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: galaxy-user@lists.bx.psu.e

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 "dataset_

[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 ___

[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 discussi

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-boun...@lists.bx.ps

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

Further, when I try "register" I add an email address and password, but the system still doesn't log me in Maybe this is a database configuration issue? I didn't think I'd need to state any specific entries in universe as I am using physically separate directories i.e. /home/galaxy/galaxy-cte/

[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/(.*) /home/galaxy/galaxy-csiro/static/june_2007_style/blue

[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] 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 __

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 files

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 director

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 /home/galaxy/galaxy-dist/data

[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 appli

[galaxy-user] Upload directory of files .......

Hi I have a local install of Galaxy on my desktop. I performed the following steps: Created a new Library Selected "Upload directory of files" Chose the "server Directory" Selected "Copy files into Galaxy" However, when I execute I get the following error. Any ideas? Error Traceback: View a

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

Maybe you should Send this to the galaxy-dev mailing list? 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

Re: [galaxy-user] Batch jobs...

Okay cool thanks Neil From: Dannon Baker [mailto:dannonba...@me.com] Sent: Wednesday, 31 October 2012 11:14 AM To: Burdett, Neil (ICT Centre, Herston - RBWH) Cc: bjoern.gruen...@pharmazie.uni-freiburg.de; galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Batch jobs... Connect the Input Dat

Re: [galaxy-user] Batch jobs...

Thanks Dannon, I can see them now but how do I use them now? As I now have 3 steps: Input File (as before) Input Dataset (new) Atlas list (as before) I select the "Input file" in step 1, and atlases in step 3 (as before) and I can select multiple files for the Input Dataset (bu

Re: [galaxy-user] Batch jobs...

Thanks Bjorn, But I can't seem to locate the symbol/icon (looks like papers). Is there any documentation where it is located on the screen? Thanks Neil -Original Message- From: Björn Grüning [mailto:bjoern.gruen...@pharmazie.uni-freiburg.de] Sent: Friday, 26 October 2012 9:

[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 G

[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 ___

Re: [galaxy-user] Managing datasets...

Yes thanks Ross that works well Neil -Original Message- From: Ross [mailto:ross.laza...@gmail.com] Sent: Thursday, 25 October 2012 12:23 PM To: Burdett, Neil (ICT Centre, Herston - RBWH) Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Managing datasets... Neil, have you trie

[galaxy-user] Managing datasets...

Hi, We have a local instance of Galaxy installed. If a user logs into their account and uploads a file, only they can view the file in the history. Is there any way for an Admin user to also see this history? I've set up a admin account and added it to "admin_users" in universe_wsgi.ini, bu

[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 e

[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

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

Thanks very much. This did in fact solve the issue. For those following the thread the "Rewrite" statements have to be added to /etc/apache2/sites-available/defaults. Thanks Again Neil -Original Message- From: Carlos Borroto [mailto:carlos.borr...@gmail.com] Sent: Tuesday, 28 August 20

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/(.*) /home/galaxy/galaxy-dist/static/sc

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

Hi I've installed galaxy with the default settings and it works fine. On a new Ubuntu machine I am trying to get galaxy running with Apache. But I am having problems, I've followed the documentation. After installing Apache I can put my ip address into a browser and I get message saying Apac

[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 ${output.dataset.dataset.id}:${output.files_path}:${file_nam

[galaxy-user] URL file upload... and file upload renamed

1. How do I transfer files using the URL? As a test I wanted to transfer a file to my local installation of Galaxy so I put in the location of the file on my Linux box. file:///home/bmladmin/demo_data-old/file.nii.gz into the "Get Data" URL box. But it seems to think that this is code that

[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 co