Get image list from Bioshadock

[varunshankar]

Provide user with a way to choose the available images from bioshadock.

[varunshankar]

Find a way to contact the BioShaDock server, list all the images, and create a .loc file with all the images name and url. This .loc is called by the Galaxy tool to propose a list to the use.

One preliminary idea is to create a "cron" like process to update this list, stored in a .loc galaxy file every X days. Another is to "refresh" this list when the Galaxy user ask for this on the godocker galaxy tool form.

REST API for accessing bioshadock here: http://www.genouest.org/api/bioshadock-api/.

Find if there is a way to update a ".loc" file from the result of a REST API request when a user call a specifically tool.

Create a dedicated "data manager" tool https://wiki.galaxyproject.org/Admin/Tools/DataManagers ( Not sure this can be used "on-demand") when a user call the godocker galaxy tool.
-> Create a bioshadock data manager and make the godocker tool using data created by this data manager.

[varunshankar]

.loc files are in Galaxy to create lists of data files pointed by an id (or a name). These lists can be called by a xml galaxy tool form to generate a list that the user can use to select an option (id or name) and the .loc file say to galaxy which file is related to this id or name. You can have a look here: https://wiki.galaxyproject.org/Admin/DataIntegration and tool xml like for "blast"

[osallou]

You can list containers with url: https://docker-ui.genouest.org/container/all

but list is quite long. I am thinking about adding a param like https://docker-ui.genouest.org/container/all?format=light to reduce the number of parameter returned (id and description, this is all you need).

[varunshankar]

The description tag seems to be the container name.

I find https://docker-ui.genouest.org/container/all and https://docker-ui.genouest.org/container/all?format=light to contain 115 images (excluding null and "" values)

[osallou]

Name of container is field id. And description or short desc can be
useful.there are more than 1000 containers.

Le sam. 30 juil. 2016 04:43, Varun Shankar S [email protected] a
écrit :

The description tag seems to be the container name.

I find https://docker-ui.genouest.org/container/all and
https://docker-ui.genouest.org/container/all?format=light to contain 115
images (excluding null and "" values)

—
You are receiving this because you commented.

Reply to this email directly, view it on GitHub
#2 (comment),
or mute the thread
https://github.com/notifications/unsubscribe-auth/AA-gYk3WWN0MjqwxCo2TZFJhhKymTNF4ks5qarpCgaJpZM4JRLPW
.

[varunshankar]

I am not getting an idea on how to have the code tag get the result from the html file.

[osallou]

as far as I understand code tag is a script being executed on server side,
not in web browser, so cannot be used to extract list dynamically

Le sam. 20 août 2016 à 21:00, Varun Shankar S [email protected] a
écrit :

I am not getting an idea on how to have the code tag get the result from
the html file.

—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub
#2 (comment),
or mute the thread
https://github.com/notifications/unsubscribe-auth/AA-gYqx4_MyE6jiM3tVDya_LZKHGhXTIks5qh06ugaJpZM4JRLPW
.