Question: add test-data folder in repository of tool shed
1
gravatar for azf127
4.2 years ago by
azf12720
United States
azf12720 wrote:

I tried to add test-data folder to my repository in toolshed, but there aren't any option to add folder.
https://wiki.galaxyproject.org/CreateAndPopulateARepository

I found only the way to upload file. 

 

toolshed • 1.2k views
ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by azf12720
4
gravatar for fubar
4.2 years ago by
fubar1.1k
Australia
fubar1.1k wrote:

AFAIK: It's a mercurial repository so directories in an uploaded archive will add directories to the updated repository.

Make a gzipped tarball of your repository containing all of the contents - eg if ./foo is the top level directory containing the tool xml and that test-data subdirectory (./foo/test-data) then something like:

tar -cz ./foo/* > myrepo.tar.gz

Upload myrepo.tar.gz using the upload option in your tool shed repository view.

The subdirectories and other contents should appear in the updated tool repository.

Suggestion: spin up a local tool shed and experiment there BEFORE you upload to any public toolshed. Recent laptops and desktops are likely to run both servers well enough for development. 

sh run_tool_shed.sh --daemon

should just about do it - then localhost:9009 becomes your test playground - access to the logs will help a lot.

ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by fubar1.1k
1
gravatar for azf127
4.2 years ago by
azf12720
United States
azf12720 wrote:

Thank you very much for the answer. The situation is a bit more complicated than that.
First, most of these tools have been tested. They are valid. I can install it back to my local galaxy after I deposit them on public toolshed. I did that with 9 of them.

Second, when I use sh run_tool_shed.sh --daemon, I can't create repository to put my tools there. There is no admin panel for me. I only have admin panel in local8080.

Third, in main toolshed, when I click "Repositories I own" and click at my repository, I cannot see the valid tools. However, if I change revision to other version and change back, then I see four of them. Thus, I think there is something wrong with the update of the tool on toolshed.

ADD COMMENTlink written 4.2 years ago by azf12720
2

Second, when I use sh run_tool_shed.sh --daemon, I can't create repository to put my tools there. There is no admin panel for me. I only have admin panel in local8080.

To make a local administrator is the same for the toolshed as for Galaxy - add your account user email to the list of toolshed administrators in tool_shed_wsgi.ini and restart the toolshed - eg:

# this should be a comma-separated list of valid Galaxy users
admin_users = ross.lazarus@gmail.com,foo@bar.com

 

This http://gregvonkuster.org/galaxy-tool-shed-framework-building-galaxy-tools/ may also be useful.

 

ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by fubar1.1k
1
gravatar for azf127
4.2 years ago by
azf12720
United States
azf12720 wrote:

Although I still can't create repository in local toolshed, but I found out the problem of my tools. It's some prohibit in comment that I just add. The "test-data" directory works as well. Thank you so much.

ADD COMMENTlink written 4.2 years ago by azf12720

If Ross's answer helped to solve some of your other issues, "Accepting" the answer will help others to know it was a solution. Thanks! Jen

ADD REPLYlink written 4.2 years ago by Jennifer Hillman Jackson25k

Can you tell me where is the "Accepting" button?

Thank you,

ADD REPLYlink written 4.2 years ago by azf12720

On the left side of the reply you like, a grey circle with a check mark is the bottom icon. Click on this to accept an answer. Only the person that originally posted the question has this option available.

Thanks! Jen, Galaxy team

ADD REPLYlink written 4.2 years ago by Jennifer Hillman Jackson25k
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