[galaxy-dev] Question about "reference_fasta_filename" for "Map with BWA" (existing tool)

[Qian, Yingzhi]

Hi there,

This is my first time writing to the mailing list. Thanks in advance.

I want to use Map with BWA for short reads 
https://toolshed.g2.bx.psu.edu/repository/display_tool?repository_id=25bdd3c7f0d57b06&tool_config=database%2Fcommunity_files%2F000%2Frepo_253%2Fbwa_wrapper.xml&changeset_revision=b4427dbb6ced


(I have added the lines in PS (below) to the section I made in 
config/tool_conf.xml file and "Map with BWA" is showing up on galaxy interface 
when I execute run.sh. ) However, I can't pick a genome in the "Using reference 
genome" box. The drop-down box doesn't work.


I have loaded genomes and created indexes to my local galaxy. I just don't know 
where to insert the path in this file - 
shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/bwa/051eba708f43/bwa/bwa.xml
 I see it has "reference_fasta_filename" (reference genome) but I am not sure 
what it is directing to or what to modify to tell where I put the genomes. Or 
is there something else I need to do?


Regards,

Ying

PS

http://toolshed.g2.bx.psu.edu/repos/devteam/bwa/051eba708f43/bwa/bwa.xml>"
 
guid="toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.15.2">
toolshed.g2.bx.psu.edu
bwa
devteam

051eba708f43

toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.15.2
0.7.15.2


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Re: [galaxy-dev] Displaying tool select list according to user

[Mohamed Kassam]

Hi Fred,

Thanks a lot,, we are also intereted on that solution for our private
database.

Hope that we have any good news soon.

Best regards,

Mohamed

2017-09-21 16:01 GMT+02:00 SAPET, Frederic :

> Hi,
>
>
>
> I have created 3 issues!
>
>
>
> Use different .loc files depending on user's parameters
>
> https://github.com/galaxyproject/galaxy/issues/4666
>
>
>
> Access DataLibrary files from tool form
>
> https://github.com/galaxyproject/galaxy/issues/4667
>
>
>
> File upload enhancement
>
> https://github.com/galaxyproject/galaxy/issues/4668
>
>
>
> thank you Peter for pointing me out http://www.sequenceserver.com/
>
>
>
> and of course as I also develop and maintain tools, I understand that all
> ‘craziest’ ideas cannot become a reality.
>
>
>
> Fred
>
>
>
>
>
> *De :* Peter Cock [mailto:p.j.a.c...@googlemail.com]
> *Envoyé :* jeudi 21 septembre 2017 14:46
> *À :* SAPET, Frederic 
> *Cc :* Laure QUINTRIC ; Galaxy-dev <
> galaxy-dev@lists.galaxyproject.org>
> *Objet :* Re: [galaxy-dev] Displaying tool select list according to user
>
>
>
>
>
>
>
> On Thu, Sep 21, 2017 at 12:50 PM, SAPET, Frederic <
> frederic.sa...@biogemma.com> wrote:
>
> Hi Peter,
>
> Good idea, I will keep that in mind for other needs.
> I'm not sure that it will be suitable for what I want to do. Users will
> have to first import database to their history (yet another step as they
> ask me for less, even the upload process is sometimes one step they would
> like to avoid !)
>
>
>
> But it could be a way of achieving what I want, if Galaxy could get files
> (or .loc files) from a data library, within the tool form itself !
>
>
>
> Maybe I will create an issue on the Galaxy git in order to discuss about
> that. I will be glad to help if something can be done.
>
>
>
> Good idea! I wonder if the Galaxy UI team can think of a good way to
> integrate this, which would make Shared Data library files available to any
> tool without the import to current history step? Can you reply with a link
> to the new GitHub issue for this?
>
>
>
> Maybe some explanations about the fact that my users ask me for "less
> steps".
> I really want Galaxy to be the main tool of our analysis platform.
> Right now I still maintain a plain old perl/php/CGI web interface. With a
> blast tool (among a lot of others tools). This proprietary Blast interface
> is really like you will find on NCBI or EBI sites. And you can quickly
> paste your sequences, pick up a database, a Blast algorythm and then
> launch. Few seconds later I have a 'htmlized' Blast report, with a nice
> picture.
> This use case (is this sequence a part of this database ?) is still faster
> on this plain old interface. And I afraid that I will have to keep it until
> they found Galaxy better than it...
>
>
>
> We used to run wwwBLAST locally for similar reasons. If I was trying to
> setup up something similar now, I'd look at http://www.sequenceserver.com/
> for this - but making the Galaxy alternative easier to use would be neater.
>
>
>
> Maybe it could be another (or two) idea(s)  : the user can drag and drop
> his file within the tool form, Galaxy will handle the creation of this file
> within the history and then launch the tool. Or user can copy/paste a
> sequence within a text-area, and Galaxy will handle the creation of a file
> from these data within the history and then launch the tool.
> This skips upload process.
>
>
>
> The Galaxy upload does now support drag and drop, so again in principle
> the Galaxy team might be able to extend the tool interface as well. The
> tool input's expected file formats could be used to guide the data-type
> sniffer and/or short list the choices shown to the use.
>
>
>
> As well or instead, I could imagine having an upload icon associated with
> each tool input (again, creating a history item and selecting it for you)?
> This could take advantage of the fact that each tool's input parameter
> specifies the expected input file formats, so that might be mapped to known
> file extensions for a file picker?
>
>
>
>
> thank you again for sharing your ideas, it helps!
>
> Fred
>
>
>
> These are great usability ideas you are putting forward here - as a Galaxy
> Tool Author they sound positive, but I cannot comment on how complicated it
> would be for the Galaxy UI team. Or indeed if the UI would actually be
> practical - or just overly complicate things which is always a risk.
>
>
>
> Peter
>
>
>
> ___
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Re: [galaxy-dev] upload file format is data - type not recognized in galaxy

[Peter Cock]

That's a shame - I don't see anything in the log either at
first reading - it was hoping to see problems with missing
datatypes or sniffers, which might explain this.

Sorry, I am out of ideas.

Peter

On Fri, Sep 22, 2017 at 2:41 PM, Pavel Fibich  wrote:
> Hi Hans-Rudolf and Peter,
>
> thank you for replies. I tried both suggestions, but no luck.
>
> I made empty database, let galaxy run from it. Than, uploading fasta file
> again finished in the format 'data', not recognized again.
>
> Also, I did not find anything interesting in the startup logs ( logs are
> here: https://repeatexplorer-elixir.cerit-sc.cz/galstart2.log ), there are
> just fine information about datatypes, eg. for fasta:
>
> galaxy.datatypes.registry DEBUG 2017-09-22 15:11:52,810 Retrieved datatype
> module galaxy.datatypes.sequence:Fasta from the datatype registry.
> ...
> galaxy.datatypes.registry DEBUG 2017-09-22 15:11:52,929 Loaded sniffer for
> datatype 'galaxy.datatypes.sequence:Fasta'
>
> I have only config/datatypes_conf.xml.sample, so I expect that it is
> default.
>
> If you have any other ideas, I will be glad for them.
>
> Best, Pavel
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Re: [galaxy-dev] upload file format is data - type not recognized in galaxy

[Pavel Fibich]

Hi Hans-Rudolf and Peter,

thank you for replies. I tried both suggestions, but no luck.

I made empty database, let galaxy run from it. Than, uploading fasta file
again finished in the format 'data', not recognized again.

Also, I did not find anything interesting in the startup logs ( logs are
here: https://repeatexplorer-elixir.cerit-sc.cz/galstart2.log ), there are
just fine information about datatypes, eg. for fasta:

galaxy.datatypes.registry DEBUG 2017-09-22 15:11:52,810 Retrieved datatype
module galaxy.datatypes.sequence:Fasta from the datatype registry.
...
galaxy.datatypes.registry DEBUG 2017-09-22 15:11:52,929 Loaded sniffer for
datatype 'galaxy.datatypes.sequence:Fasta'

I have only config/datatypes_conf.xml.sample, so I expect that it is
default.

If you have any other ideas, I will be glad for them.

Best, Pavel

On Fri, Sep 22, 2017 at 2:25 PM, Peter Cock 
wrote:

> My first thought would be to double check the Galaxy startup logs
> (which normally tell you about the datatypes as they are setup).
> That ought to give some clues.
>
> Also check the XML files where the datatypes are defined are
> all still fine - do you have any of these and do they look fine?
>
> datatypes_conf.xml
> config/datatypes_conf.xml
> config/datatypes_conf.xml.sample
>
> (I know you said the settings and code were not changed,
> but it seems worth double checking)
>
> Peter
>
> On Fri, Sep 22, 2017 at 12:31 PM, Hans-Rudolf Hotz  wrote:
> > Hi Pavel
> >
> >
> > what happens if you connect your galaxy instance to an empty PostgreSQL
> > database, let galaxy build all the tables and then try to upload files.
> >
> >
> > Regards, Hans-Rudolf
> >
> >
> >
> >
> > On 09/22/2017 10:51 AM, Pavel Fibich wrote:
> >>
> >> Hello,
> >>
> >> do you have any idea why my galaxy 16.07 stop recognizing uploaded files
> >> and format of uploaded files is set to the format 'data'?
> >>
> >> After using older version of database backup, galaxy stop recognizing
> >> format of uploaded files (e.g. fasta, fastqc) and everything is set to
> >> format 'data'. Uploaded files are OK, I have tested them on other public
> >> galaxy servers, where they were recognized well. Before changing
> >> database (after the technical problems with the server), recognizing of
> >> the files were OK. Even in debugging level I do not see any errors or
> >> problems in the log (I have compared logs before changing database with
> >> new ones, and there are no differences). From the investigating of
> >> upload.py, I guess something happen with galaxy.datatypes.registry
> >> (settings and code of galaxy were not changed). Do you have any ideas? I
> >> cannot switch the database back and changing file format in Edit
> >> attributes is annoying.
> >>
> >> Best, Pavel
>
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Re: [galaxy-dev] upload file format is data - type not recognized in galaxy

[Peter Cock]

My first thought would be to double check the Galaxy startup logs
(which normally tell you about the datatypes as they are setup).
That ought to give some clues.

Also check the XML files where the datatypes are defined are
all still fine - do you have any of these and do they look fine?

datatypes_conf.xml
config/datatypes_conf.xml
config/datatypes_conf.xml.sample

(I know you said the settings and code were not changed,
but it seems worth double checking)

Peter

On Fri, Sep 22, 2017 at 12:31 PM, Hans-Rudolf Hotz  wrote:
> Hi Pavel
>
>
> what happens if you connect your galaxy instance to an empty PostgreSQL
> database, let galaxy build all the tables and then try to upload files.
>
>
> Regards, Hans-Rudolf
>
>
>
>
> On 09/22/2017 10:51 AM, Pavel Fibich wrote:
>>
>> Hello,
>>
>> do you have any idea why my galaxy 16.07 stop recognizing uploaded files
>> and format of uploaded files is set to the format 'data'?
>>
>> After using older version of database backup, galaxy stop recognizing
>> format of uploaded files (e.g. fasta, fastqc) and everything is set to
>> format 'data'. Uploaded files are OK, I have tested them on other public
>> galaxy servers, where they were recognized well. Before changing
>> database (after the technical problems with the server), recognizing of
>> the files were OK. Even in debugging level I do not see any errors or
>> problems in the log (I have compared logs before changing database with
>> new ones, and there are no differences). From the investigating of
>> upload.py, I guess something happen with galaxy.datatypes.registry
>> (settings and code of galaxy were not changed). Do you have any ideas? I
>> cannot switch the database back and changing file format in Edit
>> attributes is annoying.
>>
>> Best, Pavel
>>
>>
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>>
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Re: [galaxy-dev] upload file format is data - type not recognized in galaxy

[Hans-Rudolf Hotz]

Hi Pavel


what happens if you connect your galaxy instance to an empty PostgreSQL 
database, let galaxy build all the tables and then try to upload files.



Regards, Hans-Rudolf



On 09/22/2017 10:51 AM, Pavel Fibich wrote:

Hello,

do you have any idea why my galaxy 16.07 stop recognizing uploaded files
and format of uploaded files is set to the format 'data'?

After using older version of database backup, galaxy stop recognizing
format of uploaded files (e.g. fasta, fastqc) and everything is set to
format 'data'. Uploaded files are OK, I have tested them on other public
galaxy servers, where they were recognized well. Before changing
database (after the technical problems with the server), recognizing of
the files were OK. Even in debugging level I do not see any errors or
problems in the log (I have compared logs before changing database with
new ones, and there are no differences). From the investigating of
upload.py, I guess something happen with galaxy.datatypes.registry
(settings and code of galaxy were not changed). Do you have any ideas? I
cannot switch the database back and changing file format in Edit
attributes is annoying.

Best, Pavel


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[galaxy-dev] upload file format is data - type not recognized in galaxy

[Pavel Fibich]

Hello,

do you have any idea why my galaxy 16.07 stop recognizing uploaded files
and format of uploaded files is set to the format 'data'?

After using older version of database backup, galaxy stop recognizing
format of uploaded files (e.g. fasta, fastqc) and everything is set to
format 'data'. Uploaded files are OK, I have tested them on other public
galaxy servers, where they were recognized well. Before changing database
(after the technical problems with the server), recognizing of the files
were OK. Even in debugging level I do not see any errors or problems in the
log (I have compared logs before changing database with new ones, and there
are no differences). From the investigating of upload.py, I guess something
happen with galaxy.datatypes.registry (settings and code of galaxy were not
changed). Do you have any ideas? I cannot switch the database back and
changing file format in Edit attributes is annoying.

Best, Pavel
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