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 > >> 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/ > >> > > > > ___________________________________________________________ > 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/ > ___________________________________________________________ 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/
