Question: Search In Libraries
0
gravatar for Davide Cittaro
8.2 years ago by
Davide Cittaro140 wrote:
Hi all, how does the library search tool work? I'm trying on the public galaxy but I can't get any result... d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro@ifom-ieo-campus.it */
galaxy • 769 views
ADD COMMENTlink modified 8.2 years ago • written 8.2 years ago by Davide Cittaro140
0
gravatar for Davide Cittaro
8.2 years ago by
Davide Cittaro140 wrote:
I mean, does it only work at "first level"? d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro@ifom-ieo-campus.it */
ADD COMMENTlink written 8.2 years ago by Davide Cittaro140
Hi Davide, When browsing all libraries, you can currently search on the name or description of the library itself, but searching does not currently work for library contents ( folders and datasets ). It is on our development plans to enable searching on contents. Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
ADD REPLYlink written 8.2 years ago by Greg Von Kuster810
Hi, When I click the Options button in the tool pane on the left there's no option to search for tools. I can only show or hide recently used tools. Is there something I need to configure/enable to make this work? I browsed the Wiki, but could not find relevant documentation... Cheers, Pi
ADD REPLYlink written 8.1 years ago by Pieter Neerincx360
Pieter, Configuration is not necessary for tool search; it should always be available from the Options menu. Answering a couple questions should help us debug the issue: *Are you using the public/main Galaxy instance or an instance of your own? *What web browser are you using? *Are there any Javascript errors that your web browser is reporting? Thanks, J.
ADD REPLYlink written 8.1 years ago by Jeremy Goecks2.2k
Dear Jeremy, Thanks, good to know. Then I can stop searching for the magic setting on the config files :) Our own instance. I just tried the public/main Galaxy instance and tool search works just fine for me over there, so I doubt it's my web browser. I tried Camino, FireFox and Safari all on OS X. All with the same result. No, the only errors I can see are a missing favicon.ico and a missing
tag in tool_menu just before the closing </body> </html> tags... Our Galaxy is not 100% up to date, but fairly recent: it's from 03-aug-2010. Were there any recent fixes for the tool search or should our instance be recent enough? Cheers, Pi Biomolecular Mass Spectrometry & Proteomics group Utrecht University phone: +31 6 143 66 783 email: pieter.neerincx@gmail.com skype: pieter.online visiting address: H.R. Kruyt building // room O607 Padualaan 8 // 3584 CH Utrecht // The Netherlands mail address: P.O. box 80.082 // 3508 TB Utrecht // The Netherlands
ADD REPLYlink written 8.1 years ago by Pieter Neerincx360
Hmm. This should be recent enough to include the tool search and any bug fixes after we rolled it out. However, it would be nice if you could update your Galaxy instance and try again. If it still breaks, at least we're working from the current and same codebase. Is it possible for you to update your Galaxy instance and try again? Thanks, J.
ADD REPLYlink written 8.1 years ago by Jeremy Goecks2.2k
Hi Jeremy, Yes, but probably not until next week. I'll get back to you when I've tried it on the latest version... Cheers, Pi mobile: +31 6 143 66 783 e-mail: pieter.neerincx@gmail.com skype: pieter.online
ADD REPLYlink written 8.1 years ago by Pieter Neerincx360
Hi all, I used to have working sniffers for custom data formats, but the documentation on the wiki is no longer enough to make it work :(... When I start our Galaxy I do see log messages like this: galaxy.datatypes.registry INFO 2010-08-17 18:20:28,666 Loaded sniffer for datatype: galaxy.datatypes.nbic:RAW which suggests that the sniffers should be enabled, but unfortunately they don't work. If I add the sniffers to the default list in galaxy/lib/galaxy/datatypes/registry.py like this: .... # Default values - the order in which we attempt to determine data types is critical # because some formats are much more flexibly defined than others. if len(self.sniff_order) < 1: self.sniff_order = [ nbic.RAW(), nbic.OtherCustomFormat(), binary.Bam(), binary.Sff(), xml.BlastXml(), sequence.Maf(), sequence.Lav(), sequence.csFasta(), etc..... my sniffers do work, so I'm pretty sure it's not the sniff-logic. Does anyone have an idea how I can make my sniffers work again by simply adding them to datatypes_conf.xml and importing them in registry.py, but without hacking the code in registry.py that builds the list of sniffers? Cheers, Pi Biomolecular Mass Spectrometry & Proteomics group Utrecht University phone: +31 6 143 66 783 email: pieter.neerincx@gmail.com skype: pieter.online visiting address: H.R. Kruyt building // room O607 Padualaan 8 // 3584 CH Utrecht // The Netherlands mail address: P.O. box 80.082 // 3508 TB Utrecht // The Netherlands
ADD REPLYlink written 8.1 years ago by Pieter Neerincx360
Hi Pieter, Thanks for reporting this. It should be fixed in changeset 4158:03be4a0828ce. Thanks, --nate
ADD REPLYlink written 8.1 years ago by Nate Coraor3.2k
Hi Nate, Thanks for the fast reply and fix! I'll give the update a try... Cheers, Pi mobile: +31 6 143 66 783 e-mail: pieter.neerincx@gmail.com skype: pieter.online
ADD REPLYlink written 8.1 years ago by Pieter Neerincx360
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