Re: [galaxy-dev] [galaxy-user] Cannot get rid of custom build error
Hi Jim, You'll need to update your datatypes_conf.xml file to get custom builds + converters to work. This file is located in the root of your galaxy directory. If you haven't modified your datatypes_conf.xml file previously, you can just copy datatypes_conf.xml.sample to datatypes_conf.xml If you have modifed this file, please add the following lines to your datatypes_conf.xml: (a) to the fasta definition and (b) to the len definition See datatypes_conf.xml.sample for examples. Also, you'll need to download and add the UCSC program fastaToTwoBit to your path as well. You can find UCSC executables here: hgwdev.cse.ucsc.edu/~kent/exe/ Good luck, J. > Hello, > > I've tried to create a custom build (starting from the trackster page) > and clearly made some mistake. I get a NoConverterException error > which is almost certainly my fault putting something wrong in. > However, now the Custom Builds page shows this error and I cannot make > it go away. > > I have a local install, have killed and restarted, logged in and out, > but still this error stays. I cannot try to enter another custom build > because there is nothing on the page except this error. Does anyone > kow how to get rid of this? Any help in getting around this error are > appreciated. > > Jim > ___ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] [galaxy-user] Cannot get rid of custom build error
James, do you have an entry for the "fasta_to_len" convertor in your
datatypes_conf.xml? If not, you might want to update your config to include
those entries from the sample. Thanks!
-- jt
(composed on my phone)
On Nov 2, 2011, at 11:58 AM, James Vincent wrote:
> Hello Devs,
>
> I can confirm I am using the latest build:
>
> galaxy@monolith:~/galaxy-dist$ hg pull -u -r 338ead4737ba
> pulling from https://bitbucket.org/galaxy/galaxy-dist/
> searching for changes
> no changes found
> galaxy@monolith:~/galaxy-dist$
>
> Here is a copy of the error message that shows when I click on Custom
> Builds under the User main menu. Oddly, when on this page I cannot
> kill the galaxy main process. I start with ./run.sh --reload. Giving a
> control-c won't kill it until I leave that error page. Hope that
> helps.
>
>
> Error Traceback:
> View as: Interactive | Text | XML (full)
> ⇝ NoConverterException: "Conversion from 'fasta' to 'len' not possible"
> URL: http://monolith.uvm.edu:8080/user/dbkeys
> Module weberror.evalexception.middleware:364 in respond view
>>> app_iter = self.application(environ, detect_start_response)
> Module paste.debug.prints:98 in __call__ view
>>> environ, self.app)
> Module paste.wsgilib:539 in intercept_output view
>>> app_iter = application(environ, replacement_start_response)
> Module paste.recursive:80 in __call__ view
>>> return self.application(environ, start_response)
> Module paste.httpexceptions:632 in __call__ view
>>> return self.application(environ, start_response)
> Module galaxy.web.framework.base:160 in __call__ view
>>> body = method( trans, **kwargs )
> Module galaxy.web.framework:86 in decorator view
>>> return func( self, trans, *args, **kwargs )
> Module galaxy.web.controllers.user:1217 in dbkeys view
>>> len_dataset = fasta_dataset.get_converted_dataset( trans, "len" )
> Module galaxy.model:913 in get_converted_dataset view
>>> raise NoConverterException("Conversion from '%s' to '%s' not possible" %
>>> (self.extension, target_ext) )
> NoConverterException: "Conversion from 'fasta' to 'len' not possible"
>
>
>
> Extra Features
>>>Display the lines of code near each part of the traceback
>Show a debug prompt to allow you to directly debug the code at the
> traceback
> Re-GET Page
> test build.
>
> Here is a copy of the error message that shows when I click on Custom
> Builds under the User main menu:
>
>
> On Wed, Nov 2, 2011 at 10:35 AM, Jennifer Jackson wrote:
>> Hi Jim,
>>
>> I am going to post your question over to the galaxy-dev mailing list (is
>> best for local/cloud instance questions).
>>
>> Would you be able to confirm which version of Galaxy you are running? The
>> latest version of the distribution?
>>
>>http://wiki.g2.bx.psu.edu/News%20Briefs/2011_10_25
>>"upgrade: % hg pull -u -r 338ead4737ba"
>>
>> Please send your reply as a "reply-all" that includes the galaxy-dev mailing
>> list, but omits the galaxy-user mailing list.
>>
>> Thanks for the additional information,
>>
>> Jen
>> Galaxy team
>>
>> On 11/2/11 4:04 AM, James Vincent wrote:
>>>
>>> Hello,
>>>
>>> I've tried to create a custom build (starting from the trackster page)
>>> and clearly made some mistake. I get a NoConverterException error
>>> which is almost certainly my fault putting something wrong in.
>>> However, now the Custom Builds page shows this error and I cannot make
>>> it go away.
>>>
>>> I have a local install, have killed and restarted, logged in and out,
>>> but still this error stays. I cannot try to enter another custom build
>>> because there is nothing on the page except this error. Does anyone
>>> kow how to get rid of this? Any help in getting around this error are
>>> appreciated.
>>>
>>> Jim
>>> ___
>>> The Galaxy User list should be used for the discussion of
>>> Galaxy analysis and other features on the public server
>>> at usegalaxy.org. Please keep all replies on the list by
>>> using "reply all" in your mail client. For discussion of
>>> local Galaxy instances and the Galaxy source code, please
>>> use the Galaxy Development list:
>>>
>>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>>>
>>> To manage your subscriptions to this and other Galaxy lists,
>>> please use the interface at:
>>>
>>> http://lists.bx.psu.edu/
>>
>> --
>> Jennifer Jackson
>> http://usegalaxy.org
>> http://galaxyproject.org/wiki/Support
>>
>>
>
> ___
> 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:
>
> http://lists.bx.psu.edu/
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lis
Re: [galaxy-dev] [galaxy-user] Cannot get rid of custom build error
Hello Devs,
I can confirm I am using the latest build:
galaxy@monolith:~/galaxy-dist$ hg pull -u -r 338ead4737ba
pulling from https://bitbucket.org/galaxy/galaxy-dist/
searching for changes
no changes found
galaxy@monolith:~/galaxy-dist$
Here is a copy of the error message that shows when I click on Custom
Builds under the User main menu. Oddly, when on this page I cannot
kill the galaxy main process. I start with ./run.sh --reload. Giving a
control-c won't kill it until I leave that error page. Hope that
helps.
Error Traceback:
View as: Interactive | Text | XML (full)
⇝ NoConverterException: "Conversion from 'fasta' to 'len' not possible"
URL: http://monolith.uvm.edu:8080/user/dbkeys
Module weberror.evalexception.middleware:364 in respond view
>> app_iter = self.application(environ, detect_start_response)
Module paste.debug.prints:98 in __call__ view
>> environ, self.app)
Module paste.wsgilib:539 in intercept_output view
>> app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__ view
>> return self.application(environ, start_response)
Module paste.httpexceptions:632 in __call__ view
>> return self.application(environ, start_response)
Module galaxy.web.framework.base:160 in __call__ view
>> body = method( trans, **kwargs )
Module galaxy.web.framework:86 in decorator view
>> return func( self, trans, *args, **kwargs )
Module galaxy.web.controllers.user:1217 in dbkeys view
>> len_dataset = fasta_dataset.get_converted_dataset( trans, "len" )
Module galaxy.model:913 in get_converted_dataset view
>> raise NoConverterException("Conversion from '%s' to '%s' not possible" %
>> (self.extension, target_ext) )
NoConverterException: "Conversion from 'fasta' to 'len' not possible"
Extra Features
>> Display the lines of code near each part of the traceback
Show a debug prompt to allow you to directly debug the code at the
traceback
Re-GET Page
test build.
Here is a copy of the error message that shows when I click on Custom
Builds under the User main menu:
On Wed, Nov 2, 2011 at 10:35 AM, Jennifer Jackson wrote:
> Hi Jim,
>
> I am going to post your question over to the galaxy-dev mailing list (is
> best for local/cloud instance questions).
>
> Would you be able to confirm which version of Galaxy you are running? The
> latest version of the distribution?
>
> http://wiki.g2.bx.psu.edu/News%20Briefs/2011_10_25
> "upgrade: % hg pull -u -r 338ead4737ba"
>
> Please send your reply as a "reply-all" that includes the galaxy-dev mailing
> list, but omits the galaxy-user mailing list.
>
> Thanks for the additional information,
>
> Jen
> Galaxy team
>
> On 11/2/11 4:04 AM, James Vincent wrote:
>>
>> Hello,
>>
>> I've tried to create a custom build (starting from the trackster page)
>> and clearly made some mistake. I get a NoConverterException error
>> which is almost certainly my fault putting something wrong in.
>> However, now the Custom Builds page shows this error and I cannot make
>> it go away.
>>
>> I have a local install, have killed and restarted, logged in and out,
>> but still this error stays. I cannot try to enter another custom build
>> because there is nothing on the page except this error. Does anyone
>> kow how to get rid of this? Any help in getting around this error are
>> appreciated.
>>
>> Jim
>> ___
>> The Galaxy User list should be used for the discussion of
>> Galaxy analysis and other features on the public server
>> at usegalaxy.org. Please keep all replies on the list by
>> using "reply all" in your mail client. For discussion of
>> local Galaxy instances and the Galaxy source code, please
>> use the Galaxy Development list:
>>
>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>>
>> To manage your subscriptions to this and other Galaxy lists,
>> please use the interface at:
>>
>> http://lists.bx.psu.edu/
>
> --
> Jennifer Jackson
> http://usegalaxy.org
> http://galaxyproject.org/wiki/Support
>
>
___
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:
http://lists.bx.psu.edu/
Re: [galaxy-dev] [galaxy-user] Cannot get rid of custom build error
Hi Jim, I am going to post your question over to the galaxy-dev mailing list (is best for local/cloud instance questions). Would you be able to confirm which version of Galaxy you are running? The latest version of the distribution? http://wiki.g2.bx.psu.edu/News%20Briefs/2011_10_25 "upgrade: % hg pull -u -r 338ead4737ba" Please send your reply as a "reply-all" that includes the galaxy-dev mailing list, but omits the galaxy-user mailing list. Thanks for the additional information, Jen Galaxy team On 11/2/11 4:04 AM, James Vincent wrote: Hello, I've tried to create a custom build (starting from the trackster page) and clearly made some mistake. I get a NoConverterException error which is almost certainly my fault putting something wrong in. However, now the Custom Builds page shows this error and I cannot make it go away. I have a local install, have killed and restarted, logged in and out, but still this error stays. I cannot try to enter another custom build because there is nothing on the page except this error. Does anyone kow how to get rid of this? Any help in getting around this error are appreciated. Jim ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support ___ 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: http://lists.bx.psu.edu/
