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rderelle / Broccoli

orthology assignment using phylogenetic and network analyses

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Installation problem

francicco opened this issue · comments

commented

Hi Romain,

I’m interested in testing your code of my 63 genome dataset. I installed Broccoli but I’m getting this error:

(venv) [tk19812@bp1-login01 Broccoli]$ ./broccoli.py --help
./broccoli.py: line 19:
    This file is part of Broccoli.
 
    Broccoli is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.
 
    Broccoli is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.
 
    You should have received a copy of the GNU General Public License
    along with Broccoli.  If not, see <https://www.gnu.org/licenses/>.
   
    contact: romain.derelle@gmail.com
 
: No such file or directory
import: unable to open X server `' @ error/import.c/ImportImageCommand/369.
import: unable to open X server `' @ error/import.c/ImportImageCommand/369.
import: unable to open X server `' @ error/import.c/ImportImageCommand/369.
import: unable to open X server `' @ error/import.c/ImportImageCommand/369.
./broccoli.py: line 26: from: command not found
./broccoli.py: line 27: from: command not found
./broccoli.py: line 28: from: command not found
./broccoli.py: line 29: from: command not found
./broccoli.py: line 34: syntax error near unexpected token `('
./broccoli.py: line 34: `def parse_args():'

What am I doing wrong?
Cheers
F

commented

Hi,

My guess is that you forgot to call python.
The command line should be:

python broccoli.py -help

Please let me know if it works this way.

cheers,
Romain

commented

There's something off...
can't install broccoli with conda on this cluster

(venv) [tk19812@bp1-login01 Broccoli]$ python3 -m pip install ete3
Requirement already satisfied: ete3 in ./venv/lib/python3.7/site-packages (3.1.2)
(venv) [tk19812@bp1-login01 Broccoli]$ python3 broccoli.py --help

            ERROR: the ete3 library is not installed
commented

seems to be fixed

commented

so how was this fixed? I am having the exact same problem using a python virtual env