Make a repository installable

, ,
1

Hi everybody. I’m trying to upload my tool in the public tool shed following this guide (not using Planemo): How to publish a tool in the Tool Shed - Galaxy Community Hub

In my local instance of Galaxy, in the admin tab I can see the repository but it says that it is not possible to install it, which is confirmed also by the repository tab in the tool shed.

I just loaded a tar file with the xml and the python code of the tool, am I missing something else?
Thank you for the help

2

Hi @Andrea_Furlani,
does it include the .shed.yml file? Could you share the repository link with me?

Regards

1 Like
3

Hi, this is the repository link (just a test):

https://toolshed.g2.bx.psu.edu/view/andrea.furlani/infr_test/bf610d149a69

It doesn’t include a yml file, just the .py codes and .xml definitions

4

Hi, I found an error while validating the sys_heatmap.xml file:

Applying linter tool_xsd... FAIL
.. ERROR: Invalid XML found in file: pheno_sys.xml. Errors [/tmp/tmpiy7_00_p:18:0:ERROR:SCHEMASV:SCHEMAV_CVC_COMPLEX_TYPE_3_2_1: Element 'param', attribute 'labels': The attribute 'labels' is not allowed.]

I think that it is the problem; I recommend you to use planemo for developing the Galaxy wrapper.

Regards

1 Like
5

Thank you for the suggestion. I’m using planemo and I solved the error indicated in your reply, but still the lint fails retrieving this message:

Linting repository /Users/andrea/Desktop/galaxy/tools/personal_tools/impc_tool
Applying linter expansion... CHECK
.. INFO: Included files all found.
Applying linter tool_dependencies_xsd... CHECK
.. INFO: No tool_dependencies.xml, skipping.
Applying linter tool_dependencies_sha256sum... CHECK
.. INFO: No tool_dependencies.xml, skipping.
Applying linter tool_dependencies_actions... CHECK
.. INFO: No tool_dependencies.xml, skipping.
Applying linter repository_dependencies... CHECK
.. INFO: No repository_dependencies.xml, skipping.
Applying linter shed_yaml... CHECK
.. INFO: .shed.yml found and appears to be valid YAML.
Applying linter readme... CHECK
.. INFO: No README found skipping.
+Linting tool /Users/andrea/Desktop/galaxy/tools/personal_tools/impc_tool/impc_tool.xml
Applying linter tests... WARNING
.. WARNING: No tests found, most tools should define test cases.
.. WARNING: No valid test(s) found.
Applying linter output... CHECK
.. INFO: 1 outputs found.
Applying linter inputs... CHECK
.. INFO: Found 43 input parameters.
Applying linter help... CHECK
.. CHECK: Tool contains help section.
.. CHECK: Help contains valid reStructuredText.
Applying linter general... WARNING
.. WARNING: Requirement requests defines no version
.. WARNING: Requirement pandas defines no version
.. WARNING: Requirement lxml defines no version
.. CHECK: Tool defines a version [0.1.0].
.. CHECK: Tool defines a name [IMPC].
.. CHECK: Tool defines an id [IMPC_query_tool].
.. CHECK: Tool targets 16.01 Galaxy profile.
Applying linter command... CHECK
.. INFO: Tool contains a command.
Applying linter citations... WARNING
.. WARNING: No citations found, consider adding citations to your tool.
Applying linter tool_xsd... CHECK
.. INFO: File validates against XML schema.
Failed linting

Regarding the warnings: I saw that also in other tools already present in the toolshed the version of the requirements is not always indicated and the citation section often is not present or inserted in the help since they are not using bibtex or doi citations types.

In the folder there are: tool.py , tool.xml , .shed.yml
Here’s the temporary link to the repository I loaded manually.

6

I found the solution by using the following command for lint:

planemo shed_lint --tools --fail_level error

In this way it will not compile only in presence of errors.

2 Likes