Re: [galaxy-dev] login problem (redirection to the login page)

Hello, I've been struggling with the login issue with Galaxy for a while now. Try to use "incognito mode" on your browser when accessing the url for Galaxy and see what happens. Also if you don't really need for your users to activate their accounts by e-mail set the "user_activation_on=False"

Re: [galaxy-dev] FASTQ Groomer tool

Hi Edgar, it seems you are hitting this fail: https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/jobs/handler.py#L124 which hints that the tool is not properly loaded in the toolbox. Did you restart the server and handlers after you installed the tool? I cannot help with the MySQL as we

Re: [galaxy-dev] FASTQ Groomer tool

Hi Edgar, Galaxy loads tools on start so if you install a tool it will show it in the panel (because that config is independent and already updated) however the toolbox will not have it yet until the restart. I updated the wiki (

Re: [galaxy-dev] Galaxy Startup Failing

Hi Keith, I use start-stop-daemon to launch python and I pass --chuid and --group to start-stop-daemon so that galaxy does not run as root. It is my understanding that start-stop-daemon creates the pid file as root before changing user, as my /var/run/galaxy.pid is owned by root:root. I have

[galaxy-dev] R: Re: FASTQ Groomer tool

Hi Edgar, to add to Martin's explanation, it is my understanding that only the web process from which the tool installation is initiated knows about the new tool. The other web and handler processes will know about it only after a restart. Cheers, Nicola Martin Čech ha scritto

[galaxy-dev] Galaxy Url for Fasta and Bed index files

Hello, What is an appropriate galaxy URL to use to obtain bed and fasta index files? I have tried below: myGalaxy.org:port/dataset/get_metadata_file?hda_id=[fasta_dataset_id]_name=fasta.fai {for fasta index} and myGalaxy.org:port/dataset/get_metadata_file?hda_id=[bed_dataset_id]_name=bed.idx

[galaxy-dev] Error in sh manage_db.sh -c ./config/galaxy.ini upgrade

Dear Galaxy Dev Team, We upgraded our Galaxy instance to the git repository from mercurial old Galaxy-dist to Galaxy. When running the sh manage_db.sh -c ./config/galaxy.ini upgrade we get the following error. Can you explain this error and more importantly how to correct the problem>

Re: [galaxy-dev] Planemo 0.19.0 testing tools that produce dataset collections

Nicola, thanks a bunch! Your eyes are phenomenal! Greg > On Nov 4, 2015, at 8:09 PM, Nicola Soranzo wrote: > > Hi Greg, > in the inputs the param has name "input_gff", while in the test you are using > name "input". > > Cheers, > Nicola > > Von Kuster, Greg ha