Re: [galaxy-dev] GalaxyAdmins Online Meetup 15 December

2017-01-03 Thread Dave Clements
Hi All,

If you missed this, the video for it is now online
.

The video for Nick Hazekamp's August talk on Dynamic Job Expansion:
Experiences using Makeflow in Galaxy is now online too
.

Thanks to Björn Grüning, Bérénice Batut, Dannon Baker, and Nick Hazekamp
for presenting their work.

Cheers,

Dave C

On Mon, Dec 12, 2016 at 8:53 PM, Dave Clements 
wrote:

> Hello all,
>
> The next GalaxyAdmins online meetup
> 
> is this Thursday, 15 December at [see your local time
> ].  The meetup will feature two presentations:
>
>- Galaxy Training Materials: Community creation, curation, and use, by
>Björn Grüning and Bérénice Batut, University of Freiburg
>- The new Galaxy Hub: Community creation, curation, and use, by Dannon
>Baker, Johns Hopkins University.
>
> The call will last around an hour, and will include discussion.
>
> Hope to see you there,
>
> Dave C & HAns-Rudolf
>
>
> --
> http://galaxyproject.org/
> http://getgalaxy.org/
> http://usegalaxy.org/
> https://wiki.galaxyproject.org/
>



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[galaxy-dev] Dump SQlite to mySQL

2017-01-03 Thread evan clark
Is there a script someone has designed to properly dump the galaxy 
sqlite database to a mySQL database?

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[galaxy-dev] Dataset Cleanup

2017-01-03 Thread McCully, Dwayne (NIH/NIAMS) [C]
Hello Everyone,

I have datasets that go back over a year in the files/000 directory but running 
the following script does not delete the datasets.
Also, my account says I have 59 GB used and can't figure out where it's getting 
that number.  I have almost everything deleted
in my Galaxy account.

galaxy_clean.sh
#!/bin/sh -x

/home/niamsgalaxy/galaxy/scripts/cleanup_datasets/delete_userless_histories.sh
/home/niamsgalaxy/galaxy/scripts/cleanup_datasets/purge_histories.sh
/home/niamsgalaxy/galaxy/scripts/cleanup_datasets/purge_libraries.sh
/home/niamsgalaxy/galaxy/scripts/cleanup_datasets/purge_folders.sh
/home/niamsgalaxy/galaxy/scripts/cleanup_datasets/delete_datasets.sh
/home/niamsgalaxy/galaxy/scripts/cleanup_datasets/purge_datasets.sh
Exit


Any information on this issue would be appreciated.

Dwayne
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Re: [galaxy-dev] psycopg2 module and SSL connection to postgresql

2017-01-03 Thread John Chilton
I don't know what the particular issue is - I do know that after a lot
of trial and error we were able to get Postgres + SSL working at MSI
before I left my previous job there - so there is hope.

I will say however, upgrading even to one newer Galaxy - namely 16.01
might solve this issue. We re-did Galaxy's dependency handling to use
virtualenvs, pip, and wheels in 16.01. It is much closer to a standard
Python dependency management stack. I think our wheel came bundled
with SSL support and even if I'm wrong about that support any random
online tutorial about debugging this problem in Python should be
applicable after the upgrade.

-John


On Mon, Jan 2, 2017 at 12:22 PM, Floreline TOUCHARD
 wrote:
> Hi Galaxy Community,
>
> I have the same problem than Nikolay few years ago
> (http://dev.list.galaxyproject.org/connecting-to-a-DB-on-a-different-host-td4139952.html#a4139955)
> :
> I would like to connect my Galaxy instance to my postgresql database using
> SSL encryption and Auth method md5.
> I have no problems connecting to the DB via the command line with SSL
> encryption.
>
> When setting the galaxy.ini file with postgresql database connection to
> "postgresql://:@:5432/?sslmode=require", I get
> the following message :
> "OperationalError: (psycopg2.OperationalError) sslmode value "require"
> invalid when SSL support is not compiled in"
>
> Regarding the former post I thought that it might come from the module
> psycopg2's compilation.
>
>
> I followed the steps of the post but encounter a different error.
>
> What I did:
>
>  1. Downloaded a tar.gz of psycopg2 2.5.1 (I saw the needed version in the
> file eggs.ini) to /galaxy/ and unpacked it there
>  2. cd into psycopg2, modified the setup.py according to the instructions
> (added the line containing scramble_lib)
>  3. export the path to pg_config (export
> PATH=/bin:$PATH)
>  4. added the file ez_setup.py (downloaded from
> https://bootstrap.pypa.io/ez_setup.py) to  dir>/galaxy/scripts/scramble/lib/, the same dir where scramble_lib.py is
> located
>  5. ran PYTHONPATH=/galaxy/scripts/scramble/lib python setup.py
> egg_info --tag-build=_9.4.4_static bdist_egg
> And get the following error :
>
> "
> Traceback (most recent call last):
>   File "setup.py", line 57, in 
> from scramble_lib import *
>   File "/galaxy/scripts/scramble/lib/scramble_lib.py", line
> 150, in 
> use_setuptools( download_delay=8, to_dir=os.path.dirname( __file__ ) )
>   File "/galaxy/scripts/scramble/lib/ez_setup.py", line 160, in
> use_setuptools
> version = _resolve_version(version)
>   File "/galaxy/scripts/scramble/lib/ez_setup.py", line 368, in
> _resolve_version
> resp = urlopen(meta_url)
>   File "/usr/lib64/python2.6/urllib2.py", line 126, in urlopen
> return _opener.open(url, data, timeout)
>   File "/usr/lib64/python2.6/urllib2.py", line 391, in open
> response = self._open(req, data)
>   File "/usr/lib64/python2.6/urllib2.py", line 409, in _open
> '_open', req)
>   File "/usr/lib64/python2.6/urllib2.py", line 369, in _call_chain
> result = func(*args)
>   File "/usr/lib64/python2.6/urllib2.py", line 1198, in https_open
> return self.do_open(httplib.HTTPSConnection, req)
>   File "/usr/lib64/python2.6/urllib2.py", line 1165, in do_open
> raise URLError(err)
> urllib2.URLError: 
> "
>
> Could it be because I have no internet access ? What module should I install
> to enable SSL encryption ?
>
>
> Additional information :
> - Postgresql version 9.4.4
> - Galaxy version 15.10
> - I use virtualenv for python environment
>
>
> Thanks in advance,
> Floreline
>
>
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[galaxy-dev] GIE security implications

2017-01-03 Thread Tamir,Ido
Hi,
what are the security implications of GIE?
I saw the overview on the GIE page,
but its not clear to me how dangerous they are.

"They have complex interactions with numerous services, you’ll need to be a 
fairly competent SysAdmin to debug all of the possible problems that can occur 
during deployment”

Is it possible to describe what the docker container has access to
and what could possibly go wrong?

thank you very much,
ido
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