Fabiano; I help with the BioCloudCentral site, which is a community maintained way to launch CloudMan and CloudBioLinux AMIs. Sorry for any confusion between the different methods. Dannon, if you're up for it we should try to coordinate better at least on the documentation side.
In terms of your problem, it sounds like you've tried to launch the same CloudMan instance with multiple AMIs. Each AMI will have different software which can create incompatibilities: your error messages indicate different version of PostgreSQL and Python at least. Every time you launch a CloudMan instance with the same name, it will pull up the saved data volumes which is causing this incompatibility. As long as you don't have any critical data on the instance, my suggestion would be: - Start up a CloudMan cluster with any AMI and then terminate the instance, removing all data. This will clear up your data volumes and S3 data associated with this CloudMan cluster. - Pick one method and stick with that moving forward. It sounds like you want to run Galaxy exclusively so Dannon's launcher would be a good choice. Hope this fixes it for you, Brad > Hi, Dannon. > > Thank you for your reply. I was using this form: > > https://biocloudcentral.herokuapp.com/launch > > which was in turn referenced in this tutorial: > > > http://onlinelibrary.wiley.com/doi/10.1002/0471250953.bi1109s38/full#bi1109-prot-0001 > > It looks like there is a lot of outdated stuff on the net regarding the > Galaxy / Cloudman bundle. Anyway, I followed the flow of this new form and > got my instance up and running in a few minutes (I chose a Galaxy-type > cluster). However, the Galaxy, Postgres and File System services seemed to be > stuck at the "Unstarted" status. I tried to manually start them and got the > following error message at the Galaxy log: > > /mnt/galaxyTools/galaxy-central/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1: > RuntimeWarning: __builtin__.file size changed, may indicate binary > incompatibility > from csamtools import * > python path is: > /mnt/galaxyTools/galaxy-central/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg, > /mnt/galaxyTools/galaxy-central/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg, > /mnt/galaxyTools/galaxy-central/eggs/boto-2.5.2-py2.6.egg, > /mnt/galaxyTools/galaxy-central/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs4.egg, > /mnt/galaxyTools/galaxy-central/eggs/Fabric-1.4.2-py2.6.egg, > /mnt/galaxyTools/galaxy-central/eggs/ssh-1.7.14-py2.6.egg, > /mnt/galaxyTools/galaxy-central/eggs/Whoosh-0.3.18-py2.6.egg, > /mnt/galaxyTools/galaxy-central/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg, > > /mnt/galaxyTools/galaxy-central/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg, > > /mnt/galaxyTools/galaxy-central/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg, > /mnt/galaxyTools/galaxy-central/eggs/amqplib-0.6.1-py2.6.egg, > /mnt/galaxyTools/galaxy-central/eggs/pexpect-2.4-py2.6.egg, > /mnt/galaxyTools/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg, > /mnt/ga! la! > xyTools/galaxy-central/eggs/Babel-0.9.4-py2.6.egg, > /mnt/galaxyTools/galaxy-central/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg, > /mnt/galaxyTools/galaxy-central/eggs/Mako-0.4.1-py2.6.egg, > /mnt/galaxyTools/galaxy-central/eggs/WebHelpers-0.2-py2.6.egg, > /mnt/galaxyTools/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg, > /mnt/galaxyTools/galaxy-central/eggs/wchartype-0.1-py2.6.egg, > /mnt/galaxyTools/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg, > /mnt/galaxyTools/galaxy-central/eggs/docutils-0.7-py2.6.egg, > /mnt/galaxyTools/galaxy-central/eggs/WebOb-0.8.5-py2.6.egg, > /mnt/galaxyTools/galaxy-central/eggs/Routes-1.12.3-py2.6.egg, > /mnt/galaxyTools/galaxy-central/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg, > /mnt/galaxyTools/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg, > /mnt/galaxyTools/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg, > /mnt/galaxyTools/galaxy-central/eggs/Paste-1.6-py2.6.egg, > /mnt/galaxyTools/galaxy-central/lib, /usr/lib/python2.6/, ! /u! > sr/lib/python2.6/plat-linux2, /usr/lib/python2.6/lib-tk, /usr/! > lib/pyth > on2.6/lib-old, /usr/lib/python2.6/lib-dynload > Traceback (most recent call last): > File > "/mnt/galaxyTools/galaxy-central/lib/galaxy/webapps/galaxy/buildapp.py", line > 36, in app_factory > app = UniverseApplication( global_conf = global_conf, **kwargs ) > File "/mnt/galaxyTools/galaxy-central/lib/galaxy/app.py", line 29, in > __init__ > self.config.check() > File "/mnt/galaxyTools/galaxy-central/lib/galaxy/config.py", line 315, in > check > raise ConfigurationError( "Unable to create missing directory: %s\n%s" % > ( path, e ) ) > ConfigurationError: Unable to create missing directory: /mnt/galaxyData/files > [Errno 13] Permission denied: '/mnt/galaxyData/files' > Removing PID file paster.pid > > I'm still wondering if I might be doing something wrong, which would > surprise me as this time the process required much less interaction and input > than the previous ones I was following. > > Any thoughts? > > Thanks, > > F. > > -----Original Message----- > From: Dannon Baker [mailto:dannonba...@me.com] > Sent: Friday, December 07, 2012 6:19 AM > To: Fabiano Lucchese > Cc: email@example.com > Subject: Re: [galaxy-dev] Installation issue on EC2 > > Which web form did you use to start the cloud instance? The page at > usegalaxy.org/cloudlaunch will always point to the currently supported AMI, > and I'd definitely recommend using this form for launching galaxy instances. > > The problem you're running into is that the unsupported AMI already > initialized your database as postgres9, which isn't backwards compatible with > the postgres8 installed on the official AMI. At this point, if you want to > continue with this specific cluster you'll need to keep using that original > AMI (or attempt to manually migrate the database between instances, which I > wouldn't recommend). > > If you don't have any data you care to preserve on this cluster, just delete > it and start over using usegalaxy.org/cloudlaunch and you should be good to > go. If you want to try again fresh without deleting anything, just use a new > cluster name when you launch the instance. > > -Dannon > > On Dec 6, 2012, at 7:45 PM, Fabiano Lucchese <fabiano.lucch...@hds.com> wrote: > >> Hi, all. >> >> I've been trying to deploy a CloudMan/Galaxy cluster on EC2 >> for a couple of days now and have been facing all kinds of unexpected >> weirdness's. I found out that the web-based form that automatically creates >> the EC2 instance uses an image that doesn`t seem to be officially supported >> (or at least encouraged) by the Galaxy team, so I decided to launch the >> instance by hand following the instructions from here: >> >> >> http://wiki.galaxyproject.org/CloudMan/AWS/GettingStarted >> >> Up to the point before accessing Galaxy, everything looks >> ok, but the service never starts. Instead, it shows up at the CloudMan Admin >> page as "Error" and nothing happens if I try to Stop/Start or Restart >> it.There's no log either. The Postgres service displays an immutable >> "Starting" status, while its log provides the following message: >> >> FATAL: database files are incompatible with server >> DETAIL: The data directory was initialized by PostgreSQL version 9.1, which >> is not compatible with this version 8.4.7. >> >> It does look like a messed up installation, which is quite >> surprising as this is supposed to be the recommended working image. >> >> Does anybody have any clue on what might be going on? >> >> Thanks in advance. >> >> F. >> >> ___________________________________________________________ >> 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/ > > > ___________________________________________________________ > 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/ ___________________________________________________________ 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/