[galaxy-dev] customize the Upload File tool form (version 1.1.4)

Hi, As we have arranged an sftp upload system through ftp port for our Galaxy instance, we would need to customize the Upload File tool form, so that a few more line explain how-to-do in the FTP section of the form, in addition to the "This Galaxy server allows you to upload files via FTP. To uplo

[galaxy-dev] rename output dataset in workflow - input dataset variable

Hello, I want to rename ouput datasets in a workflow in such a way that the name contains the name of the input dataset. I could not find instructions in the manual (and this info is missing in the Workflow editor - would be really helpful there!). I tried #{input}, e.g. "stats on: #{input}" (wit

Re: [galaxy-dev] rename output dataset in workflow - input dataset variable

For what it's worth (not much ;), I think the dataset naming is the single least intuitive part of the galaxy system for biologists. I think there's a proposal to "fix" this problem - and mainain the connection between input data set and derived data, but It doesn't seem to have gone anywhere y

Re: [galaxy-dev] customize the Upload File tool form (version 1.1.4)

Hi Christophe, In order to apply the changes scripts have to be packed properly. Please follow these steps: 1. Go to the client/ directory and type 'npm install' 2. Now type 'grunt watch'. This will start a listener which captures code changes and repacks scripts automatically 3. Finally, make yo

Re: [galaxy-dev] customize the Upload File tool form (version 1.1.4)

I updated our wiki with this new build information. https://wiki.galaxyproject.org/Develop/JSA M. On Wed, Nov 12, 2014 at 10:11 AM, Aysam Guerler wrote: > Hi Christophe, > > In order to apply the changes scripts have to be packed properly. Please > follow these steps: > > 1. Go to the client/ d

Re: [galaxy-dev] Tool shed environment dependency - HOW TO do this?

Indeed...painful and slow :( What I need is R 3.1.1 or later...so if I can get a pre-compiled package in toolshed that works I’m also happy! I understand Dave manages this process? @Dave: can you help me? Thanks, Pieter From: bjoern.gruen...@googlemail.com [mailto:bjoern.gruen...@gmail.com] S

Re: [galaxy-dev] Tool shed environment dependency - HOW TO do this?

Pieter, I am in fact planning on compiling R 3.1.1 for depot.galaxyproject in the near future. --Dave B. On 11/12/2014 11:25 AM, Lukasse, Pieter wrote: Indeed...painful and slow :( What I need is R 3.1.1 or later...so if I can get a pre-compiled package in toolshed that works I’m also ha

Re: [galaxy-dev] Tool shed environment dependency - HOW TO do this?

Ah, great! Please let me know once I can use it. Thanks, Pieter -Original Message- From: Dave Bouvier [mailto:d...@bx.psu.edu] Sent: woensdag 12 november 2014 17:27 To: Lukasse, Pieter; 'bjoern.gruen...@googlemail.com' Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Tool shed

[galaxy-dev] large drill down selection UI component?

Hi all, I was wondering if there were any existing implementations of, or any plans for, a drill down selection component that supports thousands of items? For example a taxonomy based drill down. Thanks, Andrew ___ Please keep all replies o

Re: [galaxy-dev] customize the Upload File tool form (version 1.1.4)

Aysam and Martin, Thanks for your help. I am not familiar with JS development. To make "client" crystal clear : /client stands for the home directory where Galaxy-dist is installed ? and client/galaxy/scripts/mvc/upload stands for ~/galaxy-dist/scripts/mvc/upload (assuming that the galaxy code i

Re: [galaxy-dev] customize the Upload File tool form (version 1.1.4)

corrrect: /client is a directory within Galaxy root - it contains all the javascripts The build (grunt) process takes the /client directory and copies the scripts to /static/scripts directory within Galaxy root (and packs them and stuff) from where the files are served to the browser. If you want

[galaxy-dev] Dataset collection generation from a tool

Hello, Does anyone know if it's possible to generate as output from a tool a dataset collection when it's input is only a single file? I'm imagining a tool which takes as input a file containing a list of URLs for files outside of Galaxy and generates as output a dataset collection that can then

Re: [galaxy-dev] Dataset collection generation from a tool

I think I may have just found the answer to my question in this trello card https://trello.com/c/ndVQmt3G/1857-tools-should-be-able-to-generate-one-or-more-dataset-collections On Wed, Nov 12, 2014 at 3:15 PM, Aaron Petkau wrote: > Hello, > > Does anyone know if it's possible to generate as outpu

Re: [galaxy-dev] customize the Upload File tool form (version 1.1.4)

Ok I just noticed the new client directory in Bitbucket and the accompanying trello cards. Make things more understandable... Thanks Chris Christophe Antoniewski Drosophila Genetics and Epigenetics Institut de Biologie Paris Seine

Re: [galaxy-dev] Repeats shown upside down on galaxy-central

Hi Sam, On Thu, Nov 13, 2014 at 6:25 AM, Aysam Guerler wrote: > Hey Peter, > > I have modified the data selectors appearance by adding a single select > field as default option. It resembles the previous functionality now and I > think its an improvement. > Great. I won't be able to try this u

Re: [galaxy-dev] Repeats shown upside down on galaxy-central

I see your point maybe a maximum width will fix the issue for wide screens. I look into it. Thanks, Sam On Wed, Nov 12, 2014 at 7:42 PM, Peter Cock wrote: > Hi Sam, > > > On Thu, Nov 13, 2014 at 6:25 AM, Aysam Guerler > wrote: > >> Hey Peter, >> >> I have modified the data selectors appearance

[galaxy-dev] toolsheds down

Main and Test toolsheds are not resolving properly tonight... {u'status': u'error', u'error': u'Error attempting to retrieve installation information from tool shed http://testtoolshed.g2.bx.psu.edu for revision 7511823bdea1 of repository bedtools owned by iuc: '} Cheers, -Evan Bollig Research As