Re: [galaxy-dev] Installing S-Mart on Mac OSX local instance (updated)

2014-04-09 Thread Björn Grüning 

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 popn...@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 = popn...@gmail.com

# Set 'Tool Dependencies'
https://wiki.galaxyproject.org/Admin/Config/ToolDependencies?action=showredirect=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)}'




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Re: [galaxy-dev] Installing S-Mart on Mac OSX local instance (updated)

2014-04-09 Thread 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 bjoern.gruen...@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 popn...@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 = popn...@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  *
___
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/

[galaxy-dev] Installing S-Mart on Mac OSX local instance (updated)

2014-04-08 Thread 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 popn...@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 = popn...@gmail.com

# Set 'Tool Dependencies'
https://wiki.galaxyproject.org/Admin/Config/ToolDependencies?action=showredirect=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)}'


-- 

*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  *
___
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/