- galaxy-dev - lists.galaxyproject.org

Network errors when downloading files
by William, Van Der Pol 14 Dec '17

14 Dec '17

Hello, We've noticed when our users try to download files from our galaxy instance, they are getting a network error and receiving an empty 0 Byte file. I've checked the directory where the datasets are stored and can see that the files in question exist and contain the expected data, but something is interfering with downloading them through the GUI. Do you guys have any suggestions on what could be causing this error? Thanks -Liam Help keep the CCTS funded. Please include the following text on relevant publications: "This publication was made possible by the UAB Center for Clinical and Translational Science Grant Number UL1TR001417 from the National Center for Advancing Translational Sciences (NCATS) of the National Institutes of Health (NIH)."

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Dynamic Tool UI based on script
by Evan Clark 07 Dec '17

07 Dec '17

Is it possible to execute a script within a tool xml confit to retrieve some data and append to the ui depending on the requested data. I.e if I wanted to get a list of files and provide them as select options before hitting the execute button. --- Sent from VMware Boxer

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December 2017 News of the Galaxy
by Dave Clements 07 Dec '17

07 Dec '17

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Galaxy moves files form job directory but attempts to look for them at original path
by Evan Clark 30 Nov '17

30 Nov '17

Below is an error obtained from our galaxy install. We have custom directories sets for the files directory and the jobs directory. Galaxy appears to move the files but then attempts to look for them at the original path. I have tried unsetting these options but it still persists. galaxy.jobs DEBUG 2017-11-24 17:53:19,057 finish(): Moved /var/web_services/galaxy/database/jobs_directory/000/320/galaxy_dataset_431.dat to /mnt/ceph/home/galaxy/galaxy/files_directory/000/dataset_401.dat galaxy.model.metadata DEBUG 2017-11-24 17:53:19,128 setting metadata externally failed for HistoryDatasetAssociation 431: [Errno 2] No such file or directory galaxy.jobs.runners ERROR 2017-11-24 17:53:19,319 (320/179084) Job wrapper finish method failed Traceback (most recent call last): File "/var/web_services/galaxy/lib/galaxy/jobs/runners/__init__.py", line 630, in finish_job job_state.job_wrapper.finish( stdout, stderr, exit_code ) File "/var/web_services/galaxy/lib/galaxy/jobs/__init__.py", line 1266, in finish dataset.datatype.set_meta( dataset, overwrite=False ) File "/var/web_services/galaxy/lib/galaxy/datatypes/binary.py", line 391, in set_meta exit_code = subprocess.call( args=command, stderr=open( stderr_name, 'wb' ) ) File "/usr/lib64/python2.7/subprocess.py", line 524, in call return Popen(*popenargs, **kwargs).wait() File "/usr/lib64/python2.7/subprocess.py", line 711, in __init__ errread, errwrite) File "/usr/lib64/python2.7/subprocess.py", line 1327, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory galaxy.jobs ERROR 2017-11-24 17:53:19,337 fail(): Missing output file in working directory: [Errno 2] No such file or directory: '/var/web_services/galaxy/database/jobs_directory/000/320/galaxy_dataset_431.dat'

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TR: Close cluster
by Arnaud Cheuk 30 Nov '17

30 Nov '17

Hi, I would like to close my cluster, but when click on delete permanently, I see the cluster is still active. Could you help me to close the cluster? cduanra-galaxy-cloud-17-11-28t22-14 Appliance: Galaxy CloudMan Version: 17.05 Cloud: amazon-us-east-n-virginia RUNNING http://52.202.138.61/cloud Best, Arnaud

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external display and data editing
by Nils Paulhe 22 Nov '17

22 Nov '17

Dear list, I'm working on data visualization / display in galaxy. I'm wondering if it's possible to save a resource edited from the viewer plugin or an external display in the current history. In my opinion the easier / proper way is to use an external display to show / edit the resources and upload the edited files in the current history using galaxy API. Does anyone have tried something similar? Cheers Nils

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GMOD hackathon before PAG San Diego in January
by Scott Cain 21 Nov '17

21 Nov '17

Hi all, This January before PAG on the Wednesday and Thursday before PAG (January 10-11) in San Diego we are planning a GMOD hackathon. We expect that participants will be interested in solving problems/creating solutions related to Tripal, JBrowse, Apollo, and Galaxy but if you're interested in another GMOD project, by all means, let us know! We expect this hackathon to overlap with the Tripal hackathon that is on January 11 (I'm pretty sure; right Stephen?) If you are interested in attending this hackathon, please let me know so I can be sure we have an appropriately sized space. And if you're coming for the pre-PAG hackathon, consider staying for PAG, since there is always a lot of GMOD-related content at the meeting! Thanks, Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research

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broken after upgrade to 17.09 : uploading files via the API
by Hans-Rudolf Hotz 20 Nov '17

20 Nov '17

Dear All If I execute the following command: python import_with_dbkey.py *** file.bam hg19sub the bam files will be added to the user's history the code (import_with_dbkey.py) is as follows: import sys sys.path.append('***/bioblend-0.10.0-py2.7.egg') sys.path.append('***/requests_toolbelt-0.7.0-py2.7.egg') from bioblend.galaxy import GalaxyInstance from bioblend.galaxy.tools import ToolClient url = "http://galaxy-dev.fmi.ch" key = "***" history_id = sys.argv[1] file_path = sys.argv[2] dbkey= sys.argv[3] gi = GalaxyInstance(url=url, key=key) toolClient = ToolClient(gi) uploadedFile = toolClient.upload_file(file_path, history_id, dbkey=dbkey) Now, if I use the virtual environment from Galaxy, I get: (.venv)-bash-4.2$ python import_with_dbkey.py *** file.bam hg19sub Traceback (most recent call last): File "/***/galaxy/tools/fmi__api_helpers/import_with_dbkey.py", line 40, in <module> uploadedFile = toolClient.upload_file(file_path, history_id, dbkey=dbkey) File "/***/galaxy/.venv/lib/python2.7/site-packages/bioblend/galaxy/tools/__init__.py", line 148, in upload_file return self._tool_post(payload, files_attached=True) File "/***/galaxy/.venv/lib/python2.7/site-packages/bioblend/galaxy/tools/__init__.py", line 218, in _tool_post return Client._post(self, payload, files_attached=files_attached) File "/***/galaxy/.venv/lib/python2.7/site-packages/bioblend/galaxy/client.py", line 171, in _post files_attached=files_attached) File "/***/galaxy/.venv/lib/python2.7/site-packages/bioblend/galaxyclient.py", line 131, in make_post_request r.status_code, body=r.text) bioblend.galaxy.client.ConnectionError: Unexpected response from galaxy: 400: <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN"> <html><head> <title>400 Bad Request</title> </head><body> <h1>Bad Request</h1> <p>Your browser sent a request that this server could not understand.<br /> </p> </body></html> (.venv)-bash-4.2$ ...and the file does not get uploaded. I will continue investigating the difference between the python modules used, but maybe someone has a clue and could help me Thank you very much Hans-Rudolf

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European Galaxy Administrator Workshop, 8-12 January 2018, Oslo. FREE
by Dave Clements 16 Nov '17

16 Nov '17

Hello all, *We are pleased to announce that registration <https://skjema.uio.no/galaxy-admin-workshop-2018> is now open for the European Galaxy Administrator Workshop <https://www.elixir-europe.org/events/european-galaxy-administrator-workshop>* . - Mon 8 January 2018 to Fri 12 January 2018 CET - Python room, Blindern, UiO campus, Ole Johan Dahls hus <https://www.uio.no/english/about/getting-around/areas/gaustad/ga06/>, Gaustadalléen 23B, Oslo, 0373, Norway Participants will learn how to install, configure, customize, and extend their own Galaxy servers. Topics include tool configuration, authentication and user management, using heterogeneous storage and compute services, and many other topics that will enable you to get your own Galaxy server up and running, performing well, and used by your community. Have a look at the programme <https://github.com/elixir-no-nels/dagobah-training/blob/2018-oslo/README.md> to see more details on the planned content of the workshop. *Maximum number of participants is limited to 30, and we will manage registrations to allow for geographical distribution and proritize participants with responsibility of administrating galaxy servers.* After registering you will get a second confirmation if/when a slot has been allocated to you. Although located in Europe, and named to reflect this, the workshop is definitely *open to a world-wide audience.* The workshop is a result of the collaboration between the Elixir Galaxy WG <https://www.elixir-europe.org/about/groups/galaxy-wg> and the Galaxy Project, and so far known, this is the only Galaxy Admin workshop planned for 2018. *Participants are to cover their own travel and accomodation, while the workshop participation is free of charge.* Instructors - Björn Grüning <https://github.com/bgruening> (Elixir Galaxy WG <https://www.elixir-europe.org/about/groups/galaxy-wg>, Elixir Germany <https://www.elixir-europe.org/about-us/who-we-are/nodes/germany>, University of Freiburg <https://www.uni-freiburg.de/?set_language=en>) - Marius van den Beek <https://github.com/mvdbeek> (Elixir Galaxy WG <https://www.elixir-europe.org/about/groups/galaxy-wg>, Institute Curie <https://science.institut-curie.org/>, France) - Nicola Soranzo <http://www.earlham.ac.uk/nicola-soranzo> (Elixir Galaxy WG <https://www.elixir-europe.org/about/groups/galaxy-wg>, Earlham Institute <http://www.earlham.ac.uk/>, UK) - Enis Afgan <https://galaxyproject.org/people/enis-afgan/> (Galaxy Project <https://galaxyproject.org/>, Johns Hopkins University <https://jhu.edu/>, USA) - Abdulrahman Azab <http://www.usit.uio.no/om/organisasjon/itf/ft/ansatte/azab/index.html> (Elixir Norway <https://www.elixir-europe.org/about-us/who-we-are/nodes/norway>, USIT <http://www.usit.uio.no/>, University of Oslo <http://www.uio.no/>, Norway) -- https://galaxyproject.org/ https://usegalaxy.org/

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Active Directory Authentication question
by Hakeem Almabrazi 13 Nov '17

13 Nov '17

Hello, I have installed the latest galaxy and I would like to use the MS Active Directory 2012 for authentication. I tried to follow the instructions outlined here https://galaxyproject.org/admin/config/external-user-auth/ without touching the lib/galaxy/auth/providers/ldap_ad_py since I thought this is related to ldap not AD. Here is the exact auth_config.xml file +++++++++++++++++++++++++ <?xml version="1.0"?> <auth> <authenticator> <type>ldap</type> <options> <allow-register>True</allow-register> <auto-register>True</auto-register> <allow-password-change>False</allow-password-change> <login-use-username>True</login-use-username>  <search-fields>sAMAccountName,mail</search-fields> <search-base>dc=dc1,dc=example,dc=com</search-base>  <search-filter>(&(objectClass=user)(sAMAccountName={username}))</search-filter> </options> </authenticator> </auth> +++++++++++++++++ When I try to login using a real user email and pwd, it says "No user of valid password" in the Galaxy page. And here is the error log I keep getting. galaxy.webapps.galaxy.controllers.user DEBUG 2017-11-09 13:55:37,940 trans.app.config.auth_config_file: ./config/auth_conf.xml galaxy.auth.providers.ldap_ad DEBUG 2017-11-09 13:55:37,940 LDAP authenticate: email is user(a)example.com galaxy.auth.providers.ldap_ad DEBUG 2017-11-09 13:55:37,940 LDAP authenticate: username is None galaxy.auth.providers.ldap_ad DEBUG 2017-11-09 13:55:37,940 LDAP authenticate: options are {'search-fields': 'sAMAccountName,mail', 'login-use-username': 'True', 'allow-register': 'True', 'auto-register': 'True', 'search-base': 'dc=dc1,dc=example,dc=com', 'search-filter': '(&(objectClass=user)(sAMAccountName={username}))', 'allow-password-change': 'False'} galaxy.auth.providers.ldap_ad DEBUG 2017-11-09 13:55:37,940 LDAP authenticate: username must be used to login, cannot be None galaxy.auth DEBUG 2017-11-09 13:55:37,941 Email: , Username , stopping due to failed non-continue Is there anything missing from my auth_config.xml file? I appreciate any kind of help figuring this out. Best regards, Hak Disclaimer: This email and its attachments may be confidential and are intended solely for the use of the individual to whom it is addressed. If you are not the intended recipient, any reading, printing, storage, disclosure, copying or any other action taken in respect of this e-mail is prohibited and may be unlawful. If you are not the intended recipient, please notify the sender immediately by using the reply function and then permanently delete what you have received. Any views or opinions expressed are solely those of the author and do not necessarily represent those of Sidra Medical and Research Center.

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