Error getting Detrprok_wf working on local Galaxy instance

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Error getting Detrprok_wf working on local Galaxy instance

Bernardo Bello
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.




Thanks for your help, Bernardo

Command and actions up to now:

python --version
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 = [hidden email] 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
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  




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Re: Error getting Detrprok_wf working on local Galaxy instance

Bernardo Bello
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 <[hidden email]>:
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.




Thanks for your help, Bernardo

Command and actions up to now:

python --version
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 = [hidden email] 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
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  






--

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  




___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/