[galaxy-user] How to upload multiple files......

Hi, I've recently installed galaxy. I was trying to find how to upload multiple files without the need to compress them into a zip/gz file first. Is this possible? As the Get Data option allows only one file at a time. I searched the galaxy archive mailing list but didn't find anything

[galaxy-user] file upload renamed

When uploading a file using “Get Data” it seems the file is renamed to dataset_’id’.dat in ~/database/files/000/. Is it possible for the file to keep its name rather than being renamed? It seems this is being done because of the line

Re: [galaxy-user] Installing galaxy with Apache ...

Hi Jelle, I'm still having issues with Apache. I've moved RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*)

[galaxy-user] Downloading a zip file .......

Hi I can modify the upload.py file by commenting out the uncompress stuff and hence upload a zip file containing many files. However, when I click on the save icon and try and download the file, it seems the tar file is corrupt. I can only assume that during the upload the contents of the

[galaxy-user] No output produced.....

Hi, I have my own image registration tool that I've created on my own local instance of galaxy. The method takes in two images (*.nii.gz) formats and registers them together, and produces one registered *.nii.gz file and a *.trsf matrix file. The first issue encountered was the method was

[galaxy-user] Batch jobs...

Hi, I've created a workflow that works well. The workflow accepts 2 input files. After uploading all my input files (there is a lot). How can I batch the process, because I don't want to select files manually and run each job manually. Is there a way to batch this action? Thanks Neil

[galaxy-user] Manage Jobs...

Hi I have a local install of Galaxy running on my desktop. When I'm running a task I expected to see the process under Admin-Manage Jobs but it doesn't appear here. Do I need to set something to see the processes here? Neil ___ The

Re: [galaxy-user] Using syncing tool in Galaxy

Maybe you should Send this to the galaxy-dev mailing list? galaxy-...@lists.bx.psu.edumailto:galaxy-...@lists.bx.psu.edu Neil From: galaxy-user-boun...@lists.bx.psu.edu [mailto:galaxy-user-boun...@lists.bx.psu.edu] On Behalf Of Sachit Adhikari Sent: Wednesday, 31 October 2012 7:09

[galaxy-user] Upload files from filesystem paths

Hi, I have a local galaxy installation. I've created a data library, selected Upload files from filesystem paths, pasted a path in the path to upload window, and I've selected to preserve the directory structure. And the files get imported. How do I now access these files from my

Re: [galaxy-user] Upload files from filesystem paths

Hi Ross, I think I need to clarify. I have a file in /home/galaxy/data-test/dir1/dir2/somefile.txt Under the Upload files from filesystem paths, In the path to upload window I paste /home/galaxy/data-test. This then puts the somefile.txt in the

Re: [galaxy-user] Upload files from filesystem paths

Hi Ross, I don't know of any tools that work in the way I want, but I'm not an expert on tools within Galaxy. Essentially the data in the directories will be fixed. We run a tool from Galaxy that generates some output data, this data then checks the data located under the

Re: [galaxy-user] Upload files from filesystem paths

Thanks for the help Ross. Any chance you can point me to the examples you mentioned? Thanks again Neil From: Ross [mailto:ross.laza...@gmail.com] Sent: Friday, 4 January 2013 8:35 AM To: Burdett, Neil (ICT Centre, Herston - RBWH) Cc: galaxy-user Subject: Re: [galaxy-user] Upload files from

[galaxy-user] Uploading files to history via API

Hi, It seems the API documentation is a bit scarce. I'd like to upload a file from the command line using the API rather than the GUI, but would like to see the file in the history. Does anyone have any information how to do this/ any tools that are available. Thanks Neil

[galaxy-user] Workflows

Hi Sorry if these questions are obvious but I just don't know how to find the answers. I'm trying to get one of the API examples to work in http://wiki.galaxyproject.org/Learn/API/Examples . I've got my API key but how do I get/find the workflow id (f2db41e1fa331b3e in the examples). I've

[galaxy-user] History not updating for multiple instances of Galaxy

Hi, I have three instances of galaxy running on the same Linux box. My /etc/apache2/sites-available/default is: RewriteEngine on RewriteRule ^/galaxy-csiro$ /galaxy-csiro/ [R] RewriteRule ^/galaxy-csiro/static/style/(.*)

Re: [galaxy-user] Is anyone using Galaxy with NeuroScience ?

Hi Zeeshan, We're starting to use Galaxy fro neuro-imaging projects particularly detecting the onset on Alzheimer's disease by quantifying the loss of grey matter in the cortex, so we have methods to register and segment brains etc ... Neil From:

[galaxy-user] Monitoring usage

Hi, I have a local install of Galaxy. Is there something that I could use to monitor the usage on the system, users logged i/using the tools, CPU usage, disk space etc Thanks Neil ___ The Galaxy User list should be used for the

[galaxy-user] download contains the html file

Hi, I have a tool that works well. However, when I download the results, the results are zipped up but included into the zip file is the *.html file (with the same name as the tool output) do you know how I can stop this from being zipped up? Thanks Neil

Re: [galaxy-user] download contains the html file

Sorry I should have provided more detail. After I have executed my tool, I write the html into the dataset_'id'.dat file listing all the output files which I store in extra_files_path (named as dataset_id_files in the database). Thus when I do a download I only want the files stored in

Re: [galaxy-user] download contains the html file

For those following this thread. I, finally, managed to stop zipping up the html file by commenting out the try block (around line 260) in ~/lib/galaxy/datatypes/data.py Thanks Neil From: Burdett, Neil (CCI, Herston - RBWH) Sent: Friday, 10 January 2014 3:28 PM To: