Re: [galaxy-dev] Python script can't can't import BioPython modules in Galaxy 16.01

[Makis Ladoukakis]

Yeah Linda, this was the case for me. When I started the virtual environment I 
reinstalled BioPython and everything worked again. I suggest you do the same to 
any packages you need for your tools.

Makis

To: galaxy-dev@lists.galaxyproject.org
From: linda.bak...@wur.nl
Date: Thu, 3 Mar 2016 14:10:44 +0100
Subject: Re: [galaxy-dev] Python script can't can't import BioPython modules in 
Galaxy 16.01


  

  
  
I guess this relates directly to my
  question as well...

  

  

  

  On 03/03/2016 01:06 PM, Makis Ladoukakis wrote:



  
  
  Hello everyone,



I've recently upgraded to Galaxy 16.01 and i have some issues
with a python wrapper from a tool. When I run it via Galaxy I
get the following error:



Traceback (most recent call last):
  File "/home/galaxy_user/galaxy/tools/myTools/know_parser/know_parser.py", 
line 12, in 
from Bio import SeqIO
ImportError: No module named Bio


However when I click on the "view details" icon to copy the
command from the tool and run it on my command line the tool
works perfectly. In addition this issue occurs while I already
have installed BioPython.



When I type Python and write  "from Bio import SeqIO" I get no
error.



Can this be an issue related to the virtual environment that is
initialized each time Galaxy starts?



Thank you in advance,

Makis Ladoukakis





  
  

  
  

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-- 
Linda Bakker
Bioinformatics Research Assistant
Plant Research International, Wageningen UR
Building 107 (Radix), room W1.Fa.054
Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
tel: +31-317-480756
email: linda.bak...@wur.nl
  


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Re: [galaxy-dev] Python script can't can't import BioPython modules in Galaxy 16.01

[Linda Bakker]

I guess this relates directly to my question as well...



On 03/03/2016 01:06 PM, Makis Ladoukakis wrote:

Hello everyone,

I've recently upgraded to Galaxy 16.01 and i have some issues with a 
python wrapper from a tool. When I run it via Galaxy I get the 
following error:


Traceback (most recent call last):
   File "/home/galaxy_user/galaxy/tools/myTools/know_parser/know_parser.py", line 12, 
in 
 from Bio import SeqIO
ImportError: No module named Bio

However when I click on the "view details" icon to copy the command 
from the tool and run it on my command line the tool works perfectly. 
In addition this issue occurs while I already have installed BioPython.


When I type Python and write  "from Bio import SeqIO" I get no error.

Can this be an issue related to the virtual environment that is 
initialized each time Galaxy starts?


Thank you in advance,
Makis Ladoukakis





___
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   https://lists.galaxyproject.org/

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--
Linda Bakker
Bioinformatics Research Assistant
Plant Research International, Wageningen UR
Building 107 (Radix), room W1.Fa.054
Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
tel: +31-317-480756
email: linda.bak...@wur.nl

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Re: [galaxy-dev] Python script can't can't import BioPython modules in Galaxy 16.01

[Peter Cock]

On Thu, Mar 3, 2016 at 12:06 PM, Makis Ladoukakis
 wrote:
> Hello everyone,
>
> I've recently upgraded to Galaxy 16.01 and i have some issues with a python
> wrapper from a tool. When I run it via Galaxy I get the following error:
>
> Traceback (most recent call last):
>   File "/home/galaxy_user/galaxy/tools/myTools/know_parser/know_parser.py",
> line 12, in 
> from Bio import SeqIO
> ImportError: No module named Bio
>
>
> However when I click on the "view details" icon to copy the command from the
> tool and run it on my command line the tool works perfectly. In addition
> this issue occurs while I already have installed BioPython.
>
> When I type Python and write  "from Bio import SeqIO" I get no error.
>
> Can this be an issue related to the virtual environment that is initialized
> each time Galaxy starts?
>
> Thank you in advance,
> Makis Ladoukakis

Almost certainly, yes, this is due to the new venv setup in Galaxy.

If you had manually installed Biopython, I would suggest you install it
again but inside the venv.

If you installed Biopython via the Tool Shed package, that is more troubling.
Try doing a re-install via the Tool Shed.

Peter
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[galaxy-dev] Python script can't can't import BioPython modules in Galaxy 16.01

[Makis Ladoukakis]

Hello everyone,

I've recently upgraded to Galaxy 16.01 and i have some issues with a python 
wrapper from a tool. When I run it via Galaxy I get the following error:

Traceback (most recent call last):
  File "/home/galaxy_user/galaxy/tools/myTools/know_parser/know_parser.py", 
line 12, in 
from Bio import SeqIO
ImportError: No module named Bio
However when I click on the "view details" icon to copy the command from the 
tool and run it on my command line the tool works perfectly. In addition this 
issue occurs while I already have installed BioPython.

When I type Python and write  "from Bio import SeqIO" I get no error.

Can this be an issue related to the virtual environment that is initialized 
each time Galaxy starts?

Thank you in advance,
Makis Ladoukakis




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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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