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', 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 = 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 Auṭnoma de Barcelona

Edifici CReSA

08193  Bellaterra (Barcelona, Spain)

Tel.: 647 42 52 63 www.cresa.es