Biopython as repo dependency

Question: Biopython as repo dependency

4.0 years ago by

Germany

I am currently writing a tool in python that uses biopython for accessing Entrez. For this I tried to add Biopython as a dependency according to their Manual.
Unfortunately, when I add the file repository_depencies.xml:

<?xml version="1.0"?>
<repositories description="Requires Biopython as a dependency.">
  <repository name="package_biopython_1_64" owner="biopython" />
</repositories>

and pack everything in a tar-ball, when uploading to out tool-shed I get the message:

#The repository_dependencies.xml file contains an invalid tag. Unable to locate repository with name package_biopython_1_64 and owner biopython.

This makes sense insofar that I did not specify the tool-shed the repository is located at. So I added:

toolshed="http://toolshed.g2.bx.psu.edu"

to the third line of the file but still got the same error (even though the mentioned package does exist in the tool-shed and I followed all manuals.

I am very grateful for any suggestions :)

biopython dependency • 1.0k views

ADD COMMENT • link •

modified 4.0 years ago by Bjoern Gruening ♦ 5.1k • written 4.0 years ago by Philipp Rentzsch • 0

I also tried it with a tool_dependency as in this case and then got the error message:

Unable to locate repository with name package_biopython_1_64 and owner biopython. The tool_dependencies.xml file contains an invalid tag.

ADD REPLY • link modified 4.0 years ago • written 4.0 years ago by Philipp Rentzsch • 0

4.0 years ago by

Bjoern Gruening ♦ 5.1k

Germany

Bjoern Gruening ♦ 5.1k wrote:

Hi Phillipp,

are you uploading this to the test tool shed or main tool shed or to your private one? The bioüython package needs to exist in the same tool shed your are uploading. You don't need to specify the toolshed, because this will be automatically populated during upload. Currently, cross-tool-shed dependencies are not supported.

Hope this helps,

Bjoern

ADD COMMENT • link written 4.0 years ago by Bjoern Gruening ♦ 5.1k

Ah okay, that explains it. I was testing on a private tool-shed without Biopython installed so that's probably the issue here.

ADD REPLY • link written 4.0 years ago by Philipp Rentzsch • 0

Yep. When developing tools and packages I try to do everything on the public TestToolShed before the (main) ToolShed, which generally works since the dev-team and IUC core packages are on both.

ADD REPLY • link written 4.0 years ago by Peter Cock • 1.4k

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