Question: Can't run newly installed shed tools
gravatar for shaunmwebb
3.7 years ago by
United Kingdom
shaunmwebb10 wrote:

I have recently updated my Galaxy instance to the January '15 release and I am having trouble getting new tools to run once I install them from the tool shed. There are no issues with installation and previously installed tools work without issue. It appears that jobs are not started, the full error in my handler.log is below.

I'd appreciate if anyone can give me some help on where to start looking to solve this issue.

Thanks in advance!

-------------------------------- WARNING 2015-03-16 16:24:46,252 (315) Tool '' removed from tool config, unable to run job ERROR 2015-03-16 16:24:46,335 failure running job 315
Traceback (most recent call last):
  File "/storage/home/galaxy/test/test-version/galaxy-dist/lib/galaxy/jobs/", line 273, in __monitor_step
    job_state = self.__check_job_state( job )
  File "/storage/home/galaxy/test/test-version/galaxy-dist/lib/galaxy/jobs/", line 342, in __check_job_state
    state, job_destination = self.__verify_job_ready( job, job_wrapper )
  File "/storage/home/galaxy/test/test-version/galaxy-dist/lib/galaxy/jobs/", line 362, in __verify_job_ready e )
  File "/storage/home/galaxy/test/test-version/galaxy-dist/lib/galaxy/jobs/", line 920, in fail
  File "/storage/home/galaxy/test/test-version/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/", line 114, in do
    return getattr(self.registry(), name)(*args, **kwargs)
  File "/storage/home/galaxy/test/test-version/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/", line 1718, in flush
  File "/storage/home/galaxy/test/test-version/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/", line 1789, in _flush
  File "/storage/home/galaxy/test/test-version/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/", line 331, in execute
  File "/storage/home/galaxy/test/test-version/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/", line 475, in execute
  File "/storage/home/galaxy/test/test-version/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/", line 59, in save_obj
    mapper, table, update)
  File "/storage/home/galaxy/test/test-version/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/", line 485, in _emit_update_statements
    execute(statement, params)
  File "/storage/home/galaxy/test/test-version/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/", line 1449, in execute
  File "/storage/home/galaxy/test/test-version/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/", line 1584, in _execute_clauseelement
    compiled_sql, distilled_params
  File "/storage/home/galaxy/test/test-version/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/", line 1698, in _execute_context
  File "/storage/home/galaxy/test/test-version/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/", line 1691, in _execute_context
  File "/storage/home/galaxy/test/test-version/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/", line 331, in do_execute
    cursor.execute(statement, parameters)

File "/storage/home/galaxy/test/test-version/galaxy-dist/eggs/MySQL_python-1.2.3c1_5.1.41_static-py2.7-linux-x86_64-ucs4.egg/MySQLdb/", line 173, in execute 

self.errorhandler(self, exc, value)

File "/storage/home/galaxy/test/test-version/galaxy-dist/eggs/MySQL_python-1.2.3c1_5.1.41_static-py2.7-linux-x86_64-ucs4.egg/MySQLdb/", line 36, in defaulterrorhandler
    raise errorclass, errorvalue

ProgrammingError: (ProgrammingError) (1064, "You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near '), blurb='tool error' WHERE = 474' at line 1") 'UPDATE history_dataset_association SET update_time=%s, info=%s, blurb=%s WHERE = %s' (datetime.datetime(2015, 3, 16, 16, 19, 4, 823905), ('This tool qwas disabled before the job completed.  Please contact your Galaxy administrator.',), 'tool error', 474L)


tools config install local • 1.2k views
ADD COMMENTlink modified 2.3 years ago by christophe.habib340 • written 3.7 years ago by shaunmwebb10
gravatar for Jennifer Hillman Jackson
3.7 years ago by
United States
Jennifer Hillman Jackson25k wrote:


What was your prior distribution before the upgrade? Significant changes were implemented in the Oct 2014 release. I am wondering if your galaxy.ini and tool_conf.xml/shed_tool_conf.xml are set up correctly.

You can review the changes made to config file organization in that release here:

And the latest release (Mar 2015) has sample config files that you can review to make sure things are current.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 3.7 years ago by Jennifer Hillman Jackson25k
gravatar for Re7ab
2.3 years ago by
Re7ab0 wrote:

I think I have the same issue here. Some tools do not work fairly after you install them directly. I had this problem with Hisat2 and stringtie..but eventually they worked very well.

Now I successful y installed bedtools but I am getting this erreor message: Fatal error: Exit code 127 () / line 9: bedtools: command not found!!

Any explanation?

ADD COMMENTlink written 2.3 years ago by Re7ab0
gravatar for christophe.habib
2.3 years ago by
christophe.habib340 wrote:


Do you have several handler with your instance ? I had this error when installing new tools after setting 2 handlers + uwsgi. See here :

This tool was disabled before the job completed

Did you try to reboot your instance after installing a new tools ?

ADD COMMENTlink written 2.3 years ago by christophe.habib340
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