Question: tool integration with planemo
0
gravatar for n.goue
7 months ago by
n.goue30
n.goue30 wrote:

Hi,

I have been through planemo documentations, read the galaxy-iuc-standards but I still need help to create a local repository.

  • First, could someone explain me the difference between those 2 commands : sh run_tool_shed.sh (which open port 9009) and planemo serve --port 9090 ?

  • I have been successful with the inital steps to create the tool, with the wrapper creation and the tool tests. Also I can visualize my tool on the "Galaxy / Configured by Planemo" local server.

However when I run the command :

$ planemo shed_create --shed_target local

I got the result : 'ToolShedInstance' object has no attribute 'categories'

Previously, I have created the .shed.yml file in my tool folder :

name: my_cool_tool

owner: nagoue

description: what my_cool_tool 's doing

long_description: what my_cool_tool is doing

categories:

-Fasta Manipulation

  • Finally, after running the command sh run_tool_shed.sh, I can open a web page "Galaxy Tool Shed", but I can't log in despite I filled the tool_shed.ini with my email.

May someone give me a hand to understand what's I'm doing wrong ? Many thanks,

planemo galaxy • 154 views
ADD COMMENTlink modified 7 months ago • written 7 months ago by n.goue30
2
gravatar for Bjoern Gruening
7 months ago by
Bjoern Gruening4.9k
Germany
Bjoern Gruening4.9k wrote:

Hi,

can I recommend to use the https://testtoolshed.g2.bx.psu.edu or the main toolshed. You need to configure the local toolshed properly with a user and then configure planemo to use it etc...

Ciao, Bjoern

ADD COMMENTlink written 7 months ago by Bjoern Gruening4.9k
1
gravatar for n.goue
7 months ago by
n.goue30
n.goue30 wrote:

Hi Bjoern, Your explanation makes sense to me! The testtoolshed will come as the next step. I first wanted to understand how it works locally.

Thank you!!

ADD COMMENTlink written 7 months ago by n.goue30
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