Question: biopython not installed?
1
gravatar for valdirbarth
8 months ago by
valdirbarth60
valdirbarth60 wrote:

hi, I am using Ribo Tools in a local instance installed from the tool_shed (https://toolshed.g2.bx.psu.edu/repository?repository_id=f81548109cd9dd88).

When i run it on my sample, it gives me the error: "line 16, in from Bio import SeqIO ImportError: No module named Bio"

Which I googled and it means that biopython is not installed.

The bipython package is not listed as dependency for the tool, but I tried to install the biopython package separately from the tool shed and I still get the error. I also have it installed in my computer.

Anyone knows how make Ribotools aware that there is a version of Biopython installed on my galaxy and/or computer?

biopython ribotools • 431 views
ADD COMMENTlink modified 5 months ago by taxicar00290 • written 8 months ago by valdirbarth60
1
gravatar for Bjoern Gruening
8 months ago by
Bjoern Gruening5.1k
Germany
Bjoern Gruening5.1k wrote:

Best way is to contact the RiboTools developers and make them aware of this. An other possibility is to add the biopython dependency to the tool description file as a requirement. This was Galaxy will install the missing dependency.

ADD COMMENTlink written 8 months ago by Bjoern Gruening5.1k
1
gravatar for valdirbarth
7 months ago by
valdirbarth60
valdirbarth60 wrote:

Ok, I managed to get through this error by adding it as a requirement as a "package" instead of "python module" in the dependency XML file of the tool and installing the biopython package.

thx

ADD COMMENTlink written 7 months ago by valdirbarth60

Hi

Could you please describe your steps in detail? It means how to add the requirement and how to install the biopython in galaxy?

Thx

ADD REPLYlink written 5 months ago by chenzhuod30

you need to find the xml file of each tool (eg. get_codon_frequency.xml, it is inside the shed_tools folder somewhere). If you open that xml file, at the top you'll see the requirements for that tool inside <requirements> tags. All you need to do is add biopython package as a requirement so it also installs it as a dependency. I edited the biopython line in there to a package:

<requirement type="package">biopython</requirement>

I also added python 2.7 for some reason (compatibility? this may not be necessary in yours, but just in case you also need it):

<requirement type="package" version="2.7">python</requirement>

After that I believe you need to repair the tool via admin interface.

Then it worked for me.

ADD REPLYlink modified 5 months ago • written 5 months ago by valdirbarth60

Thx !

But, I add these two requiement, it also could not run. (My custom tool is CPC2, a coding potential calculator), and I have install biopython in /home/software/shed_tools/toolshed.g2.bx.psu.edu/repos/biopython and my tool and xml are in /home/software/galaxy/tools/myTools/.

Need I do some more?

ADD REPLYlink written 4 months ago by chenzhuod30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 120 users visited in the last hour