Install issues

[Roni L]

Hi there, 

I am new to Bali-phy and fairly new to Linux and have been having some issues getting installed and set up. The main issue I am having at the moment is not having bali-phy in my terminal even though I have installed it and added it to my path (i think!). What is strange to me is when i input bali-phy --version or locate it I receive a blank response, not comman not found or file doesn't exist.

As I said I am pretty new to this so it is likely something basic I am missing! I hope you ca help :)

[Benjamin Redelings]

Hi Roni,

That is indeed odd!  In order to help you out I will need a bit more information.

Here is what I see on my system when I type the commands "echo $SHELL", "asdf", "bali-phy", "bali-phy --version", and "which bali-phy".

bredelings@centromere:~$ echo $SHELL
/bin/bash
bredelings@centromere:~$ asdf
Command 'asdf' not found, did you mean:
  command 'sadf' from deb sysstat
  command 'sdf' from deb sdf
  command 'asdfg' from deb aoeui
  command 'adsf' from deb ruby-adsf
Try: sudo apt install <deb name>
bredelings@centromere:~$ bali-phy
bali-phy: Error! You must specify alignment files or a generic model (--model or --Model).

Try `bali-phy --help' for more information.
bredelings@centromere:~$ bali-phy --version
VERSION: 4.0-beta16-preview  [HEAD -> master commit 7d03c6af2]  (Nov 20 2024 20:12:55)
BUILD: Nov 21 2024 10:13:25
ARCH: linux x86_64
COMPILER: gcc 14.2.0 x86_64
bredelings@centromere:~$ which bali-phy
/home/bredelings/Devel/bali-phy/current/bin/bali-phy

Can you copy/paste the result of typing the same commands to show me what you see?  Alternatively a screenshot would also work.

-BenRI

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[roni...@icloud.com]

Hi Ben, 

Thanks for the response! So I actually managed to resolve this issue but have a new one!

I have downloaded tracer, seaview and FigTree but I am unsure how to view results through this. When I do the 25-1 and 25-2 test it works but I am not sure how to view the results? 

Hoping you can help!

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[Benjamin Redelings]

Hi Roni,

Hmm... I guess I left that out of the section you are looking at because it is an installation section -- BUT it seems like the information isn't present anywhere else either.

1. You can use tracer to view the log files.

    tracer 25-*/C1.log &

Assuming that the bp-analyze command worked successfully, you should do:

2. Use firefox to view the summary report at Results/index.html:

    firefox Results/index.html &

3. Use figuree to view the tree estimate (although this is also available from the report)

    figtree Results/c50.PP.tree &

4. Use seaview to view the alignment

    seaview Results/P1.max.fasta &

Does that help?

I will add this to the manual...

Also, not that there is a tutorial with more information at https://bali-phy.org/Tutorial6.html

-BenRI

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[Benjamin Redelings]

Hi Roni,

I released a new version -- 4.0-beta16 -- and along with that, I've
updated the manual to address the questions you asked.

    https://bali-phy.org/doc/4.0-beta16/README.xhtml

The updated sections are sections 2.8 and 3.1.  If you have other
questions, please let me know.

-BenRI

[roni...@icloud.com]

Hi Ben,

Thanks for this, I had it working well with the 3.6.1 version however the terminal did not allow typing when bali-phy was running as well as some differentiation in the bp-analyze result. Because of this I downloaded the 4.0-beta16 successfully however now I am continuing to have the original issue of blank response with all bali-phy commands? again total newbie and learning every day but hoping you can help!

Thanks,

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[Benjamin Redelings]

Hi Roni,

On 11/28/24 11:54 AM, roni.lou via bali-phy-users wrote:
> Hi Ben,
>
> Thanks for this, I had it working well with the 3.6.1 version however the terminal did not allow typing when bali-phy was running as well as some differentiation in the bp-analyze result.

This is probably not the result of the bali-phy version.  If you want to
be able to type while running any command, you need to put a "&" at the
end of the command.  The "&" tells the shell to run the command in the
background.

See for example https://www.stationx.net/unix-commands-cheat-sheet/

> Because of this I downloaded the 4.0-beta16 successfully however now I am continuing to have the original issue of blank response with all bali-phy commands? again total newbie and learning every day but hoping you can help!

This is probably not a problem with bali-phy.  In order to help you out

Also, how did you fix it the first time?

-BenRI

[roni...@icloud.com]

Hi Ben, 

So I have went back and forth between version to try and identify the error however I seem to do the same thing between both but in 4.0-beta16 the responses are blank. I have included both below. 

For 3.6.1 

wget https://github.com/bredelings/BAli-Phy/releases/download/3.6.1/bali-phy-3.6.1-win64.tar.gz

tar -zxf bali-phy-3.6.1-win64.tar.gz 

~/Applications/bali-phy-3.6.1/bin/bali-phy --version

For 4.0-beta16

Wget https://github.com/bredelings/BAli-Phy/releases/download/4.0-beta16/bali-phy-4.0-beta16-win64.tar.gz

tar -zxf bali-phy-4.0-beta16-win64.tar.gz

~/Applications/bali-phy-4.0-beta16/bin/bali-phy --version

My echo $SHELL response is the same as yours. 

asdf
bash: asdf: command not found

Bali-phy/bali-phy --version and which bali-phy return a blank response. 

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[Benjamin Redelings]

Hi Roni,

The wget commands that you are using will download the windows version of bali-phy.  If you are running on Linux, this will not work.  What kind of operating system are you using?  If it is windows, are you using cygwin or WSL?  Because 'bash' is not normally part of windows.

-BenRI

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[roni...@icloud.com]

Hi Ben, 

I am on a windows computer using Cygwin. Is this correct?

Thanks

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[Benjamin Redelings]

Yeah, windows with cygwin is correct.  In general, when you have a software problem, its good to mention which operation system you are using (windows, mac, linux), as it helps narrow down what the possible problems could be.

I will check on windows and see if I can reproduce your problem (I was looking on Linux before :-)

-BenRI

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[Benjamin Redelings]

Hi Roni,

OK, I was able to reproduce the problem.  I installed windows in a virtual machine.  Now that I can see the problem, I should be able to fix it.  However, it might take a few days.  Thanks for your patience!

-BenRI

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[Benjamin Redelings]

OK, I replaced the file bali-phy-4.0-beta16-win64.tar.gz with a new version that fixes some problems with mismatched DLLs.

If you re-download the file using `wget https://github.com/bredelings/BAli-Phy/releases/download/4.0-beta16/bali-phy-4.0-beta16-win64.tar.gz` then you should get the new, fixed version.  With this new version I no longer see a blank response.  Instead I see:

Ben@DESKTOP-S0P5EQM ~
$ ./bali-phy-4.0-beta16/bin/bali-phy --version
VERSION: 4.0-beta16  [HEAD, tag: 4.0-beta16 commit a0fe2d0e6]  (Nov 23 2024 14:47:51)
BUILD: Nov 29 2024 10:57:26
ARCH: windows x86_64
COMPILER: gcc 13.0.0 x86_64

Ben@DESKTOP-S0P5EQM ~

Note that the BUILD date is Nov 29 for the working version.

My apologies about the blank responses.  It seems that cygwin was not showing the errors.  That seems pretty problematic, so I hope it can be fixed eventually.

-BenRI

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