Hello Enis, I would like to give you another update about Galaxy on Opennebula. I haven't been working on it that much recently, but nevertheless I think it's time to merge it with the repository. Off course there is a new file opennebula.py, but I also had to make some changes to master.py, app.py, galaxy.py and comm.py. Should I make patches for these files? I hope the are not causing backward compatibility problems. Maybe you can check it first? I added comments with my name or placed if statements to check if its running opennebula. See the attached files for details. The Cloud I am using is reaching its official release on 4th October (http://sara.nl/systems/hpc-cloud). The asked me if I could give a demonstration or poster/presentation on that day to show how I am using the cloud. I think this is a good opportunity to showcase Galaxy Cloud. But off course I need your permission for that because you wrote it and the only thing I did was make it running in a different environment. I don't want to show off with others work. Hope to hear from you, Mattias On Fri, 2011-07-15 at 14:41 +0000, Enis Afgan wrote:
Great! If you fork mi-deployment project on bitbucket and issue a pull request, the new tool can be added to upstream (or send a patch via email and I'll add it manually).
Thanks, Enis
On Fri, Jul 15, 2011 at 2:03 PM, Mattias de Hollander <m.dehollander@nioo.knaw.nl> wrote: I just found out the former approach you mentioned. Its now installing perfectly. The latter approach won't work for a Qiime installation because its needs PyCogent on its path during the setup.py phase.
Thanks for clarification. If I finished adding Qiime' dependencies I will put it on bitbucket.
Greetz,
Mattias
On Fri, 2011-07-15 at 13:44 +0000, Enis Afgan wrote: > Each use of fabric's `run` method is independent so they cannot be > chained; you would either need to prepend the export command to the > command that depends on the fact PYTHONPATH is set (e.g., run("export > PYTHONPATH=...; <command that requires given PP>") or (better > approach) create an env.sh file in the Qiime's install dir so that it > includes the required 'export PYTHONPATH=...'. When Galaxy invokes > Qiime, it will automatically source that env.sh (assuming you have > config variable `tool_dependency_dir = /mnt/galaxyTools/tools` set in > Galaxy's universe_wsgi.ini). > > Enis > > On Fri, Jul 15, 2011 at 12:19 PM, Mattias de Hollander > <m.dehollander@nioo.knaw.nl> wrote: > Hello Enis, > > I am trying to add PyCogent to the PYTHONPATH, but it seems > the Fabric > run command does not recognize it. > I tried: run("export > PYTHONPATH=/mnt/galaxyTools/tools/PyCogent/1.5.1/lib/python2.6/site-packages/:$PYTHONPATH") > and then use cmd_install() to install Galaxy, but I keep > getting the > message that PyCogent is not installed. > > The normal strategy to use sys.path will not work because that > will > adjust the PYTHONPATH on my local machine, not in the image if > I am > correct. > Do you know a way to set the PYTHONPATH for Fabric' run() > command? > > Thanks, > > Mattias > > > On Thu, 2011-07-14 at 09:05 +0000, Enis Afgan wrote: > > Hi Mattias, > > PyCogent is not currently being installed as part of > mi-deployment, so > > the method for installing it should be added (if you do so, > please > > consider issuing a pull request on bitbucket so it can be > added to the > > project). > > > > > > When it comes to composing $PYTHONPATH to include the > reference to > > PyCogent via Qiime's env.sh - this should be done as part of > the Qiime > > installation method in mi-deployment (something like export > > PYHTONPATH=<path where PyCogent was installed>; export > PATH=...). > > Sourcing of the tool's env.sh script is prepended to the > execution > > command when running the tool so the appropriate environment > settings > > will be loaded before the tool is run. > > > > > > Enis > > > > On Wed, Jul 13, 2011 at 12:09 PM, Mattias de Hollander > > <m.dehollander@nioo.knaw.nl> wrote: > > Hello, > > > > I am trying to add tools (PyCogent, Qiime) to a > Cloudman image > > using the > > mi-deployment scripts. Qiime depends on PyCogent and > it needs > > to be > > accessible on the python path, otherwise I get an > error: > > PyCogent not installed but required. (Is it > installed? Is it > > in the > > current user's $PYTHONPATH or site-packages?) > > > > Is there a way to add the paths in env.sh to the > sys.path > > during > > installation using tools_fabfile.py? > > All the tools are in /mnt/galaxyTools/tools. > > I tried the DependencyManager from galaxy but then I > only > > receive the > > path to the env.sh file: > > In [43]: dependency_manager.find_dep('blast') > > Out[43]: > > ('/mnt/galaxyTools/tools/blast/2.2.25/env.sh', > > '/mnt/galaxyTools/tools/blast/2.2.25', > > '2.2.25') > > > > Is there a smarter way to add files to the > PYTHONPATH during > > the > > execution of tools_fabfile.py? > > > > Thanks, > > > > Mattias > > > > -- > > Bioinformatician > > Netherlands Institute of Ecology (NIOO-KNAW) > > Wageningen, the Netherlands > > > > > > > > -- > > Bioinformatician > Netherlands Institute of Ecology (NIOO-KNAW) > Wageningen, the Netherlands > > >
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Bioinformatician Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, the Netherlands
-- Bioinformatician Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, the Netherlands