Re: [galaxy-dev] Is there any way to restrict the access of a local Galaxy instance

2012-04-11 Thread Gianmauro Cuccuru
On 04/11/2012 01:32 AM, JIE CHEN wrote: Dear all, I installed a local Galaxy instance for my company. Different from the regular setting, we want to restrict the access of our local Galaxy instance only to the people in our company, which means it is not open to public. After new

[galaxy-dev] Nginx upload configuration question

2012-04-11 Thread Bartlett G Ailey
Dear All, When I turn on Nginx upload (as below) I get and error: Not Found The resource cannot be found No route for /data/database/tmp/upload_store The nginx upload settings for universe.ini are: # nginx can also handle file uploads (user-to-Galaxy) via nginx_upload_module. #

[galaxy-dev] Galaxy 'environment' variables

2012-04-11 Thread Joachim Jacob
Hello all, Where can I find a list of 'environment' variables in Galaxy, such as: $GALAXY_HOME ${GALAXY_DATA_INDEX_DIR} More specifically, I am looking for the temporary directory setting of a user's Galaxy (as set in the universe_wsgi.ini). Kind regards, Joachim -- Joachim Jacob, PhD

[galaxy-dev] GATK tools

2012-04-11 Thread Robert Chase
Hello, One of our users has been using the GATK (beta) tools on the main instance of galaxy and would like to have them locally accessible. I have looked at the main toolshed but I couldn't find them there. Is there a place I can download the GATK files and xml files? -Rob

Re: [galaxy-dev] Problem uploading files from filesystem paths

2012-04-11 Thread Robert Chase
Hello, I set the library_import_dir setting in my universe_wsgi.ini file so that I could upload a directory of files into galaxy. I'm getting the following error screen when I attempt the upload from /tmp. The permissions are that galaxy owns the files in /tmp. I get the same error message when