- galaxy-dev - lists.galaxyproject.org

Running Cloudlaunch against a new OpenStack cloud
by Peter van Heusden 19 Oct '18

19 Oct '18

Hi there I'd like to set up cloudlaunch to be able to set up on-demand Galaxy servers and associated clusters on the new Ilifu OpenStack cloud. From looking around the repositories it looks like Cloudlaunch is at least 2 components: 1. The cloudlaunch server 2. The UI - either cloudlaunch-ui or cloudlaunch-cli I'm trying to get cloudlaunch server installed on a Ubuntu 18.04 VM. The only requirement seems to be python3-pip. For postgresql support I installed the python3-psycopg2 module, the postgresql-10 server and create a user and db (both named cloud). Then I installed the server with `pip3 install cloudlaunch-server` and ran commands: cloudlaunch-server django migrate cloudlaunch-server django createsuperuser cloudlaunch-server django runserver The next step (https://github.com/galaxyproject/cloudlaunch) refers to redis-server. Installing this package seemed to satisfy that requirement, running it manually didn't work so I just ran the celery command as illustrated. And finally relaunched the django server. Then nodejs and npm were installed, the cloudlaunch-ui cloned from github, the various npm package specified installed and finally npm start brings up the cloudlaunch user interface. So far so good but: 1. Is there more extensive documentation anywhere? Specifically documentation about running this in production. 2. Is there a docker container that can be used instead of all this manual installation? 3. How are appliances configured and added to the Appliance Catalogue? Thanks! Peter

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Get Data and 'xlsx'
by D K 15 Oct '18

15 Oct '18

It looks like uploading 'xlsx' data through 'Get Data' is not working. When I try this on my local Galaxy (v18.05) and on usegalaxy.org it gets automatically converted to 'BLAST xml' when using Automatic Detection. If I select 'xlsx' during uploading I get the error message ( Warning: The file 'Type' was set to 'xlsx' but the file does not appear to be of that type ) Does anyone have any suggestions?

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error and question from using galaxy kickstart
by Rui Wang 13 Oct '18

13 Oct '18

Hi Folks, So I managed to ran through the ansible. What I did was to remove certain steps. For example, I don't need slurm-drmaa and docker, then I skipped the update cache. After these minor changes, it finished successfully(?) with an error message it ignored. Then I tried to access the UI, but nothing worked. I pasted it below for your reference. If anyone has seen this before, please help. :-) Sorry for the beginner question, so once the ansible playbook ran through...seems the galaxy and the postgresql etc were started. How do I start/stop them manually? Do I have to run the playbook every time I want to run galaxy or only after I modify the playbook? Also, if I don't look at the log, I don't even know that the UI is at 127.0.0.1:4001. Is there any documentation for this? Thanks, Rui error message: galaxy.web.stack INFO 2018-10-12 19:41:53,874 [p:102477,w:1,m:0] [MainThread] Galaxy server instance 'main.web.1' is running Starting server in PID 101567. serving on uwsgi://127.0.0.1:4001 galaxy.jobs.handler ERROR 2018-10-12 19:42:48,487 [p:102477,w:1,m:0] [JobHandlerQueue.monitor_thread] Exception in monitor_step Traceback (most recent call last): File "lib/galaxy/jobs/handler.py", line 213, in __monitor self.__monitor_step() File "lib/galaxy/jobs/handler.py", line 272, in __monitor_step .order_by(model.Job.id).all() File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2737, in all return list(self) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2889, in __iter__ return self._execute_and_instances(context) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2912, in _execute_and_instances result = conn.execute(querycontext.statement, self._params) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 948, in execute return meth(self, multiparams, params) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/sql/elements.py", line 269, in _execute_on_connection return connection._execute_clauseelement(self, multiparams, params) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1060, in _execute_clauseelement compiled_sql, distilled_params File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1200, in _execute_context context) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1413, in _handle_dbapi_exception exc_info File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 203, in raise_from_cause reraise(type(exception), exception, tb=exc_tb, cause=cause) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1193, in _execute_context context) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 507, in do_execute cursor.execute(statement, parameters) OperationalError: (psycopg2.OperationalError) server closed the connection unexpectedly This probably means the server terminated abnormally before or while processing the request. [SQL: 'SELECT EXISTS (SELECT history_dataset_association.id, history_dataset_association.history_id, history_dataset_association.dataset_id, history_dataset_association.create_time, history_dataset_association.update_time, history_dataset_association.state, history_dataset_association.copied_from_history_dataset_association_id, history_dataset_association.copied_from_library_dataset_dataset_association_id, history_dataset_association.name, history_dataset_association.info, history_dataset_association.blurb, history_dataset_association.peek, history_dataset_association.tool_version, history_dataset_association.extension, history_dataset_association.metadata, history_dataset_association.parent_id, history_dataset_association.designation, history_dataset_association.deleted, history_dataset_association.visible, history_dataset_association.extended_metadata_id, history_dataset_association.version, history_dataset_association.hid, history_dataset_association.purged, history_dataset_association.hidden_beneath_collection_instance_id \nFROM history_dataset_association, job_to_output_dataset \nWHERE job.id = job_to_output_dataset.job_id AND history_dataset_association.id = job_to_output_dataset.dataset_id AND history_dataset_association.deleted = true) AS anon_1, EXISTS (SELECT history_dataset_collection_association.id \nFROM history_dataset_collection_association, job_to_output_dataset_collection \nWHERE job.id = job_to_output_dataset_collection.job_id AND history_dataset_collection_association.id = job_to_output_dataset_collection.dataset_collection_id AND history_dataset_collection_association.deleted = true) AS anon_2, job.id AS job_id, job.create_time AS job_create_time, job.update_time AS job_update_time, job.history_id AS job_history_id, job.library_folder_id AS job_library_folder_id, job.tool_id AS job_tool_id, job.tool_version AS job_tool_version, job.state AS job_state, job.info AS job_info, job.copied_from_job_id AS job_copied_from_job_id, job.command_line AS job_command_line, job.dependencies AS job_dependencies, job.param_filename AS job_param_filename, job.runner_name AS job_runner_name_1, job.stdout AS job_stdout, job.stderr AS job_stderr, job.exit_code AS job_exit_code, job.traceback AS job_traceback, job.session_id AS job_session_id, job.user_id AS job_user_id, job.job_runner_name AS job_job_runner_name, job.job_runner_external_id AS job_job_runner_external_id, job.destination_id AS job_destination_id, job.destination_params AS job_destination_params, job.object_store_id AS job_object_store_id, job.imported AS job_imported, job.params AS job_params, job.handler AS job_handler \nFROM job \nWHERE job.state = %(state_1)s AND job.handler = %(handler_1)s AND job.id NOT IN (SELECT job.id \nFROM job JOIN job_to_input_dataset ON job.id = job_to_input_dataset.job_id JOIN history_dataset_association ON history_dataset_association.id = job_to_input_dataset.dataset_id JOIN dataset ON dataset.id = history_dataset_association.dataset_id \nWHERE job.state = %(state_2)s AND (history_dataset_association.state = %(_state_1)s OR history_dataset_association.deleted = true OR dataset.state != %(state_3)s OR dataset.deleted = true)) AND job.id NOT IN (SELECT job.id \nFROM job JOIN job_to_input_library_dataset ON job.id = job_to_input_library_dataset.job_id JOIN library_dataset_dataset_association ON library_dataset_dataset_association.id = job_to_input_library_dataset.ldda_id JOIN dataset ON dataset.id = library_dataset_dataset_association.dataset_id \nWHERE job.state = %(state_4)s AND (library_dataset_dataset_association.state IS NOT NULL OR library_dataset_dataset_association.deleted = true OR dataset.state != %(state_5)s OR dataset.deleted = true)) ORDER BY job.id'] [parameters: {'state_3': 'ok', 'handler_1': 'main.web.1', 'state_1': 'new', '_state_1': 'failed_metadata', 'state_2': 'new', 'state_5': 'ok', 'state_4': 'new'}] (Background on this error at: http://sqlalche.me/e/e3q8) galaxy.jobs.handler ERROR 2018-10-12 19:42:48,488 [p:102478,w:2,m:0] [JobHandlerQueue.monitor_thread] Exception in monitor_step Traceback (most recent call last): File "lib/galaxy/jobs/handler.py", line 213, in __monitor self.__monitor_step() File "lib/galaxy/jobs/handler.py", line 272, in __monitor_step .order_by(model.Job.id).all() File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2737, in all return list(self) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2889, in __iter__ return self._execute_and_instances(context) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2912, in _execute_and_instances result = conn.execute(querycontext.statement, self._params) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 948, in execute return meth(self, multiparams, params) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/sql/elements.py", line 269, in _execute_on_connection return connection._execute_clauseelement(self, multiparams, params) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1060, in _execute_clauseelement compiled_sql, distilled_params File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1200, in _execute_context context) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1413, in _handle_dbapi_exception exc_info File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 203, in raise_from_cause reraise(type(exception), exception, tb=exc_tb, cause=cause) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1193, in _execute_context context) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 507, in do_execute cursor.execute(statement, parameters) OperationalError: (psycopg2.OperationalError) server closed the connection unexpectedly This probably means the server terminated abnormally before or while processing the request. [SQL: 'SELECT EXISTS (SELECT history_dataset_association.id, history_dataset_association.history_id, history_dataset_association.dataset_id, history_dataset_association.create_time, history_dataset_association.update_time, history_dataset_association.state, history_dataset_association.copied_from_history_dataset_association_id, history_dataset_association.copied_from_library_dataset_dataset_association_id, history_dataset_association.name, history_dataset_association.info, history_dataset_association.blurb, history_dataset_association.peek, history_dataset_association.tool_version, history_dataset_association.extension, history_dataset_association.metadata, history_dataset_association.parent_id, history_dataset_association.designation, history_dataset_association.deleted, history_dataset_association.visible, history_dataset_association.extended_metadata_id, history_dataset_association.version, history_dataset_association.hid, history_dataset_association.purged, history_dataset_association.hidden_beneath_collection_instance_id \nFROM history_dataset_association, job_to_output_dataset \nWHERE job.id = job_to_output_dataset.job_id AND history_dataset_association.id = job_to_output_dataset.dataset_id AND history_dataset_association.deleted = true) AS anon_1, EXISTS (SELECT history_dataset_collection_association.id \nFROM history_dataset_collection_association, job_to_output_dataset_collection \nWHERE job.id = job_to_output_dataset_collection.job_id AND history_dataset_collection_association.id = job_to_output_dataset_collection.dataset_collection_id AND history_dataset_collection_association.deleted = true) AS anon_2, job.id AS job_id, job.create_time AS job_create_time, job.update_time AS job_update_time, job.history_id AS job_history_id, job.library_folder_id AS job_library_folder_id, job.tool_id AS job_tool_id, job.tool_version AS job_tool_version, job.state AS job_state, job.info AS job_info, job.copied_from_job_id AS job_copied_from_job_id, job.command_line AS job_command_line, job.dependencies AS job_dependencies, job.param_filename AS job_param_filename, job.runner_name AS job_runner_name_1, job.stdout AS job_stdout, job.stderr AS job_stderr, job.exit_code AS job_exit_code, job.traceback AS job_traceback, job.session_id AS job_session_id, job.user_id AS job_user_id, job.job_runner_name AS job_job_runner_name, job.job_runner_external_id AS job_job_runner_external_id, job.destination_id AS job_destination_id, job.destination_params AS job_destination_params, job.object_store_id AS job_object_store_id, job.imported AS job_imported, job.params AS job_params, job.handler AS job_handler \nFROM job \nWHERE job.state = %(state_1)s AND job.handler = %(handler_1)s AND job.id NOT IN (SELECT job.id \nFROM job JOIN job_to_input_dataset ON job.id = job_to_input_dataset.job_id JOIN history_dataset_association ON history_dataset_association.id = job_to_input_dataset.dataset_id JOIN dataset ON dataset.id = history_dataset_association.dataset_id \nWHERE job.state = %(state_2)s AND (history_dataset_association.state = %(_state_1)s OR history_dataset_association.deleted = true OR dataset.state != %(state_3)s OR dataset.deleted = true)) AND job.id NOT IN (SELECT job.id \nFROM job JOIN job_to_input_library_dataset ON job.id = job_to_input_library_dataset.job_id JOIN library_dataset_dataset_association ON library_dataset_dataset_association.id = job_to_input_library_dataset.ldda_id JOIN dataset ON dataset.id = library_dataset_dataset_association.dataset_id \nWHERE job.state = %(state_4)s AND (library_dataset_dataset_association.state IS NOT NULL OR library_dataset_dataset_association.deleted = true OR dataset.state != %(state_5)s OR dataset.deleted = true)) ORDER BY job.id'] [parameters: {'state_3': 'ok', 'handler_1': 'main.web.2', 'state_1': 'new', '_state_1': 'failed_metadata', 'state_2': 'new', 'state_5': 'ok', 'state_4': 'new'}] (Background on this error at: http://sqlalche.me/e/e3q8)

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Re: [galaxy-dev] can't create user on a new instance
by Rui Wang 13 Oct '18

13 Oct '18

Hey Folks, When I used the kickstart, I hit this always: TASK [galaxyprojectdotorg.galaxy-os : Update APT cache] ************************************************************************* [WARNING]: sftp transfer mechanism failed on [localhost]. Use ANSIBLE_DEBUG=1 to see detailed information fatal: [localhost]: FAILED! => {"changed": false, "failed": true, "msg": "Failed to update apt cache."} Have you seen this before? If you do, please give me a hand. :) Thanks, Rui On Fri, Oct 12, 2018 at 2:17 PM Rui Wang <ruiwang.sz(a)gmail.com> wrote: > Hi Qiang, > > Let me try that. I think the postgres might be contaminated by the attempt > to use kickstart. During that it modify the config of postgres permissions > and it took me a while to clean those to get postgres working again(which > may or may not really clean the change completely). > > I'll get back to you on this. Also I'll let you know my attempts on the > kickstart. The problem was with the updater. :-( > > Thanks, > Rui > > On Fri, Oct 12, 2018 at 12:23 PM Qiang Gu <guq(a)ohsu.edu> wrote: > >> Hi Rui, >> >> Galaxy will use the default sqlite if you comment out the db setting the >> config file (`config/galaxy.yml`). You mean the sqlite works the same as >> the postgresql, which doesn't allow you to create users? >> If that's the case, try `git clone` a new galaxy repo, in the galaxy >> folder, `git checkout remotes/original/release_18.05`, `git checkout -b >> release_18.05`, `./run.sh`. >> Basically, I would like to make the sqlite working first, then switch to >> postgresql. The above-mentioned steps may help identify the hidden issue. >> >> Good luck! >> >> -Qiang >> >> >> ------------------------------ >> *From:* Rui Wang [ruiwang.sz(a)gmail.com] >> *Sent:* Friday, October 12, 2018 1:01 AM >> *To:* Qiang Gu >> *Cc:* galaxy-dev(a)lists.galaxyproject.org >> *Subject:* Re: [galaxy-dev] can't create user on a new instance >> >> Hi Qiang, >> >> Thanks so much for the email. The default sqlite seems to be the same. I >> spent some time with the kickstart. That would be fantastic if it >> works...sadly it failed on me. :-( Let me make some more effort on that. >> Btw, do you have a better version of the instructions for the kickstart? >> >> Cheers, >> Rui >> >> On Wed, Oct 10, 2018 at 10:12 PM Qiang Gu <guq(a)ohsu.edu> wrote: >> >>> Hi Rui, >>> >>> Does the default database sqlite work for you? I guess there is certain >>> mis-configuration in your >>> postgresql settings or certain element in the config/galaxy.yml file is >>> broken. Try to enter your postgresql database in terminal using the >>> same login info and create a table to make sure you have proper privileges. >>> Alternatively, using GalaxyKickStart ( >>> https://github.com/ARTbio/GalaxyKickStart) to deploy a server >>> isn't that difficult and a postgresql database comes with it by default. >>> Good luck! >>> >>> Thanks, >>> >>> -Qiang >>> >>> ------------------------------ >>> *From:* galaxy-dev [galaxy-dev-bounces(a)lists.galaxyproject.org] on >>> behalf of Rui Wang [ruiwang.sz(a)gmail.com] >>> *Sent:* Wednesday, October 10, 2018 9:30 PM >>> *To:* galaxy-dev(a)lists.galaxyproject.org >>> *Subject:* Re: [galaxy-dev] can't create user on a new instance >>> >>> Hi Folks, >>> >>> I still could not create new user account with the same error message. >>> Has anyone happened to see this before? >>> >>> Cheers, >>> Rui >>> >>> On Tue, Oct 9, 2018 at 5:48 PM Rui Wang <ruiwang.sz(a)gmail.com> wrote: >>> >>>> Hey Folks, >>>> >>>> I just installed a new 18.05 instance with a new postgresql db created. >>>> However, the UI doesn't allow me to create any user. After I provided all >>>> input information, it says >>>> >>>> galaxy.web.framework.webapp WARNING 2018-10-09 17:28:35,735 >>>> [p:32925,w:1,m:0] [uWSGIWorker1Core2] Wrong session token found, denying >>>> request >>>> >>>> in the server log. Btw, I enabled 'allow to create user' and admin user >>>> list is empty. >>>> >>>> I looked into it, and it's a function in >>>> lib/galaxy/web/framework/webapp.py: >>>> >>>> def check_csrf_token(self): >>>> session_csrf_token = >>>> self.request.params.get("session_csrf_token", None) >>>> problem = False >>>> if not session_csrf_token: >>>> log.warning("No session_csrf_token set, denying request.") >>>> problem = True >>>> elif session_csrf_token != self.session_csrf_token: >>>> log.warning("Wrong session token found, denying request.") >>>> problem = True >>>> >>>> if problem: >>>> return self.show_warn_message("Failed to authorize action.") >>>> >>>> Could someone give me a hand? :-) >>>> >>>> Cheers, >>>> Rui >>>> >>>

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can't create user on a new instance
by Rui Wang 13 Oct '18

13 Oct '18

Hey Folks, I just installed a new 18.05 instance with a new postgresql db created. However, the UI doesn't allow me to create any user. After I provided all input information, it says galaxy.web.framework.webapp WARNING 2018-10-09 17:28:35,735 [p:32925,w:1,m:0] [uWSGIWorker1Core2] Wrong session token found, denying request in the server log. Btw, I enabled 'allow to create user' and admin user list is empty. I looked into it, and it's a function in lib/galaxy/web/framework/webapp.py: def check_csrf_token(self): session_csrf_token = self.request.params.get("session_csrf_token", None) problem = False if not session_csrf_token: log.warning("No session_csrf_token set, denying request.") problem = True elif session_csrf_token != self.session_csrf_token: log.warning("Wrong session token found, denying request.") problem = True if problem: return self.show_warn_message("Failed to authorize action.") Could someone give me a hand? :-) Cheers, Rui

3 6

Error when trying to update tool vcf_to_alignment in testtoolshed
by Peter van Heusden 12 Oct '18

12 Oct '18

Hi there I had a failed updated (network problem) of the sanbi-uwc tool vcf_to_alignment and now when I try and do an update I get: $ planemo shed_update --shed_target testtoolshed cd '/home/pvh/Documents/code/SANBI/tools-sanbi-uwc/tools/vcf_to_alignment' && git rev-parse HEAD cd '/home/pvh/Documents/code/SANBI/tools-sanbi-uwc/tools/vcf_to_alignment' && git diff --quiet Could not update vcf_to_alignment ('Connection aborted.', RemoteDisconnected('Remote end closed connection without response',)) Repository metadata updated successfully for repository 'vcf_to_alignment' on the test Tool Shed. Failed to update repository contents for repository 'vcf_to_alignment' on the test Tool Shed. Nothing that I try on my side seems to resolve this. Any ideas? Is the problem on the toolshed side? Thanks, Peter

1 0

tool data confusion
by Matthias Bernt 05 Oct '18

05 Oct '18

Dear list, I still have problems to get my head around tool data. Lets consider diamond for example (lets ignore data managers for the moment). After installation it seems that there are two relevant xml files: - `config/shed_tool_data_table_conf.xml` - `tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/diamond/64be1ac21109/tool_data_table_conf.xml` and two loc files: - `tool-data/diamond_database.loc` - `tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/diamond/64be1ac21109/diamond_database.loc` In both xml files the latter loc file is referenced. And therefor the tool-data/diamond_database.loc file is seemingly ignored. What is the rational to have a loc and xml file for each tool version? It seems that they are merged upon startup anyway. What would be the best way to administrate a single tool loc file? Cheers, Matthias -- ------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt(a)ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

3 4

[CLI] Job sent to cluster never gets back
by Estelle Ancelet 05 Oct '18

05 Oct '18

Hello Galaxy community, We are trying to connect a Galaxy web server to a remote cluster by using the "CLI" approach. We do partially succeed : jobs are submitted to the cluster but seem not to be monitored. That is, jobs are executed on the cluster but Galaxy doesn't update the status in the history (stays grey) and never gets back the outputs. The Galaxy folder on the cluster is mounted to the Galaxy Server using sshfs : sshfs galaxyuser@cluster.fr:galaxy galaxy Galaxy (v18.05) is launched by a "sh run.sh" in the galaxy folder, from the Galaxy server side. Here is an extract of our job_conf.xml: <job_conf> <plugins> <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> <plugin id="cli" type="runner" load="galaxy.jobs.runners.cli:ShellJobRunner" workers="4"/> </plugins> <destinations default="ssh_slurm"> <destination id="local" runner="local"/> <destination id="ssh_slurm" runner="cli"> <param id="shell_plugin">SecureShell</param> <param id="job_plugin">Slurm</param> <param id="shell_username">galaxyuser</param> <param id="shell_hostname">cluster.fr</param> <param id="job_time">2:00:00</param> <param id="job_ncpus">4</param> <param id="job_partition">defq</param> </destination> </destinations> <tools> <tool id="runtask" destination="ssh_slurm" /> </tools> </job_conf> Did we miss something in the configuration? Or do we have to write additional code? Sincere thanks, Estelle

1 0

learning pulsar for galaxy
by Wong, Kai Leung 04 Oct '18

04 Oct '18

Hello, We are working on a project in providing a Cloud based research platform for Health Informatics and Bioinformatics. Long story short, one of the components to be provided by the project is a Galaxy Server for our genomics researchers; and on the other hand, GWU also has a HPC system for high performance and high throughput computing. Our Galaxy Server for this project is hosing in the Cloud (Azure) and the HPC cluster is onsite at GW. To allow a galaxy server to utilize external compute power of a HPC, galaxy has provided job runner plugins of DRMAA for job schedulers as well as Pulsar. For our situation, the HPC is a remote system w.r.t. the Galaxy server in the cloud and thus there isn't a shared file system between them. It seems to me that Pulsar would be the appropriate solution for us. Am I on the right track? Any suggestions are much appreciated! Best, Adam --- Adam K. L. Wong, PhD. High Performance Computing Specialist for Genomics Division of Information Technology The George Washington University Email: aklwong(a)gwu.edu

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October 2018 Galactic News: SACNAS Workshops, European Galaxy Days, Admin Training; new Pubs, Public Servers, Job postings, and Blog posts!
by Mo Heydarian 02 Oct '18

02 Oct '18

Hello All, The October 2018 Galactic News <https://galaxyproject.org/news/2018-10-galaxy-update/> highlights what’s going on in the Galaxy this month, including: - Galactic Events: - 2018 SACNAS Workshops <https://galaxyproject.org/news/2018-10-galaxy-update/#2018-sacnas-pre-confe…>,10 October, USA - European Galaxy Days <https://galaxyproject.org/news/2018-10-galaxy-update/#european-galaxy-days-…>, 19 - 20 November, Germany - 2019 Galaxy Admin Training <https://galaxyproject.org/news/2018-10-galaxy-update/#2019-galaxy-admin-tra…>, 28 January - 1 February, USA - Other events <https://galaxyproject.org/news/2018-10-galaxy-update/#upcoming-events> across the world. - Galactic Blog <https://galaxyproject.org/news/2018-10-galaxy-update/#new-galactic-blog-pos…> : - Contributor of the Month: Yvan Le Bras <https://galaxyproject.org/news/2018-10-galaxy-update/#new-galactic-blog-pos…> - Tutorial of the month: “From Peaks to Genes” <https://galaxyproject.org/news/2018-10-galaxy-update/#new-galactic-blog-pos…> - Highlight: Hybrid Training delivering to far-reaching venues <https://galaxyproject.org/news/2018-10-galaxy-update/#new-galactic-blog-pos…> - New: - 200 publications <https://galaxyproject.org/news/2018-10-galaxy-update/#publications> - Public Galaxy Servers <https://galaxyproject.org/news/2018-10-galaxy-update/#public-galaxy-server-…>: MPDS-DM - Galactic Job Postings <https://galaxyproject.org/news/2018-10-galaxy-update/#whos-hiring> - Toolshed contributions <https://galaxyproject.org/news/2018-10-galaxy-update/#tools> - Releases <https://galaxyproject.org/news/2018-10-galaxy-update/#releases> of GVL 4.4.0, Planemo 0.55.0, and galaxy-lib. - And other news <https://galaxyproject.org/news/2018-10-galaxy-update/#other-news>. See the newslette <https://galaxyproject.org/news/2018-10-galaxy-update/>r for all of the details! Thanks for using Galaxy! Cheers, Mo, on behalf of Galaxy

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