[galaxy-dev] error running API with example_watch_folder.py

Hi, when I use the example_watch_folder.py to check for files in an input directory and process them if they are present. The workflow runs to completion successfully, but the "example_watch_folder.py" task crashes with the following errors, thus it can only process one file at a time, as th

Re: [galaxy-dev] Error executing workflow via API

Hi, It seems all my other workflows that work have a txt output feeding into a an input accepting a text input. This particular workflow (that's failing) is outputting a html output to a html input ? Could this be the reason for the failure? has anyone else got html outputs to inputs on thei

Re: [galaxy-dev] Error executing workflow via API

Hi John, Thanks for the quick response. There seems to be nothing obvious on the server side log. This is all I get: galaxy.jobs.runners DEBUG 2014-09-09 11:43:23,850 (322) command is: python /home/galaxy/milxcloud-new/tools/cte/cte_process_input_data.py '/home/galaxy/milxcloud-new/t

[galaxy-dev] Error executing workflow via API

Hi, I execute a number of workflows via the API which all work fine. However, the longest one I use (consists of three linked tasks), returns an error. I call the workflow in the python script using popen and has the format: /home/galaxy/milxcloud-new/scripts/api/workflow_execute.py d2fcd3

[galaxy-dev] API for multi-file upload

Hi, I really like the multi-file upload tool in the latest version of Galaxy. Is there an API for it so we can send files via a script rather than using the user interface? If so are there any examples? Thanks Neil ___ Please keep all r

Re: [galaxy-dev] error using get( $__user_id__ ) in xml file in new Galaxy

Thanks for the help John and Dannon. I'll see if it works tomorrow. No need to raise a trello card Thanks Neil From: Dannon Baker [dannon.ba...@gmail.com] Sent: Tuesday, August 05, 2014 11:14 PM To: John Chilton Cc: Burdett, Neil (DP&S, Herston - RBWH); galaxy-dev

[galaxy-dev] error using get( $__user_id__ ) in xml file in new Galaxy

Hi, I have recently upgraded Galaxy from a version I had last year. In my tool xml file I could state: ${ __app__.model.User.get( $__user_id__ ).api_keys[0].key } in the section to get the user's API. However, after updating to the current version of Galaxy I get the following error when u

Re: [galaxy-dev] cleanup_datasets.py not deleting files...

Thanks, but this doesn't work. As there are further checks in "_purge_datasets" which check if the data has been deleted first. Can you purge data without deleting it? If so I can remove those checks. Has anyone else needed to do this? Thanks neil -Original Message- From: Eric Rasche [m

Re: [galaxy-dev] cleanup_datasets.py not deleting files...

How does the main Galaxy server deal with it? Users data can't remain on the "project's free server" forever can it? and if not then there must be some automated way of deleting data? is that correct? Thanks Neil From: Hans-Rudolf Hotz [h...@fmi.ch] Sent:

Re: [galaxy-dev] cleanup_datasets.py not deleting files...

Thanks. Is there a script that will delete all files older than a certain date even if not marked as deleted by the user? Thanks Neil From: Hans-Rudolf Hotz [h...@fmi.ch] Sent: Thursday, July 17, 2014 5:42 PM To: Burdett, Neil (DP&S, Herston - RBWH); galax

Re: [galaxy-dev] Download URL needs user to be logged in first

Hi John, What I've implemented on our local system is the user uploads their data, then automatically a workflow is run on that data (so the user doesn't need to select a tool to execute). I email the user once the job is complete with a link to that the user can download the results.

[galaxy-dev] cleanup_datasets.py not deleting files...

Hi, I'm trying to use the cleanup_datasets.py file to remove all files on my system older than 20 days. My crontab looks like this: # m h dom mon dow command 34 10 * * * cd /export/barium-data3/galaxy-suvr && python scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 20 -1 >

[galaxy-dev] Download URL needs user to be logged in first

Hi, galaxy provides a download_url to download zipped up files. However, the user must first log into Galaxy to commence the download. Is there a way to turn this feature off, so that users can click on the link and download the data without first login Thanks Neil __

[galaxy-dev] Uploading Multiple files

Hi, It was suggested recently that Galaxy would soon be providing the ability to upload multiple files rather than single files. Does anyone know when this might be available in Galaxy? I've downloaded the most recent version of Galaxy but as yet it is not present in the "stable" version Th

Re: [galaxy-dev] How Galaxy prevents security attacks?

Thanks Dannon, The team gave this example (regarding XSS), Hope it helps Example: open firefox, log into galaxy and paste the following URL: 152.83.54.10/capaibl/visualization/list?async=false&f-free-text-search=e&f-sharing=All&f-tags=All&f-title=All&page=1&show_it

[galaxy-dev] How Galaxy prevents security attacks?

Hi, we'd like to host a version of Galaxy, but our security team have identified some potential areas that could be subjected to attack. I was wondering if Galaxy had mechanism in place to avoid the following issues: Cross site scripting Description Cross site scripting (also referred to as

Re: [galaxy-dev] Postgresql database time wrong...

Thanks, but looking at /etc/postgresql/9.1/main/postgresql.conf i have the following: #timezone = '(defaults to server environment setting)' #timezone_abbreviations = 'Default' # Select the set of available time zone # abbreviations. Currently, there ar

[galaxy-dev] Postgresql database time wrong...

Hi I have quite a strange issue. I have a local install of Galaxy setup. When I type 'date' on my Ubuntu machine I get something like: Wed Jun 18 09:25:22 EST 2014 When i then execute a job and look in the database at the create_time i.e. # select create_time from job order by create_time;

[galaxy-dev] Move galaxy/database (SQLite) to a new location

Hi, we have the default setup for galaxy hence using SQLite database and all data store in the same location as the galaxy install. In Universe_wsgi.ini file there is an entry # Dataset files are stored in this directory. #file_path = database/files How do we go about moving the database to

[galaxy-dev] stdout in history

Yes that would work. Can you supply an example if possible please? Thanks Neil Message: 3 Date: Fri, 30 May 2014 15:04:47 +0200 From: Wolfgang Maier To: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] stdout in history Message-ID: Content-Type: text/plain; charset=UTF-8; format=flowed yo

[galaxy-dev] stdout in history

Hi, It seems that the first 4/5 lines that are printed in the source code tools appear in the history (when expended) and in stdout link. Is there anyway to stop "print" statements appearing in the history panel? Thanks Neil ___ Please

Re: [galaxy-dev] Galaxy queue

Thanks a lot guys for the help. That's just what I needed. I'll have a look at the database table Neil From: Hans-Rudolf Hotz [h...@fmi.ch] Sent: Monday, May 26, 2014 6:23 PM To: Peter Cock; Burdett, Neil (CCI, Herston - RBWH) Cc: galaxy-dev@lists.bx.psu.e

[galaxy-dev] Galaxy queue

Hi, is there anyway to find out (from the command line or api) what is on the Galaxy queue? When items are queued they appear in grey or processing in yellow can I get hold of these details from the command line as I could then email the user who has just submitted a job with his place on qu

Re: [galaxy-dev] Redirecting page after tool completes

Yes. I'm looking to auto display the final history output when the job finishes. It's pretty traightforward to get the URL to display i.e. http://'servername'/capaibl/datasets/5a1cff6882ddb5b2/display/?preview=True. However, I don't know how to use the URL to set it on the galaxy webpage. i.e.

[galaxy-dev] Redirecting page after tool completes

Hi, I have a tool that generates some png files. These are viewed when you click on the "eye" symbol. I was wondering if there is a way to automatically redirect to this html page once the job completes without the user needing to click on the "eye" symbol? (as this could be a small part in

[galaxy-dev] monitoring jobs start time

Hi, I am currently using the reports tool to see what jobs have been executed etc ... When you look at the information for each job it states the time the job was put on the queue (creation time) not the actual start time of the job. Do you know if the start time of the job is stored somew

[galaxy-dev] reports page download

Hi, is there a way to download the information found on the reports page so it can be used in excel for example? Thanks Neil ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions t

[galaxy-dev] User information when creating a new user

Hi, when a new user creates a new account they only need an email address and password. This can be quite tricky to identify the user/demographics etc at a alter point. Is there a form that a user may complete where he could add optional data such as name, institution, address etc ? There is

[galaxy-dev] Adding a new menu option in the header/masthead

On the banner/masthead there is a menu with things like Home, Shared Data, Admin, help etc ... How do you add a new option here. For example if I wanted something called "About" I could change ~/templates/webapps/galaxy/base_panels.mako and copy and paste something similar to the "Admin" tab

Re: [galaxy-dev] understanding change of colours in history

Thanks for the help John. I am using a slightly older version of Galaxy. However, I was hoping that the change of colour may help me understand the name change in the history. For example when you upload a file i.e. test.txt, "test.txt" appears in the history. However, if you want the history

[galaxy-dev] Bowse button on upload data tool page...

Hi, how is the "Browse..." button implemented on the data upload tool page? When you click on it you get a new window appearing so you can select files to upload. Does anyone know where is the "Browse..." button is defined/implemented in the code? I thought it would be in "./templates/weba

[galaxy-dev] understanding change of colours in history

Hi, Can someone point me in the direction of where the code in Galaxy is called to change the history background for example when a job changes from Yellow to red on error, or yellow to green on success. I've been going around in circles now trying to figure out, how this is implemented and

[galaxy-dev] Check file before uploading

Hi When selecting a file or after clicking on "Execute" to upload a file is it possible to check the file is appropriate i.e. by checking file extension etc, before the file is actually uploaded and put into the database? So the user can't upload the wrong file/format Thanks Neil Neil Burd

[galaxy-dev] popup window possible?

Hi, Is it possible to get a popup dialog box to appear for a tool? If so any examples on this please? i.e. the popup may just give a warning or an info message etc... that the user can confirm before proceeding. Or maybe another way to achieve the same thing? Thanks Neil Neil Burdett Softw

Re: [galaxy-dev] Import workflows via API

Hi Nicola, I've merged your changes into my version of the galaxy code (slightly older than galaxy-central) I believe, however, I get the following error when I try and execute your script: Traceback (most recent call last): File "get_wfs.py", line 13, in common.post(api_key,

Re: [galaxy-dev] Can't view file_name in histories via API unless admin?

Thanks Dannon, Apologies for the length of the email, I'll try and be as succint as possible. I am using Galaxy as a tool for medical image processing. We have a number of organisations (researchers and clinicians ) who would like to use the medical imaging tools we have d

[galaxy-dev] Import workflows via API

Hi Nicola, that is exactly what I'm looking for, however, how do I execute the script/tool? I would like to import all published workflows. What is the name of the script to run and the arguments ? Can you give an example please? Thanks again Neil

Re: [galaxy-dev] Can't view file_name in histories via API unless admin?

Hi Charles, not a problem. In my previous post I specified the command line: /home/galaxy/milxcloud/scripts/api/display.py http://barium-rbh:9100/extras/api/histories/ebfb8f50c6abde6d/contents/4a56addbcc836c23 The in your question refers to the api_key of an "admin" user, howev

Re: [galaxy-dev] Can't view file_name in histories via API unless admin?

I need to get the file_name so I can get the file_id, because to execute the "workflow_execute.py" I need: =hda= Unless there is another way to execute the "workflow_execute.py" or to get the Thanks Neil From: Burdett, Neil (CCI, Herston - RBWH) Sent: Friday, 17 January 2014 4:36 PM To: gala

[galaxy-dev] Can't view file_name in histories via API unless admin?

Hi, it seems that the entry "file_name:" does not appear when running the command /home/galaxy/milxcloud/scripts/api/display.py http://barium-rbh:9100/extras/api/histories/ebfb8f50c6abde6d/contents/4a56addbcc836c23 unless you are stated as as admin user in the "universe_wsgi.ini" i.e. admi

[galaxy-dev] Import workflows via API

Hi, I execute workflows via the API. However, if I want another user to use my workflows, I can publish my workflows, but the new user then has to go on to the web browser and import this workflow. Is there a method/script which I can call via the API which can import all available (publish

Re: [galaxy-dev] how to stop extra html file inserted into download zip

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 3:27 PM To: galaxy-dev@lists.bx.psu.edu

Re: [galaxy-dev] how to stop extra html file inserted into download zip

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-dev] how to stop extra html file inserted into download zip

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-dev] How to get an API key during execution?

Hi, I know that if I put : ${ __app__.model.User.get( $__user_id__ ).api_keys[0].key } in my tools xml file I am able to get the current api key. The xml calls my python script with this value, which i then use to execute workflows via the API. However, if this is value empty/blank is ther

[galaxy-dev] Auto hide tool and history panels

Hi When starting Galaxy the tool panel and history panels appear as default. On the bottom of these panels are two arrows to minimise / hide the panels. Can someone show me how to make the panels be hidden by default rather than shown ? Thanks Neil __

Re: [galaxy-dev] How to display tool instead of html WWFSMD page at start-up?

Yes I tried that but I still only see the default welcome.html page. Have you got this to work? Thanks Neil From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] Sent: Tuesday, 30 July 2013 12:37 PM To: Burdett, Neil (ICT Centre, Herston - RBWH) Cc: ross.laza...@gmail.com; galaxy-dev@lists.bx.psu.

Re: [galaxy-dev] How to display tool instead of html WWFSMD page at start-up?

Thanks Jeremy, But this doesn't seem to work. If I add the welcome_url to the universe_wsgi.ini (is this the universe config file you mentioned?) as shown below, I continue to get the welcome.html page # Galaxy --

[galaxy-dev] How to display tool instead of html WWFSMD page at start-up?

Hi, When Galaxy is started the centre column displays the "Hello world! It's running ..." WWFSMD? Html Page. How can this be changed so that a tool i.e. get data tool is shown up on start-up with all its text boxes etc rather than the default html file? Is this possible? Thanks Neil _

Re: [galaxy-dev] Creating multiple datasets in a libset

Further, when I look in the ~galaxy-dist/database/files/000 I can see both files have been uploaded but only the second file has a history associated to it Thanks Neil -Original Message- From: Burdett, Neil (ICT Centre, Herston - RBWH) Sent: Wednesday, 29 May 2013 2:45 PM To: galaxy-dev

Re: [galaxy-dev] Creating multiple datasets in a libset

Hi Guys, Did you manage to get multiple datasets working? I can't seem to upload multiple files. Only the last file appears in the history. I changed my code as mentioned in the thread below in "example_watch_folder.py" to add multiple files separated by a new line and increased the sle

Re: [galaxy-dev] Workflow refresh

Hi Dannon, I've modified the end of ~/galaxy-dist/tools/data_source/upload.py so that once the file has been uploaded, it calls a script which gets the current history file ID, workflow ID, ID if dataset uploaded and then calls execute_workflow.py with these inputs So the d

[galaxy-dev] Workflow refresh

Hi, I upload files which then automatically call execute_workflow.py. The files background turn to green , but to see the workflow running on the GUI I need to refresh the display. Does anyone know how I can add a refresh command to the code, and where in the code to add it. Thanks Neil

Re: [galaxy-dev] Bug in history when using Admin account ??

Hans, You are correct. When I look at the "Save Histories" and I double click on them I can see everything. Thanks for the help Neil -Original Message- From: Hans-Rudolf Hotz [mailto:h...@fmi.ch] Sent: Friday, 17 May 2013 4:58 PM To: Burdett, Neil (ICT Centre, Herston - RBWH) Cc:

[galaxy-dev] Bug in history when using Admin account ??

Hi, I believe I have found a bug? Or maybe I'm not using Galaxy correctly? These are the steps I used: * Downloaded the latest version of Galaxy * Created a user m...@me.com * Uploaded several files * Logged out * Create a user y

Re: [galaxy-dev] Getting example_watch_folder.py to work...

Hi all, I finally resolved the issue I'll mention it here to help anyone else who has the same issue. In "Edit" mode on the workflow you add the "Workflow control->Inputs" to use the api. Final question Everything gets created and stored in the database, but the history column on

[galaxy-dev] Getting example_watch_folder.py to work...

Hi, I'm still struggling to get the example_watch_folder.py to work. So any help much appreciated. I've created a simple workflow, which essentially opens a text file and then writes out the data to a html file. My xml file: Test $__root_dir__/tools/copy/copy.pl --input_im

Re: [galaxy-dev] Getting example_watch_folder.py to work...

It looks like the problem may have to do with the file I am using ??? It is a *.nii.gz file. Does galaxy try to uncompress ? do something to *.gz files when using the api (as it tries to do in ~/galaxy-dist/tools/data_source/upload.py Does anyone know of where in the code I can edit so my mile

Re: [galaxy-dev] Getting example_watch_folder.py to work...

Further, it seems that it doesn't manage to get hold of the file specified in the input directory as I can see from the output: http://barium-rbh/csiro/api/histories/964b37715ec9bd22/contents/2faba7054d92b2df { "data_type": "html", "deleted": false, "download_url": "/csiro/datasets/

[galaxy-dev] Getting example_watch_folder.py to work...

Hi, I'm trying to get the example_watch_folder.py to run but it seems to fail, and I'm not sure why? I run: ./example_watch_folder.py 64f3209856a3cf4f2d034a1ad5bf851c http://barium-rbh/csiro/api/ /home/galaxy/galaxy-drop/input /home/galaxy/galaxy-drop/output "My API Import" f597429621d6e

Re: [galaxy-dev] Command Line Tool for Creating New Users

Thanks Ross. I was missing __init__.py It now works thanks Neil From: Ross [mailto:ross.laza...@gmail.com] Sent: Tuesday, 30 April 2013 12:14 PM To: Burdett, Neil (ICT Centre, Herston - RBWH) Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Command Line Tool for Creating New Users Funn

Re: [galaxy-dev] Command Line Tool for Creating New Users

Thanks for the info Ross But I still get the same error "ImportError: No module named scripts.db_shell" After chmod 777 scripts/db_shell.py When you get "ImportError: No module named galaxy" for example it's because the PYTHONPATH isn't set so I guess there's some variable I need to set for t

[galaxy-dev] Command Line Tool for Creating New Users

Hi, I'm trying to use the tool, however, when I run it I get: python create_galaxy_users.py Traceback (most recent call last): File "create_galaxy_users.py", line 2, in from scripts.db_shell import * ImportError: No module named scripts.db_shell I've set my PYTHONPATH to be ~/galaxy

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

Thanks all that solved the problem. I also deleted my cache and cookies Thanks for the help Neil From: Ross [mailto:ross.laza...@gmail.com] Sent: Thursday, 21 February 2013 8:27 PM To: Peter Cock; Burdett, Neil (ICT Centre, Herston - RBWH); galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] H

Re: [galaxy-dev] 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-dev] 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

Re: [galaxy-dev] Multiple Instances ...

Thanks Ross. I did mean separate Galaxy instances like test and main with their own independent backend databases. How could I run say a test and a main from the same node? I guess I'd need to modify the port number for each instance and then multiple entries in the apache config file i.e. So

[galaxy-dev] Multiple Instances ...

Hi, Can someone point me to the documentation to set up /configure multiple instances of Galaxy running on the same node please? I think this is the best method of hiding tools based upon users email logon... Thanks Neil ___ Please keep

[galaxy-dev] 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-dev] 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-dev] XNAT and Galaxy.

Hi Does anyone have any experience / tools that allow Galaxy to work with a archiving/storage platform such as XNAT? Or maybe point me in the right direction to search, as I believe both platforms are using the REST API Neil ___ Please k

[galaxy-dev] 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 applic

Re: [galaxy-dev] Importing files into Libraries

Thanks for the information. Much appreciated Neil From: Enis Afgan [mailto:eaf...@emory.edu] Sent: Thursday, 25 October 2012 7:38 AM To: Burdett, Neil (ICT Centre, Herston - RBWH) Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Importing files into Libraries Hi Niel, I'm assuming the d

[galaxy-dev] Importing files into Libraries

Hi, If we upload data and then import the data into libraries, how is that data then accessed when running a tool in the cloud. For example if we have hundreds of template files that we need to analyse the data, and we have a tool that is instantiated on a number of nodes in the clous, is th

[galaxy-dev] Method to copy files....

Hi, Can you tell me the part of the Galaxy code or method responsible for actually copying over the data from one machine to another? i.e. it looks like data is first copied over to the ~/galaxy-dist/database/tmp area first before being moved on, which method copies over the data to ~/galaxy

Re: [galaxy-dev] Uploading composite datatypes.....

Thanks Nate. Maybe you could explain how to use/implement composite datatypes so I can understand fully how it works? The mvb file created is just a list of files i.e. The contents of Test.mvb could be: a.txt b.img c.log So, to get composite datatypes to "work" do I have to upload "

[galaxy-dev] Uploading composite datatypes.....

Hi, I was under the impression that when a composite datatype (basic) file is uploaded then the files contained within the composite file are also uploaded is this not the case? I was hoping my script would be able to have a file as an input. The file contains multiple files. Each one would