Re: [galaxy-dev] apache proxy
Hey Thon, I'd probably recommend using a simple supervisord (http://supervisord.org/) configuration to do this. Here's a link to some great reference material that might help you out: https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay/AdminWalkthrough#Configure_supervisord -Dannon On Wed Feb 18 2015 at 11:11:36 AM Michael Thon mike.t...@gmail.com wrote: If I use apache to proxy connections to the galaxy run.sh process, what is the best way to launch galaxy at boot time? Can apache do it? ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] problem with latest toolshed devteam cuffmerge wrapper multi-select
And, yes, all of the gtf files have the correct database build associated with them. On Wed, Feb 18, 2015 at 6:29 PM, Nikhil Joshi najo...@ucdavis.edu wrote: Hi all, We run our own custom galaxy instance in the Amazon Cloud and I am updating our instance with the latest toolshed files. For cuffmerge, in past revisions, we would just have a button to add another GTF input. However, this latest one (10:b6e3849293b1 https://toolshed.g2.bx.psu.edu/repository/view_changelog?id=84bbebf45888f374) that has been replaced with a multi-select. We also have a few built-in genomes that we use with cuffmerge. When I choose the first GTF file (using locally cached sequence data) it will populate the reference genome correctly with our built-in genomes. However, once I choose more than one GTF file, I get one of two errors: No reference genome is available for the build associated with the selected input dataset OR An invalid option was selected, please verify The built-in genomes are definitely there and available for cuffmerge, but for some reason choosing more than one GTF file in the multi-select causes an error. Is this a bug or am I doing something wrong? - Nik. -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w) -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w) ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Hooking a dataset full deletion
Thanks Dannon! Actually I’d like to avoid code hacking enforcing NTCC (no touch core code!). Anyway, if there is no other way I’ll share the hack with the community, maybe could be part of next core improvements. Bests, — Raffaele On 18 Feb 2015, at 07:19, Dannon Baker dannon.ba...@gmail.com wrote: There isn't a hook that already exists for this, but if this is for a custom instance and you're looking to hack something in, you could add extra logic to lib/galaxy/managers/hdas.py in the 'purge' method. Let me know if you need more information, good luck! -Dannon On Tue Feb 17 2015 at 6:37:52 PM Raffaele Montella raffaele.monte...@uniparthenope.it mailto:raffaele.monte...@uniparthenope.it wrote: Hi, I need to perform some actions when a dataset if fully deleted. Does it exist a hook in datatype definition to do that? Thanks, Raffaele ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] fastq format recognition
Thanks Martin - allow_library_path_paste did the job. Mike On Feb 18, 2015, at 6:14 AM, Martin Čech mar...@bx.psu.edu wrote: Hello Mike, you probably want to set library_import_dir or allow_library_path_paste in the config. Details here: https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles Martin On Tue Feb 17 2015 at 11:40:37 PM Michael Thon mike.t...@gmail.com wrote: On Feb 13, 2015, at 1:35 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Fri, Feb 13, 2015 at 12:08 PM, Michael Thon mike.t...@gmail.com wrote: I have a new galaxy installation on my server. I uploaded two fastq files and now I'm trying to run trimmomatic and fastqc. In both cases I am presented with a drop down list of fastq files to select from but the lists are empty. I double checked the fastq file attributes and they are both set to fastq. Any ideas what's wrong? You probably need to change the format to the more specific fastqsanger datatype (FASTQ using the Sanger encoding). It may be time for Galaxy to change their default, since the old Solexa and Illumina variants are no longer widely used. Another question: I have fastq files already on the same server as the galaxy installation. How can I get them into galaxy? I have not set up ftp yet. Can I move them into a data directory somewhere? One option is to import them into a library (which can link to the files rather than coping them). Are you a Galaxy administrator? Peter I just tried adding them to a library. On the library admin page there is an option to upload files or to import data from my history. There is no option to link to files on the filesystem. Does this need to be activated in the config somewhere? Thanks ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
