ImportError: No module named dendropy

[jaaguirresant]

Hi, I'm struggling to run discoVista, which I installed from the source code (I tried with docker but failed to understand the tutorial for this as I never used docker before). When I execute the command ./discoVista.py (located in DiscoVista/src/utils/) I get the following error: "ImportError: No module named dendropy." I did install dendropy. However, it installed it with pyhton3 instead of python2.7. Maybe that's the issue? if so, should I try to install dendropy again with python2.7 and try again?

Thanks

[esayyari]

Hi,

Can you please send me the exact commands that you used for installation as well as how you run DiscoVista.

Best, Erfan

On Jun 27, 2020, at 4:10 PM, Julián Aguirre-Santoro [email protected] wrote:

Hi, I'm struggling to run discoVista, which I installed from the source code (I tried with docker but failed to understand the tutorial for this as I never used docker before). When I execute the command ./discoVista.py (located in DiscoVista/src/utils/) I get the following error: "ImportError: No module named dendropy." I did install dendropy. However, it installed it with pyhton3 instead of python2.7. Maybe that's the issue? if so, should I try to install dendropy again with python2.7 and try again?

Thanks

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[jaaguirresant]

Hi Erfan, thank you for your quick reply! Here's what I did:

1. Created the environmental variable WS_HOME:

export WS_HOME=/users/juliansoda/repository/

2. Installed Dendropy:

python3 -m pip install --upgrade git+https://github.com/jeetsukumaran/DendroPy.git

# Output message: "Successfully installed DendroPy-4.4.0"

3. Executed DiscoVista following the instructions in your GitHub page:

Try 1:

cd $WS_HOME/DiscoVista/ ./discoVista.py # Output message: "-bash: ./discoVista.py: No such file or directory"

Try 2:

cd $WS_HOME/DiscoVista/src/utils/ ./discoVista.py # Output message: "Traceback (most recent call last): File "./discoVista.py", line 8, in <module> import find_clades File "/Users/juliansoda/repository/DiscoVista/src/utils/find_clades.py", line 7, in <module> import dendropy ImportError: No module named dendropy"

I hope this is useful. Thank you for your help.

Julián

[jaaguirresant]

Erfan, I forgot to say that I also tried the following:

python3 ./discoVista.py # Output message: "Traceback (most recent call last): File "./discoVista.py", line 8, in <module> import find_clades File "/Users/juliansoda/repository/DiscoVista/src/utils/find_clades.py", line 124 print "In %s, %s is not defined before" %(r[0],e.args[0]) ^ SyntaxError: invalid syntax"

[esayyari]

Hi Julian,

Thanks for your follow-up! DiscoVista needs python2.7 (python2 in general). If you prefer condo please try this:

Conda create -n py2.7 python=2.7 Conda activate py2.7 Pip install dendropy

And try ./discovista.py and let me know if you still have the same issue or not.

Thanks for using DiscoVista, Erfan

On Jul 11, 2020, at 1:31 PM, Julián Aguirre-Santoro [email protected] wrote:

Hi Erfan, thank you for your quick reply! Here's what I did:

Created the environmental variable WS_HOME: export WS_HOME=/users/juliansoda/repository/

Installed Dendropy: python3 -m pip install --upgrade git+https://github.com/jeetsukumaran/DendroPy.git

Output message: "Successfully installed DendroPy-4.4.0"

Executed DiscoVista following the instructions in your GitHub page: Try 1:

cd $WS_HOME/DiscoVista/ ./discoVista.py

Output message: "-bash: ./discoVista.py: No such file or directory"

Try 2:

cd $WS_HOME/DiscoVista/src/utils/ ./discoVista.py

Output message: "Traceback (most recent call last): File "./discoVista.py", line 8, in import find_clades File "/Users/juliansoda/repository/DiscoVista/src/utils/find_clades.py", line 7, in import dendropy ImportError: No module named dendropy"

I hope this is useful. Thank you for your help.

Julián

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