Upload Data To Galaxy Using Terminal

Question: Upload Data To Galaxy Using Terminal

4.7 years ago by

do kadya • 130

do kadya • 130 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 COMMENT • link •

modified 4.7 years ago by Martin Čech ♦♦ 4.9k • written 4.7 years ago by do kadya • 130

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 https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFil 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- central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html #module-galaxy.webapps.galaxy.api.library_contents Martin

ADD COMMENT • link written 4.7 years ago by Martin Čech ♦♦ 4.9k

Thank you very much Martin Äech 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 http://cli-mate.lumc.nl/define# 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 REPLY • link written 4.7 years ago by do kadya • 130

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 (http://bioblend.readthedocs.org/en/latest/ and https://github.com/afgane/bioblend). 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 REPLY • link written 4.7 years ago by Martin Čech ♦♦ 4.9k

Similar posts • Search »