Problem with PAMLX on Ubuntu 18

[Carin Tarasyan]

Hello everyone!

Could you help me with PamlX installation?

I have installed Paml4.9  correctly and would like to do the same with PamlX (I want GUI). According to instruction in readme file from pamlX1.3.1-src.tgz, I ran "qmake" without any problem, but next step "make release" has error:

"make: *** No rule to make target 'release'. Stop.

I am new linux user and would be grateful for a hint, what exactly is the cause of the error.

Thank you in advance, 

Karina Tarasyan

[Sandra AC]

Hi Karina, 

First, please note that you should use the latest version of PAML, which is available from GitHub (see here). Given to PAMLX relying on the Qt package, the compilation may not always work if the Linux distribution has issues with Qt. You may want to try the following:

1. I think the version of Qt you need is Qt4. So I recommend you remove other Qt packages if you had installed them as it may cause issues to have different versions. You can do this via Synaptic or by typing:
sudo apt-get --purge remove qt*

2. Then, install Qt4:

sudo apt-get install qt4-default

3. After that, you may want to move to the PAMLX folder with the source code and type:

qmake pamlX.pro

make

If there are no issues, the software should start compiling and, at the end, you should see an executable file called "pamlX" appear.

If after following the steps above PAMLX cannot compile, it would be good that you try to run the PAML programs from the terminal as it will help you to better understand the models you are using (i.e., never run anything by default: understand the dataset you have and use the best model according to your biological question and your dataset). If you want to use CODEML using a GUI, you may want to try EasyCODEML (Gao et al. 2019), a GUI that implements some CODEML models for detecting selection. I have not tried this tool myself as I only run CODEML from the terminal, but perhaps you may find it useful! I am not aware of other GUIs for other PAML programs, but perhaps others are and can suggest them below.

All the best,
Sandra

[Carin Tarasyan]

Thanks a lot for the answer!

You are absolutely right: paml software is requires qt4 not the qt5, which included to Ubuntu 18 and 20. 

I consulted with IT-specialists and got the decision, which is very close to yours:

1) install qt4-devtools (because I need not only libs)

2) qmake-qt4 (because qmake has changed for qt5 too)

3) make

4) ./pamlX

After these four steps I have got pamlX and enjoy GUI interface.

Thanks for recommendation of EasyCODEML, I am going to try it too.

All the best,

Karina

понедельник, 12 декабря 2022 г. в 16:40:51 UTC+3, sandr...@gmail.com: