Question: Upload Data To Galaxy Using Terminal
gravatar for do kadya
4.7 years ago by
do kadya130
do kadya130 wrote:
Hi, Can I upload data (mostly link the data) using terminal ? MuSiC 2 tool integration is not available in their website nor in tool shed. MuSiC 2 creates folder and files by itself, which is hard to track by Galaxy. So is there any way to link files to galaxy current work space so that I can link those distracted files which are created by MuSiC 2. ex: if you run music2 bmr calc-bmr file_of_input output is 3 files, ./file1.txt ./folder1/file2.txt ./folder2/file3.txt we can not mention that we need this output filename or save file at specific location, we can not give this option. Galaxy will not able to track this output, hence i have to do it manually. So is it possible to upload this files manually by terminal ? Waiting for positive reply. Thank You - Chetan
galaxy • 1.1k views
ADD COMMENTlink modified 4.7 years ago by Martin Čech ♦♦ 4.9k • written 4.7 years ago by do kadya130
gravatar for Martin Čech
4.7 years ago by
Martin Čech ♦♦ 4.9k
United States
Martin Čech ♦♦ 4.9k wrote:
Hi, yes, you can link files to a Galaxy Library without copying - please see es(the last part 'Upload files from filesystem paths'). And there is an API for libraries (although it is under construction). The flow of controllers for upload is api/library_contents > controllers/library_common https://galaxy- #module-galaxy.webapps.galaxy.api.library_contents Martin
ADD COMMENTlink written 4.7 years ago by Martin Čech ♦♦ 4.9k
Thank you very much Martin Čech for reply. Currently I am uploading data by using linking method only, But what I wanted is NO API, that means via terminal only. As you can see my first mail where I am explaining query, MuSiC2 creating folders and files by itself, and hence galaxy will not be able to track those files. hence I want to collect those files and upload to current history (as data sets) using Terminal. Is that thing is possible ? else how can I tell Galaxy that tool is creating folder first and then writing files ? I am using to create xml file for galaxy. I know I can hide output (from main command), but how can i track file which is inside folder ? Waiting for positive reply.
ADD REPLYlink written 4.7 years ago by do kadya130
I don't understand your question. What is stopping your from using the API from terminal? However the easiest way to do it would probably be with Python and the BioBlend project ( and Another way is to set up a watcher in the folder that your tool is creating files in and upload to Galaxy on change. If none of these make sense to you please clarify your need. thanks Martin
ADD REPLYlink written 4.7 years ago by Martin Čech ♦♦ 4.9k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 173 users visited in the last hour