galaxy-dev September 2018

galaxy-dev@lists.galaxyproject.org

16 participants
11 discussions

Galaxy Administrator Training, Jan 28 - Feb 1, Penn State University
by Dave Clements 20 Dec '18

20 Dec '18

Hello all, We are pleased to announce that* the 2019 Galaxy Admin Training <https://galaxyproject.org/events/2019-admin-training/> will be offered January 28 through February 1 at Penn State University* (where the Galaxy Project got started over ten years ago). The workshop offers a 2 day introductory session <https://github.com/galaxyproject/dagobah-training#basic-sessions> followed by a 3 day advanced topics session <https://github.com/galaxyproject/dagobah-training#advanced-sessions>. Participants can register for one or both sessions. This workshop will cover what you need to know to set up your own high-performance and multi-user production Galaxy instance. Sessions will be *intensive and hands-on*, and taught by experienced instructors from the Galaxy Community. 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. Registration <https://galaxyproject.org/events/2019-admin-training/#registration> is now open and starts at $40 / day for participants from non-profits and academia. Early registration ends October 31. However, the 2016 and 2018 admin training were both full, so you are strongly encouraged to *register now*. *The workshop does have prerequisites <https://galaxyproject.org/events/2019-admin-training/#prerequisites>. Please read them before you register.* Cheers, Dave C. *About Galaxy * Galaxy is an open web based platform for biomedical data integration and analysis. It is deployed at large and small organizations around the world and used in a broad range of biomedical research domains, and across the tree of life. -- https://galaxyproject.org/ https://usegalaxy.org/

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Using Singularity images to resolve dependences in Galaxy 18.05
by Peter van Heusden 19 Sep '18

19 Sep '18

Hi there Is it possible to use Singularity images to resolve dependencies in Galaxy 18.05? If so is there documentation somewhere? I have a Galaxy server where for at least some of the dependencies conda will not be a good option so I would like to be able to use singularity if at all possible. Thanks! Peter

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Issue with deseq2
by Previti 18 Sep '18

18 Sep '18

Dear all, I have been trying to get deseq2 (latest version 17, 2018-09-05 from iuc; we are still running on galaxy version 17.09) to work properly but to no avail. Older versions have other errors, I have focused on the latest version. I get this cryptic error when I run it: /opt/galaxy/galaxy/database/dependencies/_conda/envs/mulled-v1-dbc1e05d0db06d983572e7eca0df68af225d8f398b6e11dd4d586075518c4101/lib/R/bin/exec/R: symbol lookup error: /opt/galaxy/galaxy/database/dependencies/_conda/envs/mulled-v1-dbc1e05d0db06d983572e7eca0df68af225d8f398b6e11dd4d586075518c4101/lib/R/bin/exec/../../lib/../../libreadline.so.6: undefined symbol: PC /opt/galaxy/galaxy/database/dependencies/_conda/envs/mulled-v1-dbc1e05d0db06d983572e7eca0df68af225d8f398b6e11dd4d586075518c4101/lib/R/bin/exec/R: symbol lookup error: /opt/galaxy/galaxy/database/dependencies/_conda/envs/mulled-v1-dbc1e05d0db06d983572e7eca0df68af225d8f398b6e11dd4d586075518c4101/lib/R/bin/exec/../../lib/../../libreadline.so.6: undefined symbol: PC Does anybody know what to do about this? Thanks and best regards, Christopher -- *Dr. Christopher Previti* Genomics and Proteomics Core Facility High Throughput Sequencing (W190) Bioinformatician German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany Room: B2.102 (INF580/TP3) Phone: +49 6221 42-4661 christopher.previti(a)dkfz.de <http://www.dkfz.de/> www.dkfz.de <http://www.dkfz.de/> Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta VAT-ID No.: DE143293537 Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die Personen bestimmt, an die sie adressiert ist. Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte Informationen enthalten. Sollten Sie nicht der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den Absender und löschen Sie die Mitteilung. Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist untersagt.

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"Merging tabular data tables with non-matching columns is not allowed"
by Peter van Heusden 18 Sep '18

18 Sep '18

Hi there I'm working on a data manager to keep track of the reference data collection used by the SHAPEIT2 tool. I had to add a column to the data manager but when I try and do a `planemo shed_update` I get the error: Unexpected HTTP status code: 500: {"err_msg": "Error attempting to parse file tool_data_table_conf.xml.sample: Merging tabular data tables with non matching columns is not allowed: shapeit_ref:{'path': 2, 'reference_prefix': 3, 'name': 1, 'value': 0, 'map_prefix': 4} != shapeit_ref:{'name': 1, 'value': 0, 'sample_prefix': 5, 'path': 2, 'reference_prefix': 3, 'map_prefix': 4}"} This is for data_manager_shapeit_reference in testtoolshed, which is on github at https://github.com/pvanheus/data_manager_shapeit_reference As far as I can tell the columns do accord. Is there any way to see which files are being merged to help try and debug this error? Thanks! Peter

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Update from 17.10 to 18.05
by Jochen Bick 18 Sep '18

18 Sep '18

Hi, today we tried to update from 17.10 to 18.05 your server is running but with out any interface, its just white after loading? <title> Galaxy | AP - Group </title> <link rel="index" href="/"/> <link href="/static/style/jquery.rating.css?v=1537264325" media="screen" rel="stylesheet" type="text/css" /> <link href="/static/style/jquery-ui/smoothness/jquery-ui.css?v=1537264325" media="screen" rel="stylesheet" type="text/css" /> <link href="/static/style/base.css?v=1537264325" media="screen" rel="stylesheet" type="text/css" /> <link href="/static/style/bootstrap-tour.css?v=1537264325" media="screen" rel="stylesheet" type="text/css" /> # tail ./galaxy-dist/dsmerror.log 09/05/2018 11:18:21 ANS0361I DIAG: TransErrno: Unexpected error from GetFSInfo:stat, errno = 6 09/05/2018 11:18:22 ANS0361I DIAG: TransErrno: Unexpected error from GetFSInfo:stat, errno = 6 09/05/2018 11:57:19 ANS0361I DIAG: TransErrno: Unexpected error from GetFSInfo:stat, errno = 6 09/05/2018 11:57:39 ANS0361I DIAG: TransErrno: Unexpected error from GetFSInfo:stat, errno = 6 09/05/2018 11:57:39 ANS0361I DIAG: TransErrno: Unexpected error from GetFSInfo:stat, errno = 6 09/05/2018 11:57:40 ANS0361I DIAG: TransErrno: Unexpected error from lstat, errno = 6 09/05/2018 11:57:40 ANS0361I DIAG: TransErrno: Unexpected error from GetFSInfo:stat, errno = 6 09/05/2018 11:57:40 ANS1999E Incremental processing of '/' stopped. Cheers Jochen

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September 2018 News of the Galaxy
by Dave Clements 13 Sep '18

13 Sep '18

Hello all, The *September 2018 Galactic News* is here! This is a summary of what is going on in the Galaxy community. Here's what's happening: - Events - 2018 SACNAS Workshops <https://galaxyproject.org/news/2018-09-galaxy-update/#2018-sacnas-pre-confe…> - European Galaxy Days <https://galaxyproject.org/news/2018-09-galaxy-update/#european-galaxy-days-…>, 19-20 November, Freiburg, Germany - All upcoming events <https://galaxyproject.org/news/2018-09-galaxy-update/#upcoming-events> - New: - 80 publications <https://galaxyproject.org/news/2018-09-galaxy-update/#publications> - Galactic Blog entry: Contributor of the Month: Carrie Ganote <https://galaxyproject.org/news/2018-09-galaxy-update/#contributor-of-the-mo…> - Public Galaxy Server News <https://galaxyproject.org/news/2018-09-galaxy-update/#public-galaxy-server-…>: epiGeEC and MetaCentrum - ToolShed contributions <https://galaxyproject.org/news/2018-09-galaxy-update/#toolshed-contributions> - Hub and Documentation updates <https://galaxyproject.org/news/2018-09-galaxy-update/#hub-and-doc-updates> - CloudBridge v1 <https://galaxyproject.org/news/2018-09-cloudbridge-v1-release/> has been released! - Releases <https://galaxyproject.org/news/2018-09-galaxy-update/#releases> - And other news <https://galaxyproject.org/news/2018-09-galaxy-update/#other-news> too If you have anything to add to next month's newsletter, then please send it to outreach(a)galaxyproject.org. Thanks, Dave C on behalf of the Galaxy Community -- https://galaxyproject.org/ https://usegalaxy.org/

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good practice for Galaxy admin and updates ?
by julie dubois 07 Sep '18

07 Sep '18

Hi Galaxy Community, I manage a Galaxy local instance on a standalone station since 6 years. Regarding the numerous troubleshoots I have encountered (and the very long time I spent) during these years with Galaxy updates trying to minimize impact for my users, trying in the same time to keep safe our customization of this instance. I'm wondering about the best solution to manage my instance and to test my own dev and also Galaxy updates before pushing them on my production server. So I want to test a new way and I'd appreciate community feedback on this idea or let me know if other practices could be more appropriate in my situation. So my basic idea is: First install a new Galaxy from scratch, not by cloning the stable branch of Galaxy but by forking it. And use the master branch of this fork as production server. Then to manage an update of the Galaxy stable, my idea is to make a test branch on my fork, then pull Galaxy update on this test branch and run this test instance as a dev server in another station to be sure that update will not override our customization or any crucial tools/functionality for my users. Finally when I'll be sure this update is safe, I'll merge the test branch with the master branch of my forked Galaxy. Is anyone already acting in this way? Is it a good (the best) way to manage local instance of Galaxy? Have you other good practices? Thanks a lot for your help. Julie

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Salmon references and data manager
by Previti 07 Sep '18

07 Sep '18

Dear Björn, I just installed Salmon on our Galaxy instance and I have a couple of basic questions. Currently the reference transcriptomes are put in the same data table as the genomes, would it be of interest to separate this and give the transcriptomes their own table? I could probably try to do this... There is a data manager available that unfortunately has a bug. We fixed that and it now populates the reference genome data table. I would probably modify this as well use the new table. Could this be useful? I'm not sure how to proceed...would I give you the modified Salmon wrapper for inclusion in the package? Best regards, Christopher -- *Dr. Christopher Previti* Genomics and Proteomics Core Facility High Throughput Sequencing (W190) Bioinformatician German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany Room: B2.102 (INF580/TP3) Phone: +49 6221 42-4661 christopher.previti(a)dkfz.de <http://www.dkfz.de/> www.dkfz.de <http://www.dkfz.de/> Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta VAT-ID No.: DE143293537 Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die Personen bestimmt, an die sie adressiert ist. Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte Informationen enthalten. Sollten Sie nicht der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den Absender und löschen Sie die Mitteilung. Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist untersagt.

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Local galaxy of release_18.05 is too slow
by 沈维燕(Steven Shen) 05 Sep '18

05 Sep '18

Hi list, I use Anaconda2-5.2.0-Linux-x86_64.sh and galaxy release_18.05 for my local galaxy, but I found it was too slow to open the web pages. The release_17.09 on the same server is much faster. I can see some limit when release_18.05 start: your processes number limit is 4096 your memory page size is 4096 bytes detected max file descriptor number: 65535 !!! no /etc/mime.types file found !!! lock engine: pthread robust mutexes Is this related to my problem? or which options could I set ? Thank you. Steven

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Re: [galaxy-dev] galaxy config from 17.05 to 18.05
by Fernandez Edgar 04 Sep '18

04 Sep '18

Hey gents, I would really appreciate some help with this. If you can find some kind of error in my configuration. I believe I have found all the configuration to run galaxy on port 7112 and have an apache proxy on 8081. Also I would like two handlers one for local and one for drama. I however still getting the following error in the apache logs: [Tue Sep 04 12:22:57 2018] [debug] mod_proxy_http.c(56): proxy: HTTP: canonicalising URL //localhost:7112/ [Tue Sep 04 12:22:57 2018] [debug] proxy_util.c(1544): [client 10.33.158.247] proxy: *: found reverse proxy worker for http://localhost:7112/ [Tue Sep 04 12:22:57 2018] [debug] mod_proxy.c(1026): Running scheme http handler (attempt 0) [Tue Sep 04 12:22:57 2018] [debug] mod_proxy_http.c(2018): proxy: HTTP: serving URL http://localhost:7112/ [Tue Sep 04 12:22:57 2018] [debug] proxy_util.c(2102): proxy: HTTP: has acquired connection for (*) [Tue Sep 04 12:22:57 2018] [debug] proxy_util.c(2158): proxy: connecting http://localhost:7112/ to localhost:7112 [Tue Sep 04 12:22:57 2018] [debug] proxy_util.c(2289): proxy: connected / to localhost:7112 [Tue Sep 04 12:22:57 2018] [debug] proxy_util.c(2540): proxy: HTTP: fam 2 socket created to connect to * [Tue Sep 04 12:22:57 2018] [debug] proxy_util.c(2672): proxy: HTTP: connection complete to 127.0.0.1:7112 (localhost) [Tue Sep 04 12:23:01 2018] [error] [client 10.33.158.247] (20014)Internal error: proxy: error reading status line from remote server localhost [Tue Sep 04 12:23:01 2018] [debug] mod_proxy_http.c(1499): [client 10.33.158.247] proxy: NOT Closing connection to client although reading from backend server localhost failed. [Tue Sep 04 12:23:01 2018] [error] [client 10.33.158.247] proxy: Error reading from remote server returned by /galaxy-prod/ [Tue Sep 04 12:23:01 2018] [debug] proxy_util.c(2120): proxy: HTTP: has released connection for (*) [Tue Sep 04 12:23:01 2018] [debug] mod_deflate.c(687): [client 10.33.158.247] Zlib: Compressed 497 to 333 : URL /galaxy-prod/ Hers is some of my config: diff galaxy.yml.sample galaxy.yml 19a20 > socket: 127.0.0.1:7112 24c25 < http: 127.0.0.1:8080 --- > #http: 127.0.0.1:8080 30c31 < buffer-size: 16384 --- > buffer-size: 32768 35c36 < processes: 1 --- > processes: 2 53c54 < master: false --- > master: true 68c69 < thunder-lock: false --- > thunder-lock: true 87a89,92 > mule: lib/galaxy/main.py > mule: lib/galaxy/main.py > farm: job-handlers:1,2 > 88a94 > server_name: main 93c99 < #filter-with: proxy-prefix --- > filter-with: proxy-prefix 100c106 < #cookie_path: null --- > cookie_path: /galaxy-prod 107a114 > database_connection: mysql://galaxy:qaz1wsx2@localhost/galaxy_db_prod?unix_socket=/var/lib/mysql/mysql.sock 122a130 > database_engine_option_pool_recycle: 7200 168a177 > file_path: /home/galaxy/galaxy-prod/database/files 171a181 > new_file_path: /home/galaxy/galaxy-prod/database/tmp 177a188 > tool_config_file: '/home/galaxy/galaxy-prod/config/tool_conf.xml,/home/galaxy/galaxy-prod/config/shed_tool_conf.xml' 192a204 > migrated_tools_config: /home/galaxy/galaxy-prod/config/migrated_tools_conf.xml 199a212 > integrated_tool_panel_config: /home/galaxy/galaxy-prod/config/integrated_tool_panel.xml 214a228 > tool_dependency_dir: /home/galaxy/galaxy-prod/database/dependencies 281a296 > tool_sheds_config_file: /home/galaxy/galaxy-prod/config/tool_sheds_conf.xml 342a358 > tool_data_table_config_path: /home/galaxy/galaxy-prod/config/tool_data_table_conf.xml 351a368 > shed_tool_data_table_config: /home/galaxy/galaxy-prod/config/shed_tool_data_table_conf.xml 441a459 > job_working_directory: /home/galaxy/galaxy-prod/database/jobs_directory 445a464 > cluster_files_directory: /home/galaxy/galaxy-prod/database/pbs 508a528 > smtp_server: smtp.umontreal.ca:25 522a543 > smtp_ssl: false 535a557 > error_email_to: edgar.fernandez(a)umontreal.ca 542a565 > email_from: Galaxy ESI Project <esi-galaxy-no-reply(a)umontreal.ca> 564a588 > user_activation_on: true 775a800 > apache_xsendfile: true 786a812 > upstream_gzip: false 989a1016 > use_interactive: false 1204a1232 > id_secret: 3s1G@l@xyPr0j3ct 1256a1285 > admin_users: rootbac(a)esi.umontreal.ca 1259a1289 > require_login: true 1263a1294 > show_welcome_with_login: true 1267a1299 > allow_user_creation: false 1270a1303 > allow_user_deletion: true 1273a1307 > allow_user_impersonation: true 1282a1317 > allow_user_dataset_purge: true 1288a1324 > new_user_dataset_access_role_default_private: true 1493a1530 > enable_quotas: true 1499a1537 > expose_dataset_path: true 1532a1571 > job_config_file: /home/galaxy/galaxy-prod/config/job_conf.xml 1622a1662 > cleanup_job: onsuccess Also, cat job_conf.xml <?xml version="1.0"?> <job_conf> <plugins> <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/> <plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/> </plugins> <handlers default="main.job-handlers.1"> <handler id="main.web.1" tags="handlers"><plugin id="local"/></handler> <handler id="main.job-handlers.1" tags="handlers"><plugin id="drmaa"/></handler> </handlers> <destinations default="torque"> <destination id="local" runner="local"></destination> <destination id="torque" runner="drmaa"><param id="native_specification">-l nodes=1:ppn=8</param></destination> </destinations> <tools> <tool id="upload1" handler="main" destination="local"/> </tools> </job_conf> Finally, cat /etc/httpd/vhosts.d/galaxy_prod.conf User galaxy Group users Listen 8081 NameVirtualHost *:8081 <VirtualHost *:8081> # don't decode encoded slashes in path info AllowEncodedSlashes NoDecode # enable compression on all relevant types AddOutputFilterByType DEFLATE text/html text/plain text/xml AddOutputFilterByType DEFLATE text/css AddOutputFilterByType DEFLATE application/x-javascript application/javascript application/ecmascript AddOutputFilterByType DEFLATE application/rss+xml AddOutputFilterByType DEFLATE application/xml AddOutputFilterByType DEFLATE application/json # allow access to static content <Directory "/home/galaxy/galaxy-prod/static"> AllowOverride None Require all granted </Directory> # allow up to 3 minutes for Galaxy to respond to slow requests before timing out ProxyTimeout 180 # uWSGI on a TCP socket ProxyPass /galaxy-prod/ uwsgi://127.0.0.1:7112/ # serve framework static content RewriteEngine On RewriteRule ^/galaxy-prod$ /home/galaxy/galaxy-prod/ [R] RewriteRule ^/galaxy-prod/static/style/(.*) /home/galaxy/galaxy-prod/static/style/blue/$1 [L] RewriteRule ^/galaxy-prod/static/(.*) /home/galaxy/galaxy-prod/static/$1 [L] RewriteRule ^/galaxy-prod/favicon.ico /home/galaxy/galaxy-prod/static/favicon.ico [L] RewriteRule ^/galaxy-prod/robots.txt /home/galaxy/galaxy-prod/static/robots.txt [L] RewriteRule ^/galaxy-prod(.*) http://localhost:7112$1 [P] # enable caching on static content <Location "/static"> ExpiresActive On ExpiresDefault "access plus 24 hours" </Location> # serve visualization and interactive environment plugin static content <Directory "/home/galaxy/galaxy-prod/config/plugins/(.+)/(.+)/static"> AllowOverride None Require all granted </Directory> RewriteRule ^/galaxy-prod/plugins/(.+)/(.+)/static/(.*)$ /home/galaxy/galaxy-prod/config/plugins/$1/$2/static/$3 [L] <Location "/"> XSendFile on XSendFilePath / </Location> # Log levels LogLevel debug ErrorLog /var/log/httpd/galaxy-prod-error_log CustomLog /var/log/httpd/galaxy-prod-access_log common </VirtualHost> Please let me know what you guys think... Thank you, Edgar Fernandez Administrateur Système (Linux) Technologies de l'Information Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-210 * Bur. : 1-514-343-6111 poste 16568 From: Fernandez Edgar Sent: August 31, 2018 10:52 AM To: 'galaxy-dev(a)bx.psu.edu' <galaxy-dev(a)bx.psu.edu> Subject: galaxy config from 17.05 to 18.05 Hello gents, I would greatly appreciate some help configuring my new installation of galaxy 18.05. I found most of the configuration I needed but I'm missing the following configuration in green. Here is my galaxy 17.05: [galaxy@esilbac3a ~]$ diff galaxy-17.05/config/galaxy.ini galaxy-17.05/config/galaxy.ini.sample 32c32 < port = 7112 --- > #port = 8080 37c37 < host = 0.0.0.0 --- > #host = 127.0.0.1 50,59d49 < # ---- HTTP PBS DRMAA HANDLER ----------------------------------------------- < < # Configuration of the pbs drmaa handler < < [server:handler0] < use = egg:Paste#http < port = 8088 < use_threadpool = True < threadpool_workers = 10 < 74c64 < prefix = /galaxy-prod --- > prefix = /galaxy 95c85 < filter-with = proxy-prefix --- > #filter-with = proxy-prefix 109c99 < database_connection = mysql://galaxy:qaz1wsx2@localhost/galaxy_db_prod2?unix_socket=/var/lib/mysql/mysql.sock --- > #database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE 119c109 < database_engine_option_pool_recycle = 7200 --- > #database_engine_option_pool_recycle = -1 152c142 < file_path = /home/galaxy/galaxy-prod/database/files --- > #file_path = database/files 155c145 < new_file_path = /home/galaxy/galaxy-prod/database/tmp --- > #new_file_path = database/tmp 161c151 < tool_config_file = /home/galaxy/galaxy-prod/config/tool_conf.xml,/home/galaxy/galaxy-prod/config/shed_tool_conf.xml --- > #tool_config_file = config/tool_conf.xml,config/shed_tool_conf.xml 197c187 < tool_dependency_dir = /home/galaxy/galaxy-prod/tool-data/toolshed.dependency.dir --- > #tool_dependency_dir = database/dependencies 401c391 < job_working_directory = /home/galaxy/galaxy-prod/database/jobs_directory --- > #job_working_directory = database/jobs_directory 466c456 < smtp_server = smtp.umontreal.ca:25 --- > #smtp_server = None 475c465 < smtp_ssl = False --- > #smtp_ssl = False 486c476 < error_email_to = edgar.fernandez(a)umontreal.ca<mailto:edgar.fernandez@umontreal.ca> --- > #error_email_to = None 493c483 < email_from = Galaxy ESI Project <rootbac(a)esi.umontreal.ca<mailto:rootbac@esi.umontreal.ca>> --- > #email_from = None 679c669 < apache_xsendfile = True --- > #apache_xsendfile = False 693c683 < upstream_gzip = False --- > #upstream_gzip = False 848c838 < debug = False --- > #debug = False 861c851 < use_interactive = False --- > use_interactive = True 989c979 < id_secret = 3s1G@l@xyPr0j3ct --- > #id_secret = USING THE DEFAULT IS NOT SECURE! 1038c1028 < admin_users = rootbac(a)esi.umontreal.ca<mailto:rootbac@esi.umontreal.ca> --- > #admin_users = None 1041c1031 < require_login = True --- > #require_login = False 1049c1039 < allow_user_creation = False --- > #allow_user_creation = True 1052c1042 < allow_user_deletion = True --- > #allow_user_deletion = False 1055c1045 < allow_user_impersonation = True --- > #allow_user_impersonation = False 1060c1050 < allow_user_dataset_purge = True --- > #allow_user_dataset_purge = True 1066c1056 < new_user_dataset_access_role_default_private = True --- > #new_user_dataset_access_role_default_private = False 1200c1190 < enable_quotas = True --- > #enable_quotas = False 1234c1224 < job_config_file = /home/galaxy/galaxy-prod/config/job_conf.xml --- > #job_config_file = config/job_conf.xml 1292c1282 < retry_job_output_collection = 20 --- > #retry_job_output_collection = 0 1310c1300 < cleanup_job = onsuccess --- > #cleanup_job = always Please help me find what I am missing. Best regards, Edgar Fernandez Administrateur Système (Linux) Technologies de l'Information Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-210 * Bur. : 1-514-343-6111 poste 16568

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galaxy-dev September 2018