Thanks Nate,

For now I downloaded:
https://bitbucket.org/galaxy/galaxy-central/raw/e74e89a4c03a/tools/ngs_rna/cuffcompare_wrapper.py
https://bitbucket.org/galaxy/galaxy-central/raw/d1f2d2e5246a/tools/ngs_rna/cuffcompare_wrapper.xml

I saved to current versions of these files, so I'll make sure to
replace them before updating to the next stable version to avoid
merging errors.

Thanks again,
--
Carlos Borroto
Baltimore, MD



On Mon, Jun 20, 2011 at 3:30 PM, Nate Coraor <n...@bx.psu.edu> wrote:
> Hi Carlos,
>
> We're expecting to release a stable distribution this week, but you are
> always free to pull changes from the central repository.  The suggested
> method would be to just pull all changesets up to the one you want, or
> up to the tip changeset.
>
> It's not trivial to pull single changesets, you have to export them from
> central, import them to your local repository, and then you'll have to
> merge when we release a new stable distribution.
>
> --nate
>
> Carlos Javier Borroto wrote:
>> I see there is this changeset:
>> https://bitbucket.org/galaxy/galaxy-central/changeset/f4b98c453389
>>
>> As I have cufflinks 1.0.3, I wonder if this is the cause of the error.
>> Maybe I should move to galaxy-central if I want to use cufflinks. Is
>> there any clean way to backport a changeset from -central to -dist?
>>
>> Thanks,
>> --
>> Carlos Borroto
>> Baltimore, MD
>>
>>
>>
>> On Mon, Jun 20, 2011 at 2:01 PM, Carlos Javier Borroto
>> <carlos.borr...@gmail.com> wrote:
>> > Hi John,
>> >
>> > I'm finding the exact same error while going through Jeremy's tutorial
>> > in a local instance of galaxy-dist. I was wonder if you found the
>> > solution.
>> >
>> > I see cuffcompare wrapper outputs these files:
>> > cc_output.combined.gtf
>> > cc_output.input1.refmap
>> > cc_output.input1.tmap
>> > cc_output.loci
>> > cc_output.stats
>> > cc_output.tracking
>> >
>> > and in the logs I'm seing this:
>> > galaxy.jobs DEBUG 2011-06-20 13:34:49,902 finish(): Could not move
>> > /home/galaxy/galaxy_dist/database/job_working_directory/47/cc_output
>> > to /home/galaxy/galaxy_dist/database/files/000/dataset_68.dat as
>> > directed by from_work_dir
>> > galaxy.jobs DEBUG 2011-06-20 13:34:49,917 finish(): Could not move
>> > /home/galaxy/galaxy_dist/database/job_working_directory/47/input1.tmap
>> > to /home/galaxy/galaxy_dist/database/files/000/dataset_69.dat as
>> > directed by from_work_dir
>> > galaxy.jobs DEBUG 2011-06-20 13:34:49,932 finish(): Could not move
>> > /home/galaxy/galaxy_dist/database/job_working_directory/47/input1.refmap
>> > to /home/galaxy/galaxy_dist/database/files/000/dataset_70.dat as
>> > directed by from_work_dir
>> > galaxy.jobs DEBUG 2011-06-20 13:34:49,948 finish(): Moved
>> > /home/galaxy/galaxy_dist/database/job_working_directory/47/cc_output.combined.gtf
>> > to /home/galaxy/galaxy_dist/database/files/000/dataset_71.dat as
>> > directed by from_work_dir
>> >
>> > Only cc_output.combined.gtf is correctly being moved, the rest aren't
>> > being call by the correct filenames.
>> >
>> > Thanks,
>> > --
>> > Carlos Borroto
>> > Baltimore, MD
>> >
>> >
>> >
>> > 2011/6/10 吳正華 <joh...@ibms.sinica.edu.tw>:
>> >> Dear galaxy team:
>> >>
>> >>
>> >>
>> >> I was testing local galaxy of our lab by analyzing RNA-seq data in 
>> >> Jeremy’s
>> >> RNA-seq tutorial.
>> >>
>> >>
>> >>
>> >> http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise
>> >>
>> >>
>> >>
>> >> I could run TopHat, cufflinks, and cuffdiff and got results correctly,
>> >>
>> >> but when I executed cuffcompare through galaxy, the following error
>> >> occurred:
>> >>
>> >>
>> >>
>> >> Tool execution generated the following error message:
>> >>
>> >> Error running cuffcompare. [Errno 2] No such file or directory: 
>> >> 'cc_output'
>> >>
>> >> The tool produced the following additional output:
>> >>
>> >> cuffcompare v1.0.3 (2403)
>> >>
>> >> cuffcompare -o cc_output  -s
>> >> /home/galaxy/data/galaxy_data/sam_index/hg19.fasta ./input1
>> >>
>> >>
>> >>
>> >> and error messages in log file (galaxy.log) are:
>> >>
>> >>
>> >>
>> >> galaxy.jobs INFO 2011-06-10 14:02:15,161 job 130 dispatched
>> >>
>> >> galaxy.jobs.runners.local DEBUG 2011-06-10 14:02:15,466 executing: python
>> >> /home/galaxy/software/galaxy_dist/tools/ngs_rna/cuffcompare_wrapper.py
>> >>                             -s                     --ref_file="None"
>> >>                 --dbkey=hg19
>> >> --index_dir=/home/galaxy/software/galaxy_dist/tool-data
>> >> /home/galaxy/software/galaxy_dist/database/files/000/dataset_398.dat
>> >>
>> >>
>> >>
>> >> galaxy.jobs.runners.local DEBUG 2011-06-10 14:02:27,834 execution 
>> >> finished:
>> >> python
>> >> /home/galaxy/software/galaxy_dist/tools/ngs_rna/cuffcompare_wrapper.py
>> >> -s                     --ref_file="None"
>> >>   --dbkey=hg19
>> >> --index_dir=/home/galaxy/software/galaxy_dist/tool-data
>> >> /home/galaxy/software/galaxy_dist/database/files/000/dataset_398.dat
>> >>
>> >>
>> >>
>> >> galaxy.jobs DEBUG 2011-06-10 14:02:27,943 finish(): Could not move
>> >> /home/galaxy/software/galaxy_dist/database/job_working_directory/130/cc_output
>> >> to /home/galaxy/software/galaxy_dist/database/files/000/dataset_399.dat as
>> >> directed by from_work_dir
>> >>
>> >> galaxy.jobs DEBUG 2011-06-10 14:02:27,971 finish(): Could not move
>> >> /home/galaxy/software/galaxy_dist/database/job_working_directory/130/input1.tmap
>> >> to /home/galaxy/software/galaxy_dist/database/files/000/dataset_400.dat as
>> >> directed by from_work_dir
>> >>
>> >> galaxy.jobs DEBUG 2011-06-10 14:02:27,999 finish(): Could not move
>> >> /home/galaxy/software/galaxy_dist/database/job_working_directory/130/input1.refmap
>> >> to /home/galaxy/software/galaxy_dist/database/files/000/dataset_401.dat as
>> >> directed by from_work_dir
>> >>
>> >> galaxy.jobs DEBUG 2011-06-10 14:02:28,027 finish(): Moved
>> >> /home/galaxy/software/galaxy_dist/database/job_working_directory/130/cc_output.combined.gtf
>> >> to /home/galaxy/software/galaxy_dist/database/files/000/dataset_402.dat as
>> >> directed by from_work_dir
>> >>
>> >> galaxy.jobs DEBUG 2011-06-10 14:02:28,174
>> >>
>> >>
>> >>
>> >> job 130 ended
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> I’ve tried to manually execute cuffcompare to analyze dataset_398.dat 
>> >> (which
>> >> is the output of tophat) and I could get correct cuffcompare output.
>> >>
>> >>
>> >>
>> >> $ cuffcompare -o cc_output  -s
>> >> /home/galaxy/data/galaxy_data/sam_index/hg19.fasta dataset_398.dat
>> >>
>> >>
>> >>
>> >> It seems that the coffcompare_wrapper might have something to do with this
>> >> error…
>> >>
>> >>
>> >>
>> >> Thanks in advance for your help!
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> Best
>> >>
>> >> John Wu
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> ___________________________________________________________
>> >> The Galaxy User list should be used for the discussion of
>> >> Galaxy analysis and other features on the public server
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>> >> use the Galaxy Development list:
>> >>
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>> >>
>> >> To manage your subscriptions to this and other Galaxy lists,
>> >> please use the interface at:
>> >>
>> >>  http://lists.bx.psu.edu/
>> >>
>> >
>>
>> ___________________________________________________________
>> 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
>>
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>> please use the interface at:
>>
>>   http://lists.bx.psu.edu/
>>
>

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