Peter, Can you confirm that you are running 10639:8045e137464f or later when this problem occurs? Fabric was upgraded in 10638, and the paramiko egg was added in 10639. --Dave B. On 09/24/2013 12:21 PM, Peter Cock wrote:
Hmm.
This error message is unhelpful, no hint of if this is a local configuration error (like the egg paths) or remote (e.g. the Galaxy egg cache):
$ python ./scripts/fetch_eggs.py Warning: paramiko (a dependent egg of Fabric) cannot be fetched
(Meanwhile working from the stable branch avoids this)
Peter
On Tue, Sep 24, 2013 at 5:08 PM, Dave Bouvier <dave@bx.psu.edu> wrote:
Peter,
We recently upgraded the Fabric egg, which now depends on paramiko. You should be able to resolve this issue by running
python ./scripts/fetch_eggs.py
--Dave B.
On 09/24/2013 11:42 AM, Peter Cock wrote:
Hi all,
Has something changed recently on galaxy-central with the fabric egg, and a possible missing dependency?
$ ./run.sh ... galaxy.jobs.handler INFO 2013-09-24 16:40:21,849 job handler stop queue started galaxy.jobs.handler INFO 2013-09-24 16:40:21,867 job handler queue started galaxy.sample_tracking.external_service_types DEBUG 2013-09-24 16:40:21,870 Loaded external_service_type: Simple unknown sequencer 1.0.0 galaxy.sample_tracking.external_service_types DEBUG 2013-09-24 16:40:21,873 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0 galaxy.web.framework.base DEBUG 2013-09-24 16:40:21,899 Enabling 'data_admin' controller, class: DataAdmin galaxy.web.framework.base DEBUG 2013-09-24 16:40:21,903 Enabling 'requests_common' controller, class: RequestsCommon galaxy.web.framework.base DEBUG 2013-09-24 16:40:21,905 Enabling 'forms' controller, class: Forms galaxy.web.framework.base DEBUG 2013-09-24 16:40:21,974 Enabling 'workflow' controller, class: WorkflowController galaxy.web.framework.base DEBUG 2013-09-24 16:40:21,975 Enabling 'async' controller, class: ASync galaxy.web.framework.base DEBUG 2013-09-24 16:40:21,975 Enabling 'library' controller, class: Library galaxy.web.framework.base DEBUG 2013-09-24 16:40:21,982 Enabling 'data_manager' controller, class: DataManager galaxy.web.framework.base DEBUG 2013-09-24 16:40:21,983 Enabling 'error' controller, class: Error galaxy.web.framework.base DEBUG 2013-09-24 16:40:22,213 Enabling 'cloudlaunch' controller, class: CloudController galaxy.eggs WARNING 2013-09-24 16:40:22,480 Warning: paramiko (a dependent egg of Fabric) cannot be fetched Traceback (most recent call last): File "/mnt/galaxy/galaxy-central/eggs/Fabric-1.7.0-py2.6.egg/fabric/network.py", line 24, in <module> import paramiko as ssh ImportError: No module named paramiko
There was a problem importing our SSH library (see traceback above). Please make sure all dependencies are installed and importable ...
Also what is this CloudController and can I turn it off instead?
Thanks,
Peter ___________________________________________________________ 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/
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