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.

On Jun 29, 2010, at 8:37 AM, Davide Cittaro wrote:

On Jun 29, 2010, at 2:29 PM, Davide Cittaro wrote:

...

Hi all, how does the library search tool work? I'm trying on the public galaxy but I can't get any result...

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 */

---

galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user

Greg Von Kuster Galaxy Development Team greg@bx.psu.edu

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...

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.

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 ------------------------------------------------------------------

Hi Pieter,

Thanks for reporting this. It should be fixed in changeset 4158:03be4a0828ce.

Thanks, --nate

Pieter Neerincx wrote:

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

---

---

galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user

Hi Nate,

Thanks for the fast reply and fix! I'll give the update a try...

Cheers,

Pi

On Aug 18, 2010, at 9:16 PM, Nate Coraor wrote:

Hi Pieter,

Thanks for reporting this. It should be fixed in changeset 4158:03be4a0828ce.

Thanks, --nate

Pieter Neerincx wrote:

...

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

---

---

galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user

------------------------------------------------------------- mobile: +31 6 143 66 783 e-mail: pieter.neerincx@gmail.com skype: pieter.online -------------------------------------------------------------