Re: [galaxy-dev] Non-admin tool install/import

[John Chilton]

Galaxy doesn't really support this use case and it will be major
effort to get it work this way I suspect. Pieces to look at include:

The Galaxy Tool Factory (it has the ability to create reusable tools
from scripts):

http://www.ncbi.nlm.nih.gov/pubmed/23024011

You may be able to modify it in such a way that each tool is tagged
with who created and then use ToolBox filters to limit added tools to
a given user:

https://wiki.galaxyproject.org/UserDefinedToolboxFilters

I think the latest version of Galaxy has improved support for adding
tools without requiring restarts (using message queues). I don't know
if this will automatically work with the tool factory or not.

I suspect fighting Galaxy at every step on this will frustrate you and
the users - and you are exposing all of your users data to every user
you give this privilege to. Is this a shared cluster or is dedicated
to Galaxy? If it is shared - it might be better for advanced users to
just get importing and exporting data to user directories really well.
In my previous position at MSI we created a set of tools that allowed
Galaxy to SCP files as the user to our login nodes (using a SSH key
scheme) - likewise creating directories user's can upload files can
enabled power users.

Hopefully this helps,

-John

On Sat, Jun 7, 2014 at 1:12 PM, Karthik Gururaj
gururaj.kart...@gmail.com wrote:
 Hello,
   We have a centralized Galaxy installation for out cluster which can be
 used by many users (backend interfaces with HTCondor to run jobs). Is there
 any way for non-administrator users to import/install their own tools so
 that they may use it in their workflows (under a subsection called
 unstable, for example? Ideally, without having to restart the Galaxy
 daemons whenever a change is made.
 It would be fine if these tools are not visible to other users till the
 administrator says so.
 Thanks,
 Karthik

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[galaxy-dev] Galaxy updated botched?

[Kandalaft, Iyad]

Hi everyone

I was looking to upgrade galaxy to the latest verison.  I did the usual hg 
pull; hg update;.  I start up galaxy, it fetches some eggs, and then it tells 
me that I need a DB schema update.  Fine, I ran sh db_manage.sh upgrade.

All I see is a list of stack traces similar to the following.  I'm using mysql 
and all the tables that galaxy had created are running under the myisam 
engine  Hence, no foreign key constraints allowed.  Why did this happen and 
can I simply convert all my tables to InnoDB to complete the database upgrade?  
Should I restore the DB from a backup?

IntegrityError: (IntegrityError) (1215, 'Cannot add foreign key constraint') 
'\nCREATE TABLE history_dataset_collection_rating_association (\n\tid INTEGER 
NOT NULL AUTO_INCREMENT, \n\thistory_dataset_collection_id INTEGER, \n\tuser_id 
INTEGER, \n\trating INTEGER, \n\tPRIMARY KEY (id), \n\tFOREIGN 
KEY(history_dataset_collection_id) REFERENCES 
history_dataset_collection_association (id), \n\tFOREIGN KEY(user_id) 
REFERENCES galaxy_user (id)\n)\n\n' ()
(IntegrityError) (1215, 'Cannot add foreign key constraint') '\nCREATE TABLE 
history_dataset_collection_tag_association (\n\tid INTEGER NOT NULL 
AUTO_INCREMENT, \n\thistory_dataset_collection_id INTEGER, \n\ttag_id INTEGER, 
\n\tuser_id INTEGER, \n\tuser_tname VARCHAR(255), \n\tvalue VARCHAR(255), 
\n\tuser_value VARCHAR(255), \n\tPRIMARY KEY (id), \n\tFOREIGN 
KEY(history_dataset_collection_id) REFERENCES 
history_dataset_collection_association (id), \n\tFOREIGN KEY(tag_id) REFERENCES 
tag (id), \n\tFOREIGN KEY(user_id) REFERENCES galaxy_user (id)\n)\n\n' ()
Creating history_dataset_collection_tag_association table failed: 
(IntegrityError) (1215, 'Cannot add foreign key constraint') '\nCREATE TABLE 
history_dataset_collection_tag_association (\n\tid INTEGER NOT NULL 
AUTO_INCREMENT, \n\thistory_dataset_collection_id INTEGER, \n\ttag_id INTEGER, 
\n\tuser_id INTEGER, \n\tuser_tname VARCHAR(255), \n\tvalue VARCHAR(255), 
\n\tuser_value VARCHAR(255), \n\tPRIMARY KEY (id), \n\tFOREIGN 
KEY(history_dataset_collection_id) REFERENCES 
history_dataset_collection_association (id), \n\tFOREIGN KEY(tag_id) REFERENCES 
tag (id), \n\tFOREIGN KEY(user_id) REFERENCES galaxy_user (id)\n)\n\n' ()
Traceback (most recent call last):
  File lib/galaxy/model/migrate/versions/0120_dataset_collections.py, line 
179, in __create
table.create()
  File build/bdist.linux-x86_64/egg/sqlalchemy/schema.py, line 593, in create
checkfirst=checkfirst)
  File build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py, line 2302, in 
_run_visitor
conn._run_visitor(visitorcallable, element, **kwargs)
  File build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py, line 1972, in 
_run_visitor
**kwargs).traverse_single(element)
  File build/bdist.linux-x86_64/egg/sqlalchemy/sql/visitors.py, line 106, in 
traverse_single
return meth(obj, **kw)
  File build/bdist.linux-x86_64/egg/sqlalchemy/engine/ddl.py, line 86, in 
visit_table
self.connection.execute(schema.CreateTable(table))
  File build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py, line 1449, in 
execute
params)
  File build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py, line 1542, in 
_execute_ddl
compiled
  File build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py, line 1698, in 
_execute_context
context)
  File build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py, line 1691, in 
_execute_context
context)
  File build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py, line 331, 
in do_execute
cursor.execute(statement, parameters)
  File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/cursors.py, line 173, in 
execute
self.errorhandler(self, exc, value)
  File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py, line 36, in 
defaulterrorhandler
raise errorclass, errorvalue


Regards,

Iyad Kandalaft
Bioinformatics Programmer
Microbial Biodiversity Bioinformatics
Science  Technology Branch
Agriculture  Agri-Food Canada
iyad.kandal...@agr.gc.ca | (613) 759-1228

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