Installing S-Mart on Mac OSX local instance (updated)

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Installing S-Mart on Mac OSX local instance (updated)

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 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.


cd galaxy-dist
hg update stable

sh run.sh # gave errors, so see below

% export LC_ALL='en_US.UTF-8'
% sh run.sh

done # Go to http://localhost:8080/ and register as [hidden email]
# 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 = [hidden email]

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)}'


--

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: Installing S-Mart on Mac OSX local instance (updated)

Björn Grüning-3
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@.../msg13354.html)
> % export LC_ALL='en_US.UTF-8'
> % sh run.sh
>
> done # Go to http://localhost:8080/ and register as [hidden email]
> # 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 = [hidden email]
>
> # 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/
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Re: Installing S-Mart on Mac OSX local instance (updated)

Bernardo Bello
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 <[hidden email]>:
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@.../msg13354.html)
% export LC_ALL='en_US.UTF-8'
% sh run.sh

done # Go to http://localhost:8080/ and register as [hidden email]
# 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 = [hidden email]

# 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  




___________________________________________________________
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/