Re: [galaxy-user] Installing Galaxy on SGE Cluster - Questions
On Tue, Oct 2, 2012 at 2:15 PM, Nate Coraor wrote: > On Oct 2, 2012, at 12:45 PM, greg wrote: > >> Hi guys, >> >> I'm following the instructions here to install Galaxy on our SGE cluster. >> http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster >> (I'm aiming for the unified install) >> >> Here are a couple of questions I'm hoping someone could clear up for me: >> >> How exactly do I use virtual env to make Galaxy install all the Python >> libraries there instead of on the system? How will Galaxy know to use >> the virtualenv to run and to use it for grid jobs? > > Hi Greg, > > You should start at the top level documentation for production servers: > > http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server > > This includes instructions on how to set up a virtualenv. You can make this > the default by setting the $PATH in the Galaxy user's ~/.bash_profile to > include the virtualenv's bin directory (at the beginning of $PATH). This makes sense, but I ultimately want to run the jobs as the logged in user as per this page: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster#Submitting_Jobs_as_the_Real_User It wouldn't be feasible to add the virtualenv to every users' path. I'm hoping there's some kind of other way? Thanks again, Greg ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Installing Galaxy on SGE Cluster - Questions
On Oct 2, 2012, at 12:45 PM, greg wrote: > Hi guys, > > I'm following the instructions here to install Galaxy on our SGE cluster. > http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster > (I'm aiming for the unified install) > > Here are a couple of questions I'm hoping someone could clear up for me: > > How exactly do I use virtual env to make Galaxy install all the Python > libraries there instead of on the system? How will Galaxy know to use > the virtualenv to run and to use it for grid jobs? Hi Greg, You should start at the top level documentation for production servers: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server This includes instructions on how to set up a virtualenv. You can make this the default by setting the $PATH in the Galaxy user's ~/.bash_profile to include the virtualenv's bin directory (at the beginning of $PATH). > Do I need to install all of the dependencies listed on this page: > http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies > If so what's a good way to make sure they're contained in the > galaxy-dist directory and make sure Galaxy and all of the jobs know to > find these tools there? You only need to install the dependencies for the tools that you plan to use. Setting them up is explained in more detail here: http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies --nate > > Thanks, > > Greg > ___ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Installing Galaxy on SGE Cluster - Questions
Hi guys, I'm following the instructions here to install Galaxy on our SGE cluster. http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster (I'm aiming for the unified install) Here are a couple of questions I'm hoping someone could clear up for me: How exactly do I use virtual env to make Galaxy install all the Python libraries there instead of on the system? How will Galaxy know to use the virtualenv to run and to use it for grid jobs? Do I need to install all of the dependencies listed on this page: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies If so what's a good way to make sure they're contained in the galaxy-dist directory and make sure Galaxy and all of the jobs know to find these tools there? Thanks, Greg ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Galaxy download
Hi all I downloaded galaxy om my Mac OS 10.6.8 and have followed the following steps: Install Galaxy on MacBook Pro OS10.7.4 (08-10-2012) • Install Mercurial http://mercurial.selenic.com/wiki/ • Open Applications/Utilities/Terminal.app • Confirm Mercurial installation by pasting in "hg version", no quotes and hit return response = version 2.3+20120807 • Check Python version by pasting in "python -V", no quotes and hit return response = Python 2.7.1 • Go to your home directory by pasting in "cd", no quotes and hit return • Get Galaxy by pasting in "hg clone http://bitbucket.org/galaxy/galaxy-dist/";, no quotes and hit return • Go to the Galaxy directory by pasting in "cd galaxy-dist", no quotes and hit return • Start up Galaxy by pasting in "sh run.sh", no quotes and hit return • Open web browser and paste in “http://localhost:8080”, no quotes and hit return I started galaxy by pasting sh run.sh and it fetched everything and updated whats needed. Upon pasting http://localhost:8080 in my browser GoogleChrome and Safari respectively, it didn't work. I even changed the host setting in the universe_wsgi.ini to 0.0.0.0 and still didn't open. Any suggestions? Kind regards Lizex Husselmann This message is confidential and may be covered by legal professional privilege. It must not be read, copied, disclosed or used in any other manner by any person other than the addressee(s). Unauthorised use, disclosure or copying is strictly prohibited and may be unlawful. The views expressed in this email are those of the sender, unless otherwise stated. If you have received this email in error, please contact ARC Service Desk immediately. (mailto:serviced...@arc.agric.za) To report incidents of fraud and / or corruption in the ARC use our Ethics Hotline by: Phone number : 0800 000 604 Fax number : 0800 00 7788 Email address : a...@tip-offs.com Please Call me : 32840 Website: www.tip-offs.com For more information on the ARC Ethics Hotline, please visit our website at www.arc.agric.za. ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
