fastq format recognition

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fastq format recognition

Michael Thon
I have a new galaxy installation on my server.  I uploaded two fastq files and now I'm trying to run trimmomatic and fastqc. In both cases I am presented with a drop down list of fastq files to select from but the lists are empty.  I double checked the fastq file attributes and they are both set to fastq. Any ideas what's wrong?

Another question: I have fastq files already on the same server as the galaxy installation.  How can I get them into galaxy? I have not set up ftp yet. Can I move them into a data directory somewhere?

Thanks!


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Re: fastq format recognition

Björn Grüning-3
Hi Michael,

have a look at this biostar question.

https://biostar.usegalaxy.org/p/8070/

Hope this helps,
Bjoern

Am 13.02.2015 um 13:08 schrieb Michael Thon:

> I have a new galaxy installation on my server.  I uploaded two fastq files and now I'm trying to run trimmomatic and fastqc. In both cases I am presented with a drop down list of fastq files to select from but the lists are empty.  I double checked the fastq file attributes and they are both set to fastq. Any ideas what's wrong?
>
> Another question: I have fastq files already on the same server as the galaxy installation.  How can I get them into galaxy? I have not set up ftp yet. Can I move them into a data directory somewhere?
>
> Thanks!
>
>
> ___________________________________________________________
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Re: fastq format recognition

Peter Cock
In reply to this post by Michael Thon
On Fri, Feb 13, 2015 at 12:08 PM, Michael Thon <[hidden email]> wrote:
> I have a new galaxy installation on my server.  I uploaded two fastq files and now I'm trying to run trimmomatic and fastqc. In both cases I am presented with a drop down list of fastq files to select from but the lists are empty.  I double checked the fastq file attributes and they are both set to fastq. Any ideas what's wrong?
>

You probably need to change the format to the more specific
fastqsanger datatype (FASTQ using the Sanger encoding).

It may be time for Galaxy to change their default, since the old
Solexa and Illumina variants are no longer widely used.

> Another question: I have fastq files already on the same server as the galaxy installation.  How can I get them into galaxy? I have not set up ftp yet. Can I move them into a data directory somewhere?

One option is to import them into a library (which can link to the
files rather than coping them). Are you a Galaxy administrator?

Peter
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Re: fastq format recognition

Michael Thon

> On Feb 13, 2015, at 1:35 PM, Peter Cock <[hidden email]> wrote:
>
> On Fri, Feb 13, 2015 at 12:08 PM, Michael Thon <[hidden email]> wrote:
>> I have a new galaxy installation on my server.  I uploaded two fastq files and now I'm trying to run trimmomatic and fastqc. In both cases I am presented with a drop down list of fastq files to select from but the lists are empty.  I double checked the fastq file attributes and they are both set to fastq. Any ideas what's wrong?
>>
>
> You probably need to change the format to the more specific
> fastqsanger datatype (FASTQ using the Sanger encoding).
>
> It may be time for Galaxy to change their default, since the old
> Solexa and Illumina variants are no longer widely used.
>
>> Another question: I have fastq files already on the same server as the galaxy installation.  How can I get them into galaxy? I have not set up ftp yet. Can I move them into a data directory somewhere?
>
> One option is to import them into a library (which can link to the
> files rather than coping them). Are you a Galaxy administrator?
>
> Peter

Yes I am the admin. I will look into that.
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Re: fastq format recognition

Michael Thon
In reply to this post by Björn Grüning-3
Thanks, that did it.
Mike

> On Feb 13, 2015, at 1:26 PM, Björn Grüning <[hidden email]> wrote:
>
> Hi Michael,
>
> have a look at this biostar question.
>
> https://biostar.usegalaxy.org/p/8070/
>
> Hope this helps,
> Bjoern
>
> Am 13.02.2015 um 13:08 schrieb Michael Thon:
>> I have a new galaxy installation on my server.  I uploaded two fastq files and now I'm trying to run trimmomatic and fastqc. In both cases I am presented with a drop down list of fastq files to select from but the lists are empty.  I double checked the fastq file attributes and they are both set to fastq. Any ideas what's wrong?
>>
>> Another question: I have fastq files already on the same server as the galaxy installation.  How can I get them into galaxy? I have not set up ftp yet. Can I move them into a data directory somewhere?
>>
>> Thanks!
>>
>>
>> ___________________________________________________________
>> 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/
>>

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Re: fastq format recognition

Michael Thon
In reply to this post by Peter Cock

> On Feb 13, 2015, at 1:35 PM, Peter Cock <[hidden email]> wrote:
>
> On Fri, Feb 13, 2015 at 12:08 PM, Michael Thon <[hidden email]> wrote:
>> I have a new galaxy installation on my server.  I uploaded two fastq files and now I'm trying to run trimmomatic and fastqc. In both cases I am presented with a drop down list of fastq files to select from but the lists are empty.  I double checked the fastq file attributes and they are both set to fastq. Any ideas what's wrong?
>>
>
> You probably need to change the format to the more specific
> fastqsanger datatype (FASTQ using the Sanger encoding).
>
> It may be time for Galaxy to change their default, since the old
> Solexa and Illumina variants are no longer widely used.
>
>> Another question: I have fastq files already on the same server as the galaxy installation.  How can I get them into galaxy? I have not set up ftp yet. Can I move them into a data directory somewhere?
>
> One option is to import them into a library (which can link to the
> files rather than coping them). Are you a Galaxy administrator?
>
> Peter

I just tried adding them to a library.  On the library admin page there is an option to upload files or to import data from my history.  There is no option to link to files on the filesystem.  Does this need to be activated in the config somewhere?
Thanks

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Re: fastq format recognition

Martin Čech
Hello Mike,

you probably want to set library_import_dir or allow_library_path_paste in the config.

Martin

On Tue Feb 17 2015 at 11:40:37 PM Michael Thon <[hidden email]> wrote:

> On Feb 13, 2015, at 1:35 PM, Peter Cock <[hidden email]> wrote:
>
> On Fri, Feb 13, 2015 at 12:08 PM, Michael Thon <[hidden email]> wrote:
>> I have a new galaxy installation on my server.  I uploaded two fastq files and now I'm trying to run trimmomatic and fastqc. In both cases I am presented with a drop down list of fastq files to select from but the lists are empty.  I double checked the fastq file attributes and they are both set to fastq. Any ideas what's wrong?
>>
>
> You probably need to change the format to the more specific
> fastqsanger datatype (FASTQ using the Sanger encoding).
>
> It may be time for Galaxy to change their default, since the old
> Solexa and Illumina variants are no longer widely used.
>
>> Another question: I have fastq files already on the same server as the galaxy installation.  How can I get them into galaxy? I have not set up ftp yet. Can I move them into a data directory somewhere?
>
> One option is to import them into a library (which can link to the
> files rather than coping them). Are you a Galaxy administrator?
>
> Peter

I just tried adding them to a library.  On the library admin page there is an option to upload files or to import data from my history.  There is no option to link to files on the filesystem.  Does this need to be activated in the config somewhere?
Thanks

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Re: fastq format recognition

Michael Thon
Thanks Martin - allow_library_path_paste did the job.
Mike

> On Feb 18, 2015, at 6:14 AM, Martin Čech <[hidden email]> wrote:
>
> Hello Mike,
>
> you probably want to set library_import_dir or allow_library_path_paste in the config.
> Details here:
> https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles
>
> Martin
>
> On Tue Feb 17 2015 at 11:40:37 PM Michael Thon <[hidden email]> wrote:
>
> > On Feb 13, 2015, at 1:35 PM, Peter Cock <[hidden email]> wrote:
> >
> > On Fri, Feb 13, 2015 at 12:08 PM, Michael Thon <[hidden email]> wrote:
> >> I have a new galaxy installation on my server.  I uploaded two fastq files and now I'm trying to run trimmomatic and fastqc. In both cases I am presented with a drop down list of fastq files to select from but the lists are empty.  I double checked the fastq file attributes and they are both set to fastq. Any ideas what's wrong?
> >>
> >
> > You probably need to change the format to the more specific
> > fastqsanger datatype (FASTQ using the Sanger encoding).
> >
> > It may be time for Galaxy to change their default, since the old
> > Solexa and Illumina variants are no longer widely used.
> >
> >> Another question: I have fastq files already on the same server as the galaxy installation.  How can I get them into galaxy? I have not set up ftp yet. Can I move them into a data directory somewhere?
> >
> > One option is to import them into a library (which can link to the
> > files rather than coping them). Are you a Galaxy administrator?
> >
> > Peter
>
> I just tried adding them to a library.  On the library admin page there is an option to upload files or to import data from my history.  There is no option to link to files on the filesystem.  Does this need to be activated in the config somewhere?
> Thanks
>
> ___________________________________________________________
> 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/

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