Re: [galaxy-dev] Trimmomatic tool is not visible in the workflow editor

I have installed Galaxy using this link : https://bitbucket.org/apetkau/galaxy-dist/get/b065a7a.tar.gz I’m using Galaxy along with an open source project so this instance is built specifically for that project I guess. In that case do you know how I should update it? Thanks, Dineli From:

Re: [galaxy-dev] Trimmomatic tool is not visible in the workflow editor

Hi Martin, It’s 15.03. Regards, Dineli From: Martin Čech [mailto:mar...@bx.psu.edu] Sent: Tuesday, September 13, 2016 10:31 PM To: Amarathunga A. Dineli Karunath; galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Trimmomatic tool is not visible in the workflow editor Hi Dineli, what version of

Re: [galaxy-dev] Trimmomatic tool is not visible in the workflow editor

I think you might need to update since I believe the trimmomatic tool uses features that are not available in the 15.03 Galaxy workflow editor/engine. M. On Tue, Sep 13, 2016, 21:45 Amarathunga A. Dineli Karunath < dineli_karunathil...@nuhs.edu.sg> wrote: > Hi Martin, > > > > It’s 15.03. > > >

Re: [galaxy-dev] Send repeat parameter to code file for multiple select list

If anyone was wondering, I ended up sending the name of the repeat to the function in the code file which is a list of dictionaries and in the dictionaries you have an index and the other parameters in the repeat so as long as you know the name of the parameters you are golden. On Fri, Sep 2,

[galaxy-dev] Odd error, solution not understood

Hi all, I'm getting the following error when attempting to do a trackster visualization: Error: The requested genome file (/vectorbase/web/Galaxy/galaxy/tool-data/shared/ucsc/chrom/?.len) could not be opened. Exiting! Couldn't open /vectorbase/web/Galaxy/galaxy/tool-data/shared/ucsc/chrom/?.len

Re: [galaxy-dev] Can't log in to Galaxy instance using Safari web browser

Stephanie: can you log in to usegalaxy.org or test.galaxyproject.org using Safari? Also please try to login to your instance using Safari private window. Martin On Tue, Sep 13, 2016 at 11:33 AM Stephanie LE GRAS wrote: > Hi Martin, > > > > Thank you for your feedback. We

Re: [galaxy-dev] Can't log in to Galaxy instance using Safari web browser

Hello Stephanie, I have just tested this on 16.07 and on `dev` branch of Galaxy and it works for both in my case. Can you please check the browser's console for javascript errors? Thanks, Martin On Tue, Sep 13, 2016 at 10:22 AM Stephanie LE GRAS wrote: > Hi there (again), >

Re: [galaxy-dev] Can't log in to Galaxy instance using Safari web browser

Hi Martin, Thank you for your feedback. We don’t have any javascript errors… Stephanie De : Martin Čech Date : mardi 13 septembre 2016 16:36 À : Stephanie Le Gras , "galaxy-dev@lists.galaxyproject.org" Objet : Re:

Re: [galaxy-dev] apache on ubuntu

Hi Keith, > You say you can see the Apache instance from other machines on the network. I > assume you are accessing your machine via its local IP address (something > like 192.168.1.x); what happens when you try to access Galaxy via > http://192.168.1.x:8080? > Yes I used my local IP and

[galaxy-dev] bowtie2 data_manager issue

I am indexing reference genomes for bowtie2/tophat2, using the corresponding data manager. I am getting some successful indexes and others are giving an error. For the successful ones I see the genomes are appearing in the "built in index" drop down for both bowtie2 and tophat2. For the

Re: [galaxy-dev] apache on ubuntu

Jochen, Two quick questions for you: You say you can see the Apache instance from other machines on the network. I assume you are accessing your machine via its local IP address (something like 192.168.1.x); what happens when you try to access Galaxy via http://192.168.1.x:8080? I see you

Re: [galaxy-dev] Trimmomatic tool is not visible in the workflow editor

Hi Dineli, what version of Galaxy do you have installed? thanks Martin On Tue, Sep 13, 2016 at 10:27 AM Amarathunga A. Dineli Karunath < dineli_karunathil...@nuhs.edu.sg> wrote: > Hi, > > I have a local galaxy instance and have installed many tools from the > galaxy tool shed. Recently I have

[galaxy-dev] Can't display tools in the middle panel of Galaxy

Hi there (again again), The last problem we are facing is that sometime when clicking on a tool name in the tool panel, the form don’t get displayed in the middle panel. We’ve checked the log of galaxy and it seems that the HTML request arrives but nothing happens. We have noticed that this

[galaxy-dev] Can't log in to Galaxy instance using Safari web browser

Hi there (again), Another problem we are currently facing is that we cannot log in anymore on our galaxy instance using Safari. It’s working with Firefox and Chrome but when we are using Safari (with the right password and login) we just see a green box saying that we successfully logged in

[galaxy-dev] Problem downloading HTML datasets

Hi there, I’m currently facing several problems with the galaxy instance I’m managing. I’m going to send a mail per problem so sorry in advance : for flooding ! The first problem I’m facing is that we can’t download HTML datasets from Galaxy. Here is the error I got when I try to do download

Re: [galaxy-dev] apache on ubuntu

a2enmod adds an apache module to your list of enabled modules. Previously enabled modules will remain enabled. -Will On Tue, Sep 13, 2016 at 12:10 AM, Jochen Bick wrote: > Hi Will and Ray, > > > > You may need to load the mod_rewrite module. This can be done via: > >

Re: [galaxy-dev] apache on ubuntu

Hi Will and Ray, > You may need to load the mod_rewrite module. This can be done via: > sudo a2enmod rewrite I will try that. Is this also resetting the modules of apache? > > -Will > >> >> I presume you've restarted the web server after making this change? >> >> Apache's mod_rewrite (the