biopython not installed?

Question: biopython not installed?

9 months ago by

valdirbarth • 60 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 • 506 views

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modified 6 months ago by taxicar0029 • 0 • written 9 months ago by valdirbarth • 60

9 months ago by

Bjoern Gruening ♦ 5.1k

Germany

Bjoern Gruening ♦ 5.1k 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 COMMENT • link written 9 months ago by Bjoern Gruening ♦ 5.1k

9 months ago by

valdirbarth • 60

valdirbarth • 60 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 COMMENT • link written 9 months ago by valdirbarth • 60

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 REPLY • link written 6 months ago by chenzhuod • 30

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 REPLY • link modified 6 months ago • written 6 months ago by valdirbarth • 60

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 REPLY • link written 6 months ago by chenzhuod • 30

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