that begin with e.g. C:/, but ~/Applications is a unix-style filename.  "25.fasta" works with both.  Very tricky.

Also note that you need to use the cygwin installer to install python3 in order for the bp-analyze script to work.

I updated the user guide for both issues.

Any other problems?

-BenRI

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[bobbyr...@gmail.com]

Sorry to bother you again but I think i have done as you suggested, but am still not progressing. Below is my code where I: 1) made a local copy of the directory 2) attempted to run but received an error 3) checked that the file did exist on my local drive (but received a message saying "permission denied") 4) attempted to run the software using that same path as above, however still got an error!

br33@PC18417 ~/Applications

$ cp ~/Applications/bali-phy-3.5.0 /cygdrive/c/Users/br33 -r

 

br33@PC18417 ~/Applications

$ bali-phy 25.fasta --iter=150

-bash: /home/br33/Applications/local_bali-phy-3.5.0/bin/bali-phy: No such file or directory

 

br33@PC18417 ~/Applications

$ /cygdrive/c/Users/br33/bali-phy-3.5.0/share/doc/bali-phy/examples/sequences/5S-rRNA/25.fasta

-bash: /cygdrive/c/Users/br33/bali-phy-3.5.0/share/doc/bali-phy/examples/sequences/5S-rRNA/25.fasta: Permission denied

 

br33@PC18417 ~/Applications

$ bali-phy /cygdrive/c/Users/br33/bali-phy-3.5.0/share/doc/bali-phy/examples/sequences/5S-rRNA/25.fasta --iter=150

-bash: /home/br33/Applications/local_bali-phy-3.5.0/bin/bali-phy: No such file or directory

If you can see any blatant mistakes please let me know... my PhD supervisor has tasked me with learning how to use the software during Covid-lockdown but i have no experience in using command lines so I could just be making silly mistakes! 

[Benjamin Redelings]

Hi,

I might be able to help you out.  I also updated the section on windows and unix filenames in the README -- take a look at that.

On 5/4/20 2:02 PM, bobbyr...@gmail.com wrote:

Sorry to bother you again but I think i have done as you suggested, but am still not progressing. Below is my code where I: 1) made a local copy of the directory 2) attempted to run but received an error 3) checked that the file did exist on my local drive (but received a message saying "permission denied") 4) attempted to run the software using that same path as above, however still got an error!

br33@PC18417 ~/Applications

$ cp ~/Applications/bali-phy-3.5.0 /cygdrive/c/Users/br33 -r

This copies the whole directory to your current location.  The location is not the problem, the problem is that bali-phy (unfortunately) needs the WINDOWS path, while all the other programs (like "ls") are using UNIX paths.

To see what the windows path is, try (for example)

$ cygpath -w ~/Applications/bali-phy-3.5.0/share/doc/bali-phy/examples/sequences/5S-rRNA/25.fasta

br33@PC18417 ~/Applications

$ bali-phy 25.fasta --iter=150

-bash: /home/br33/Applications/local_bali-phy-3.5.0/bin/bali-phy: No such file or directory

The error message is correct here: the "25.fasta" file is not where you said it was!

If you try the instructions from the manual, it should work:

$ cp ~/Applications/bali-phy-3.5.0/share/doc/bali-phy/examples/sequences/5S-rRNA/25.fasta .
$ bali-phy 25.fasta --iter=150

 

br33@PC18417 ~/Applications

$ /cygdrive/c/Users/br33/bali-phy-3.5.0/share/doc/bali-phy/examples/sequences/5S-rRNA/25.fasta

-bash: /cygdrive/c/Users/br33/bali-phy-3.5.0/share/doc/bali-phy/examples/sequences/5S-rRNA/25.fasta: Permission denied

Here you tried to execute the 25.fasta file as if it was an executable program.  You have permission to *read* the file, but not to *execute* it, so you get "permission denied".

Take a look at section 5 in http://www.ee.surrey.ac.uk/Teaching/Unix/

 

br33@PC18417 ~/Applications

$ bali-phy /cygdrive/c/Users/br33/bali-phy-3.5.0/share/doc/bali-phy/examples/sequences/5S-rRNA/25.fasta --iter=150

-bash: /home/br33/Applications/local_bali-phy-3.5.0/bin/bali-phy: No such file or directory

Here you are using a UNIX/cygwin path again, when you need to use a Windows path.  You can use "cygwin -w <path>" to find the windows version of a cygwin path.

If you can see any blatant mistakes please let me know... my PhD supervisor has tasked me with learning how to use the software during Covid-lockdown but i have no experience in using command lines so I could just be making silly mistakes!

These tutorials might help you out:

    http://www.ee.surrey.ac.uk/Teaching/Unix/

    http://www.rain.org/~mkummel/unix.html

Also, if you try bali-phy on Linux or Mac, you would have the problem with Windows versus Unix filenames.

-BenRI

[bobbyr...@gmail.com]

Thank you, Ben! this has all worked perfectly and I can now visualise the results too in FigTree and Tracer. Amazing!