This has been solved. Detrprok workflow is working well, although asRNA step not. I will contact the author for this particular problem.
Thanks, Bernardo 2014-04-09 11:04 GMT+02:00 Bernardo Bello <popn...@gmail.com>: > Hi, > > While problems are been solved in my other Galaxy instance (MAC OSX), I > tried to install Galaxy on local Linux machine running Ubuntu 12.04. > > Surprisingly, seems I have been able to get Galaxy toolshed work. The > problem I have now is that I'm trying to run a published workflow, named ' > Detrprok_wf <http://127.0.0.1:8080/workflow/run?id=f597429621d6eb2b>', > that requires S-Mart installed and Detrprok scripts installed. Both of > them are installed, however although I've also been able to import the > corresponding wokflow 'Detrprok_wf', seems there is something wrong. See > attached files. > > > https://drive.google.com/file/d/0B8-ZAuZe8jldNE5ncktjTFZ6SG8/edit?usp=sharing > > > https://drive.google.com/file/d/0B8-ZAuZe8jldbTVxTTM3Ujluems/edit?usp=sharing > > > Thanks for your help, Bernardo > > Command and actions up to now: > > python --version > hg clone -v https://bitbucket.org/galaxy/galaxy-dist/ > cd galaxy-dist > hg update stable > sh run.sh > > #7. Workflow installation instructions > #The workflow should be run on a local Galaxy instance or one hosted on a > distant server. Refer to the tutorial ( > http://wiki.galaxyproject.org/Admin/Get_Galaxy) for creation of a #Galaxy > instance. As the workflow has several steps running in parallel, the Galaxy > instance should use a database management system supporting concurential > access such as #postgreSQL, instead of the default SQLite system. The > DETR'PROK pipeline is obtained from the Galaxy main tool shed ( > http://toolshed.g2.bx.psu.edu/), or my experiment (http://# > www.myexperiment.org), searching by name "detrprok_wf", and should be > installed by the Galaxy instance administrator. DETR'PROK requires > installation of the S-MART toolbox [13] and 3the "detrprok_scripts", both > available in the Galaxy main tool shed. > > done # replace admin = none by admin = popn...@gmail.com in > 'universe_wsgi.ini' file > lets see if this is not essential # postgreSQL installation ( > https://help.ubuntu.com/community/PostgreSQL) > > done # The DETR'PROK pipeline is obtained from the Galaxy main tool shed ( > http://toolshed.g2.bx.psu.edu/ > > done ## DETR'PROK requires installation of the S-MART toolbox [13] and the > "detrprok_scripts" > > # S-MART needs the folowing packages > R --slave --no-save --no-restore --quiet -e 'if("RColorBrewer" %in% > rownames(installed.packages()) == FALSE){install.packages("RColorBrewer", > repos = c("http://cran.rstudio.com/";), dependencies = TRUE)}' > R --slave --no-save --no-restore --quiet -e 'if("Hmisc" %in% > rownames(installed.packages()) == FALSE){install.packages("Hmisc", repos = > c("http://cran.rstudio.com/";), dependencies = TRUE)}' > > # set 'tool_dependency_dir' > mkdir tool_dependency_dir > # http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies > tool_dependency_dir = /home/usuario/tool_dependency_dir > > # install 'detrprok_wf' nad from 'repository actions' import workflow to > Galaxy > NOTE -> Workflow Detrprok_wf imported successfully. The following tools > required by this workflow are missing from this Galaxy instance: name: > bam_to_sam, id: BAM-to-SAM. > > done # install 'bam_to_sam' > Install S-MART dependencies > > > -- > > *Bernardo Bello Ortí* > > PhD student > > CReSA-IRTA > > Campus de Bellaterra-Universitat Autònoma de Barcelona > > Edifici CReSA > > 08193 Bellaterra (Barcelona, Spain) > > Tel.: 647 42 52 63 *www.cresa.es <http://www.cresa.es> * > > > > -- *Bernardo Bello Ortí* PhD student CReSA-IRTA Campus de Bellaterra-Universitat Autònoma de Barcelona Edifici CReSA 08193 Bellaterra (Barcelona, Spain) Tel.: 647 42 52 63 *www.cresa.es <http://www.cresa.es> *
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