Re: [galaxy-dev] Bypassing Data Managers?

Hi Hans-Rudolf, Thank you for getting back to me! I did take a peak at those files and they seem self-explanatory. I think I can do that. However, I was worried about the message at the top of: https://wiki.galaxyproject.org/Admin/DataPreparation It seemed the method written on that page has now been superseded by Data Managers? I was worried editing *.loc files directly with an editor would break a database and cause more headaches for me. Is that not the case or perhaps I can get away with doing it just for the FASTA files but should still use Data Managers for index generation? Thank you! Ray On Thu, Feb 18, 2016 at 3:54 PM, Hans-Rudolf Hotz <hrh(a)fmi.ch&gt; wrote: > Hi Ray > > If you already have the reference data (as you have written in your first > e-mail), then I suggest you manually add those files (file paths) to > > ~/tool-data/bowtie2_indices.loc > ~/tool-data/bowtie_indices.loc > > This way you prevent duplication of your reference data > > > Regards, Hans-Rudolf > > > >> Dear all, >> >> I have gotten a bit further and was able to install the Data Managers >> this time. Previously, I was having problems accessing the ToolShed >> web site and some Python errors in the log file, but fine ... sort of >> (I get some intermittent errors accessing the Tool Shed site; maybe >> it's a problem on my side). >> >> However, with the FASTA fetch tool installed from the Galaxy Main Tool >> Shed, I selected "Local Data" from the Administrator panel. Under >> "Run Data Manager Tools", I now have "Bowtie index", "Reference >> Genome", etc. When I click on any of the options under "Run Data >> Manager Tools", though, I get a blank page. I mean, I get a >> user-level menu on the left, history on the right, a menu along the >> top. But the center is blank. Is there something else I need to do? >> >> If I go to "View Data Manager Jobs", "Reference Genome", though, I get >> a message that says there are "There are no jobs for this data >> manager.". >> >> If possible, I would like to upload FASTA files myself to our local >> Galaxy instance. For reasons which I'm still working on (and which is >> unrelated to Galaxy), download times are very long. Since I have the >> FASTA file already, it might be easier to upload one myself; but if >> that's not something Data Managers can do, I guess I can just start >> the download and set it aside... >> >> Thank you! >> >> Ray >> >> >> >> On Thu, Feb 18, 2016 at 8:36 AM, Raymond Wan <rwan.work(a)gmail.com&gt; wrote: >>> >>> Dear all, >>> >>> I'm a bit new at being a Galaxy administrator, so apologies for the >>> basic question. >>> >>> I need to install some bowtie and bowtie2 indices. I have the indices >>> already but came across this page: >>> >>> https://wiki.galaxyproject.org/Admin/DataPreparation >>> >>> which says the steps mentioned on that page have been replaced with >>> Data Managers. I'm having problems with installing Data Managers >>> (accessing ToolShed right now and some errors which I guess I need to >>> sort out later) and was wondering if there was a way to bypass Data >>> Managers? >>> >>> Are Data Managers the only way of installing reference data? With the >>> indices already pre-calculated, can I install them without having to >>> go through re-calculating them within Galaxy? >>> >>> Thank you! >>> >>> Ray >> >> ___________________________________________________________ >> 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/ >> >