CummeRbund on Galaxy

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CummeRbund on Galaxy

Ganote, Carrie L
Hi list,

Is the cummeRbund wrapper on Galaxy yet functional? I've got some replicates that I'm trying to test for a user on our local Galaxy, but I just can't get the program to behave.

Using cuffdiff v2.2.0 604fa75232a2
cummeRbund version 0.0.7, 137aab1d9ac1
R 2.15.2 and 3.0.1 (tried both)
Last galaxy-dist/stable changeset: 7a7985a007fb

I ran cuffdiff like so:
Transcripts 83: Cuffmerge on data 6, data 67, and others: merged transcripts
Name control
Add replicate 44: Tophat2 on data 1 and data 6: accepted_hits (ran as single-end fastq)
Add replicate 54: Tophat2 on data 2 and data 6: accepted_hits (ran as single-end fastq)
Name sample
Add replicate 59: Tophat2 on data 3 and data 6: accepted_hits (ran as single-end fastq)
Add replicate 64: Tophat2 on data 4 and data 6: accepted_hits (ran as single-end fastq)
Library normalization method geometric
Dispersion estimation method pooled
False Discovery Rate 0.05
Min Alignment Count 10
Use multi-read correct No
Perform Bias Correction No
Include Read Group Datasets No
Set Additional Parameters? (not recommended for paired-end reads) No

Here's what I get when I run cummeRbund:
(From Galaxy, with R 2.15.2)
Creating database //path/job_working_directory/005/5051/galaxy_dataset_16602.dat
Reading //path/dataset_files/009/dataset_9861.dat
Checking samples table...
Populating samples table...
Writing genes table
Reshaping geneData table
Recasting
Writing geneData table
Reading //path/dataset_files/009/dataset_9861.dat
Error in function (classes, fdef, mtable)  :
  unable to find an inherited method for function 'make.db.names' for signature '"SQLiteConnection", "NULL"'
Calls: readCufflinks ... make.db.names -> .valueClassTest -> is -> <Anonymous>
Execution halted

(From R interpreter on command line, R = 3.0.1)
Reading //path/dataset_files/009/dataset_9842.dat
Checking samples table...
Populating samples table...
Writing genes table
Reshaping geneData table
Recasting
Writing geneData table
Reading //path/dataset_files/009/dataset_9842.dat
Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function 'make.db.names' for signature '"SQLiteConnection", "NULL"'
In addition: Warning message:
attributes are not identical across measure variables; they will be dropped

I tried changing the group names in cuffdiff but no luck. No spaces or funny characters.

Thanks for any insight,

Carrie Ganote


___________________________________________________________
The Galaxy User List is being replaced by the Galaxy Biostar
User Support Forum at https://biostar.usegalaxy.org/

Posts to this list will be disabled in May 2014.  In the
meantime, you are encouraged to post all new questions to
Galaxy Biostar.

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:

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Re: CummeRbund on Galaxy

Jen Hillman-Jackson
Hi Carrie,

I'll start this off by stating that I am not as familiar with this
wrapper as many of the others. I am bringing in the repository owner
(Jim Johnson) to the thread so that he can offer help. You can also
reach him (or any other repository owner) when logged in under the
"Repository Actions" menu under "Contact Repository Owner".

Just from a quick look, I am wondering if the R package dependencies are
installed with all necessary components and available to the "Galaxy
user". Or, if the ones you tried are the correct ones to be using with
this tool. The "attributes" warning is one that is given by R.

Going forward, using the [hidden email] mailing list will be best
for questions like this one. This list is being retired on Friday
(replaced by Galaxy Biostar). Please join us there for usage questions
(although there is some cross-over in questions and we are open to both,
the community is still actively using galaxy-dev for primary local
install help and you will reach more developers there):
https://wiki.galaxyproject.org/Support#Biostar

Hopefully Jim will see this thread, but also try contacting him direct
if no reply is sent here.

Sorry I could not help more,

Jen
Galaxy team

On 6/2/14 2:57 PM, Ganote, Carrie L wrote:

> Hi list,
>
> Is the cummeRbund wrapper on Galaxy yet functional? I've got some replicates that I'm trying to test for a user on our local Galaxy, but I just can't get the program to behave.
>
> Using cuffdiff v2.2.0 604fa75232a2
> cummeRbund version 0.0.7, 137aab1d9ac1
> R 2.15.2 and 3.0.1 (tried both)
> Last galaxy-dist/stable changeset: 7a7985a007fb
>
> I ran cuffdiff like so:
> Transcripts 83: Cuffmerge on data 6, data 67, and others: merged transcripts
> Name control
> Add replicate 44: Tophat2 on data 1 and data 6: accepted_hits (ran as single-end fastq)
> Add replicate 54: Tophat2 on data 2 and data 6: accepted_hits (ran as single-end fastq)
> Name sample
> Add replicate 59: Tophat2 on data 3 and data 6: accepted_hits (ran as single-end fastq)
> Add replicate 64: Tophat2 on data 4 and data 6: accepted_hits (ran as single-end fastq)
> Library normalization method geometric
> Dispersion estimation method pooled
> False Discovery Rate 0.05
> Min Alignment Count 10
> Use multi-read correct No
> Perform Bias Correction No
> Include Read Group Datasets No
> Set Additional Parameters? (not recommended for paired-end reads) No
>
> Here's what I get when I run cummeRbund:
> (From Galaxy, with R 2.15.2)
> Creating database //path/job_working_directory/005/5051/galaxy_dataset_16602.dat
> Reading //path/dataset_files/009/dataset_9861.dat
> Checking samples table...
> Populating samples table...
> Writing genes table
> Reshaping geneData table
> Recasting
> Writing geneData table
> Reading //path/dataset_files/009/dataset_9861.dat
> Error in function (classes, fdef, mtable)  :
>    unable to find an inherited method for function 'make.db.names' for signature '"SQLiteConnection", "NULL"'
> Calls: readCufflinks ... make.db.names -> .valueClassTest -> is -> <Anonymous>
> Execution halted
>
> (From R interpreter on command line, R = 3.0.1)
> Reading //path/dataset_files/009/dataset_9842.dat
> Checking samples table...
> Populating samples table...
> Writing genes table
> Reshaping geneData table
> Recasting
> Writing geneData table
> Reading //path/dataset_files/009/dataset_9842.dat
> Error in (function (classes, fdef, mtable)  :
>    unable to find an inherited method for function 'make.db.names' for signature '"SQLiteConnection", "NULL"'
> In addition: Warning message:
> attributes are not identical across measure variables; they will be dropped
>
> I tried changing the group names in cuffdiff but no luck. No spaces or funny characters.
>
> Thanks for any insight,
>
> Carrie Ganote
>
>
> ___________________________________________________________
> The Galaxy User List is being replaced by the Galaxy Biostar
> User Support Forum at https://biostar.usegalaxy.org/
>
> Posts to this list will be disabled in May 2014.  In the
> meantime, you are encouraged to post all new questions to
> Galaxy Biostar.
>
> 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/
>
> To search Galaxy mailing lists use the unified search at:
>
>    http://galaxyproject.org/search/mailinglists/

--
Jennifer Hillman-Jackson
http://galaxyproject.org

___________________________________________________________
The Galaxy User List is being replaced by the Galaxy Biostar
User Support Forum at https://biostar.usegalaxy.org/

Posts to this list will be disabled in May 2014.  In the
meantime, you are encouraged to post all new questions to
Galaxy Biostar.

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/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/
Jennifer Hillman-Jackson
http://galaxyproject.org
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Re: CummeRbund on Galaxy

Jim Johnson-2
Carrie,

We've had issues when  gene ids contain a '#' character, which is the R comment character.
We've had issues when the group names in a plot weren't exactly the same as those used in the cuffdiff inputs.

Are you linking in all the individual output files from cuffdiff?
I included a cuffdiff tool in the cummeRbund toolshed respository because the original cuffdiff galaxy tool didn't  output all 21 files that cummeRbund prefers.
Are you also including the "genome reference and Feature file". The gtf may be needed for some functions.

JJ


On 6/3/14, 11:54 AM, Jennifer Jackson wrote:

> Hi Carrie,
>
> I'll start this off by stating that I am not as familiar with this wrapper as many of the others. I am bringing in the repository owner (Jim Johnson) to the thread so that he can offer help. You can also reach him (or any other repository owner) when logged in under the "Repository Actions" menu under "Contact Repository Owner".
>
> Just from a quick look, I am wondering if the R package dependencies are installed with all necessary components and available to the "Galaxy user". Or, if the ones you tried are the correct ones to be using with this tool. The "attributes" warning is one that is given by R.
>
> Going forward, using the [hidden email] mailing list will be best for questions like this one. This list is being retired on Friday (replaced by Galaxy Biostar). Please join us there for usage questions (although there is some cross-over in questions and we are open to both, the community is still actively using galaxy-dev for primary local install help and you will reach more developers there): https://wiki.galaxyproject.org/Support#Biostar
>
> Hopefully Jim will see this thread, but also try contacting him direct if no reply is sent here.
>
> Sorry I could not help more,
>
> Jen
> Galaxy team
>
> On 6/2/14 2:57 PM, Ganote, Carrie L wrote:
>> Hi list,
>>
>> Is the cummeRbund wrapper on Galaxy yet functional? I've got some replicates that I'm trying to test for a user on our local Galaxy, but I just can't get the program to behave.
>>
>> Using cuffdiff v2.2.0 604fa75232a2
>> cummeRbund version 0.0.7, 137aab1d9ac1
>> R 2.15.2 and 3.0.1 (tried both)
>> Last galaxy-dist/stable changeset: 7a7985a007fb
>>
>> I ran cuffdiff like so:
>> Transcripts     83: Cuffmerge on data 6, data 67, and others: merged transcripts
>> Name     control
>> Add replicate     44: Tophat2 on data 1 and data 6: accepted_hits (ran as single-end fastq)
>> Add replicate     54: Tophat2 on data 2 and data 6: accepted_hits (ran as single-end fastq)
>> Name     sample
>> Add replicate     59: Tophat2 on data 3 and data 6: accepted_hits (ran as single-end fastq)
>> Add replicate     64: Tophat2 on data 4 and data 6: accepted_hits (ran as single-end fastq)
>> Library normalization method     geometric
>> Dispersion estimation method     pooled
>> False Discovery Rate     0.05
>> Min Alignment Count     10
>> Use multi-read correct     No
>> Perform Bias Correction     No
>> Include Read Group Datasets     No
>> Set Additional Parameters? (not recommended for paired-end reads)     No
>>
>> Here's what I get when I run cummeRbund:
>> (From Galaxy, with R 2.15.2)
>> Creating database //path/job_working_directory/005/5051/galaxy_dataset_16602.dat
>> Reading //path/dataset_files/009/dataset_9861.dat
>> Checking samples table...
>> Populating samples table...
>> Writing genes table
>> Reshaping geneData table
>> Recasting
>> Writing geneData table
>> Reading //path/dataset_files/009/dataset_9861.dat
>> Error in function (classes, fdef, mtable)  :
>>    unable to find an inherited method for function 'make.db.names' for signature '"SQLiteConnection", "NULL"'
>> Calls: readCufflinks ... make.db.names -> .valueClassTest -> is -> <Anonymous>
>> Execution halted
>>
>> (From R interpreter on command line, R = 3.0.1)
>> Reading //path/dataset_files/009/dataset_9842.dat
>> Checking samples table...
>> Populating samples table...
>> Writing genes table
>> Reshaping geneData table
>> Recasting
>> Writing geneData table
>> Reading //path/dataset_files/009/dataset_9842.dat
>> Error in (function (classes, fdef, mtable)  :
>>    unable to find an inherited method for function 'make.db.names' for signature '"SQLiteConnection", "NULL"'
>> In addition: Warning message:
>> attributes are not identical across measure variables; they will be dropped
>>
>> I tried changing the group names in cuffdiff but no luck. No spaces or funny characters.
>>
>> Thanks for any insight,
>>
>> Carrie Ganote
>>
>>
>> ___________________________________________________________
>> The Galaxy User List is being replaced by the Galaxy Biostar
>> User Support Forum at https://biostar.usegalaxy.org/
>>
>> Posts to this list will be disabled in May 2014.  In the
>> meantime, you are encouraged to post all new questions to
>> Galaxy Biostar.
>>
>> 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/
>>
>> To search Galaxy mailing lists use the unified search at:
>>
>>    http://galaxyproject.org/search/mailinglists/
>


--
James E. Johnson, Minnesota Supercomputing Institute, University of Minnesota
___________________________________________________________
The Galaxy User List is being replaced by the Galaxy Biostar
User Support Forum at https://biostar.usegalaxy.org/

Posts to this list will be disabled in May 2014.  In the
meantime, you are encouraged to post all new questions to
Galaxy Biostar.

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/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/
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