blackrim / treePL

Phylogenetic penalized likelihood
https://github.com/blackrim/treePL/wiki
GNU General Public License v3.0
45 stars 19 forks source link

How to run treePL? #46

Closed kjlmaurin closed 4 years ago

kjlmaurin commented 4 years ago

Hello,

Here is a very basic question, but surprisingly I cannot find any answer to it online: how do I run treePL once installed?

The test run works, but when I am trying to replace "test" in the command line brew test -v treepl by my script (a .txt file), with the path to it, I get a Unknown command: [my file] error message. I have tried many combinations of this command line, like swapping treepl and my file, not putting brew, adding ./ before treepl, adding the path to the treePL script, etc. but nothing works.

Can someone please tell me how they run it? Many thanks

kjlmaurin commented 4 years ago

Whoops sorry ignore this. I got confused about the instructions in the "Run Options" page, but not I managed to run it. I have issues with the run, will come back here if I cannot solve them :)

BiodeB commented 3 years ago

Dear Sir,

Have you solve this issue, I'm having same problem. I have installed treePL through brew install. Now how can I ran my file through this kindly guide me.

Thanks

kjlmaurin commented 3 years ago

Hello, You must open the command window of whichever plaftorm you are using, then type treePL /path/to/your/configuration/file.txt Maybe use treepl instead of treePL, I cannot remember what I used (I have not made a run in months, so this detail just slipped my mind ah ah!). And for the config file, use .txt or whichever format your config file has. This should work if treePL has been installed properly. Cheers