PROBLEM IN RUNNING PAMLX

[sima rout]

Hi everyone,

I am new to this software PAMLX so i faced problems. First  I have downloaded this software in linux from the link obtained from  Beginner's Guide on the Use of PAML to Detect Positive Selection (2023) , the repository name was paml- master. After that I have opened the terminal and run the command. After enter into src, I tried to compile the file in src by typing the command make -f Makefile. but is is shown as error. then when i tried to move the directories into the bin file, it was shown that no such file or directory . please help me.

In another user guideline, i saw it was mentioned that for PAMLX, PAML4 is required. is it correct? 

[Sandra AC]

Hi Sima, 

PAMLX is not to be used when using the CODEML protocol -- you will se that we only explain how to run PAML, specifically the CODEML program, from the terminal, not using a GUI such as PAMLX.

Nevertheless, if you want to make PAMLX work for other types of analyses, please note that it relies heavily on the Qt package, and hence the compilation may not always work if the Linux distribution has issues with Qt. You may want to try the following steps, which I previously explained on this google group conversation:

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 instead of using GUI 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). As I mentioned above, we only explain how to run CODEML from the terminal on the protocol you mention, not using a GUI :) 

Hope this helps!
Sandra

[Carin Tarasyan]

Hi Sima,

PAMLX is only GUI for PAML4, so you have to install PAML4 first.

Note that you need qt4 library for compiling PAMLX. My working decision (for UBUNTU 18) was:

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

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

3) make

4) ./pamlX

Hope it can help you.

All the best,

Karina

среда, 10 мая 2023 г. в 12:22:37 UTC+3, cutesi...@gmail.com:

[sima rout]

ohk. got it.

Thank you so much for your kind response.