Question: Biopython as repo dependency
0
gravatar for Philipp Rentzsch
4.0 years ago by
Germany
Philipp Rentzsch0 wrote:

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 COMMENTlink modified 4.0 years ago by Bjoern Gruening5.1k • written 4.0 years ago by Philipp Rentzsch0

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 REPLYlink modified 4.0 years ago • written 4.0 years ago by Philipp Rentzsch0
3
gravatar for Bjoern Gruening
4.0 years ago by
Bjoern Gruening5.1k
Germany
Bjoern Gruening5.1k 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 COMMENTlink written 4.0 years ago by Bjoern Gruening5.1k

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

ADD REPLYlink written 4.0 years ago by Philipp Rentzsch0

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 REPLYlink written 4.0 years ago by Peter Cock1.4k
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