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 popnard@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=sharin...
https://drive.google.com/file/d/0B8-ZAuZe8jldbTVxTTM3Ujluems/edit?usp=sharin...
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 = popnard@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 *