Re: [galaxy-dev] FastQC galaxy issue

Hi, I think it can. I tried it from command line and it worked. -Original Message- From: Björn Grüning [mailto:bjoern.gruen...@gmail.com] Sent: Saturday, September 12, 2015 11:19 AM To: Hakeem Almabrazi; Bjoern Gruening; galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] FastQC

[galaxy-dev] GCC2017 Needs a Host!

Hello all, The Galaxy Community Conference has been held annually since 2010. GCC2016 will be held June 25-29 at Indiana University in Bloomington, Indiana, United States. *We are now seeking proposals

Re: [galaxy-dev] simplifying Galaxy interface to the max (zen-like)

I don't have a ton of advice here, I imagine you could hack up Galaxy to do it. If you a have a fixed workflow or fixed collections of workflows and very clear vision of what the interface should be I guess I would just create a web app and target the Galaxy API. Two projects to checkout would be

Re: [galaxy-dev] simplifying Galaxy interface to the max (zen-like)

Hi Piotr, I see two basic approaches: * You can use an API to interact with any Galaxy so writing a single webapp that does just that is an option. However you would need to interact with user's credentials as API would need a user key for most of the interactions. You can use e.g. BioBlend libr

[galaxy-dev] simplifying Galaxy interface to the max (zen-like)

Dear Galaxy-Devs, I am developing a tool for biologists, I managed to integrate it with Galaxy (it's a KNIME/R-based machine learning workflow). This tool doesn't require a lot of interaction from the user - just a list of IDs pasted-in and maybe 1-2 text entry fields - then it's just Execute. Ev

[galaxy-dev] Removing LWR Support from Galaxy

Hello All, The LWR has been deprecated for over a year now. It has been renamed and replaced by Pulsar which has many advantages over the previous LWR code base. Instructions on migrating from the LWR to Pulsar can be found here - http://pulsar.readthedocs.org/en/latest/upgrading.html. There

Re: [galaxy-dev] Adding data libraries from filesystem path creating duplicates

If I had to guess, I would guess this is caused by a mis-configured proxy (nginx or Apache) that is resubmitting a POST request that is taking Galaxy to long to respond to. Order of events being something like: - User clicks to upload library items. - Proxy gets requests and passes to Galaxy - Gal

Re: [galaxy-dev] Subtleties of and escaping dollar signs

I would say it is a ways off yet, it doesn't even validate all proper XML yet, let alone have proper documentation tags. I was hoping adding the validation feature to planemo would spur some development on it, but it hasn't happened yet. Some people are trying it out though (https://github.com/gala

Re: [galaxy-dev] Opening Galaxy with a specified History Name

It looks like you can specify a tool or workflow to jump straight to but not a history. The following pull request (https://github.com/galaxyproject/galaxy/pull/725) extends this functionality to include histories. You will need the encoded history ID as returned by the workflow and history API to

Re: [galaxy-dev] Process stuck in unix 'T' State

Do you have a job runner configured or are you just using the default local job runner? I'm not sure what could cause this, is the main script actually launched by Galaxy still running or just child processes? I assume this is happening for just one script or tool and not all of them right? If yes

Re: [galaxy-dev] Galaxy configuration

This means the job has probably been queued in PBS, do you want to run qstat as the Galaxy user on the command line and see if you can see the Galaxy job - it may just be sitting there waiting for resources to run. The PBS logs might have more information at this point. -John On Mon, Sep 14, 2015

Re: [galaxy-dev] Galaxy configuration

Hi Nate, Also, the only configuration I did on my Galaxy installation is the job_conf.xml file. I have not edited any of the other xml files or used other config sample files. Should I also have edited some other XML configuration files. Also, do I need to have run any of the executbales in t