Installing S-Mart on Mac OSX local instance (updated)
Hi, I am having problems to install a tool from tool shed named S_MART on my local Galaxy. In fact, its the first tool I'm trying to install. The reason to install S-MART is to use DETR'PROK in Galaxy. Here is the 'error' Galaxy shows after installing some programs from toolshed.<https://drive.google.com/file/d/0B8-ZAuZe8jldN3ptYzE5N0p2ZGM/edit?usp=sharing> I've seen this related post, but I don't know if we are talking about the same problem.<http://dev.list.galaxyproject.org/Problem-installing-tool-Galaxy-local-td4662775.html> Here are the commands aI've used up to now: Thanks, Bernardo P.S. Sorry for the duplicated email, I mistyped the subject in the previous one. hg clone https://bitbucket.org/galaxy/galaxy-dist/ cd galaxy-dist hg update stable sh run.sh # gave errors, so see below # solve problem at startup ( https://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg13354.html) % export LC_ALL='en_US.UTF-8' % sh run.sh done # Go to http://localhost:8080/ and register as popnard@gmail.com # Setup admin user (https://wiki.galaxyproject.org/Admin/Interface). To give a user Galaxy admin privileges, add their Galaxy login ( email ) to the list in the following config setting in the Galaxy configuration file universe_wsgi.ini. admin_users = popnard@gmail.com # Set 'Tool Dependencies' https://wiki.galaxyproject.org/Admin/Config/ToolDependencies?action=show&redirect=Admin%2FConfig%2FTool+Dependencies mkdir tool_dependency_dir done # add tool dependencies folder to 'universe_wsgi.ini' -> Galaxy provides a method for managing the dependencies of Galaxy tools installed from the Tool Shed. In this case, it is simply necessary to set the tool_dependency_dir option of universe_wsgi.ini to a path writable by the Galaxy server. done # restart server First, I modified the universe_wsgi.ini file by removing the "#" before the tool_config_file and tool_path lines. # http://user.list.galaxyproject.org/Installing-new-tools-from-the-tool-shed-t... # Then, I created a shed_tools folder in my $HOME directory before modifying the shed_tool_conf.xml file <?xml version="1.0"?> <toolbox tool_path="$HOME/shed_tools"> </toolbox> done # INSTALL R done # ADD R 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)}' -- *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> *
Hi Bernado, can you try to change your $HOME/shed_tools to a full path? Also please try my small tutorial here: https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox Hope that will help you! Cheers - Bjoern Am 08.04.2014 23:39, schrieb Bernardo Bello:
Hi,
I am having problems to install a tool from tool shed named S_MART on my local Galaxy. In fact, its the first tool I'm trying to install. The reason to install S-MART is to use DETR'PROK in Galaxy.
Here is the 'error' Galaxy shows after installing some programs from toolshed.<https://drive.google.com/file/d/0B8-ZAuZe8jldN3ptYzE5N0p2ZGM/edit?usp=sharing>
I've seen this related post, but I don't know if we are talking about the same problem.<http://dev.list.galaxyproject.org/Problem-installing-tool-Galaxy-local-td4662775.html>
Here are the commands aI've used up to now:
Thanks, Bernardo
P.S. Sorry for the duplicated email, I mistyped the subject in the previous one.
hg clone https://bitbucket.org/galaxy/galaxy-dist/ cd galaxy-dist hg update stable
sh run.sh # gave errors, so see below
# solve problem at startup ( https://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg13354.html) % export LC_ALL='en_US.UTF-8' % sh run.sh
done # Go to http://localhost:8080/ and register as popnard@gmail.com # Setup admin user (https://wiki.galaxyproject.org/Admin/Interface). To give a user Galaxy admin privileges, add their Galaxy login ( email ) to the list in the following config setting in the Galaxy configuration file universe_wsgi.ini.
admin_users = popnard@gmail.com
# Set 'Tool Dependencies' https://wiki.galaxyproject.org/Admin/Config/ToolDependencies?action=show&redirect=Admin%2FConfig%2FTool+Dependencies mkdir tool_dependency_dir
done # add tool dependencies folder to 'universe_wsgi.ini' -> Galaxy provides a method for managing the dependencies of Galaxy tools installed from the Tool Shed. In this case, it is simply necessary to set the tool_dependency_dir option of universe_wsgi.ini to a path writable by the Galaxy server.
done # restart server
First, I modified the universe_wsgi.ini file by removing the "#" before the tool_config_file and tool_path lines. # http://user.list.galaxyproject.org/Installing-new-tools-from-the-tool-shed-t...
# Then, I created a shed_tools folder in my $HOME directory before modifying the shed_tool_conf.xml file <?xml version="1.0"?> <toolbox tool_path="$HOME/shed_tools"> </toolbox>
done # INSTALL R done # ADD R 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)}'
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Hi Björn, I finally got Galaxy tool shed working, installing Galaxy again following your tutorial and worked. Just skipped the san-boxed optional step. Thanks, Bernardo 2014-04-09 9:04 GMT+02:00 Björn Grüning <bjoern.gruening@gmail.com>:
Hi Bernado,
can you try to change your $HOME/shed_tools to a full path? Also please try my small tutorial here:
https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox
Hope that will help you!
Cheers - Bjoern
Am 08.04.2014 23:39, schrieb Bernardo Bello:
Hi,
I am having problems to install a tool from tool shed named S_MART on my local Galaxy. In fact, its the first tool I'm trying to install. The reason to install S-MART is to use DETR'PROK in Galaxy.
Here is the 'error' Galaxy shows after installing some programs from toolshed.<https://drive.google.com/file/d/0B8- ZAuZe8jldN3ptYzE5N0p2ZGM/edit?usp=sharing>
I've seen this related post, but I don't know if we are talking about the same problem.<http://dev.list.galaxyproject.org/Problem- installing-tool-Galaxy-local-td4662775.html>
Here are the commands aI've used up to now:
Thanks, Bernardo
P.S. Sorry for the duplicated email, I mistyped the subject in the previous one.
hg clone https://bitbucket.org/galaxy/galaxy-dist/ cd galaxy-dist hg update stable
sh run.sh # gave errors, so see below
# solve problem at startup ( https://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg13354.html) % export LC_ALL='en_US.UTF-8' % sh run.sh
done # Go to http://localhost:8080/ and register as popnard@gmail.com # Setup admin user (https://wiki.galaxyproject.org/Admin/Interface). To give a user Galaxy admin privileges, add their Galaxy login ( email ) to the list in the following config setting in the Galaxy configuration file universe_wsgi.ini.
admin_users = popnard@gmail.com
# Set 'Tool Dependencies' https://wiki.galaxyproject.org/Admin/Config/ToolDependencies?action=show& redirect=Admin%2FConfig%2FTool+Dependencies mkdir tool_dependency_dir
done # add tool dependencies folder to 'universe_wsgi.ini' -> Galaxy provides a method for managing the dependencies of Galaxy tools installed from the Tool Shed. In this case, it is simply necessary to set the tool_dependency_dir option of universe_wsgi.ini to a path writable by the Galaxy server.
done # restart server
First, I modified the universe_wsgi.ini file by removing the "#" before the tool_config_file and tool_path lines. # http://user.list.galaxyproject.org/Installing- new-tools-from-the-tool-shed-td4655241.html
# Then, I created a shed_tools folder in my $HOME directory before modifying the shed_tool_conf.xml file <?xml version="1.0"?> <toolbox tool_path="$HOME/shed_tools"> </toolbox>
done # INSTALL R done # ADD R 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)}'
___________________________________________________________ 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/
___________________________________________________________ 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/
-- *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> *
participants (2)
-
Bernardo Bello -
Björn Grüning