galaxy-dev March 2019

galaxy-dev@lists.galaxyproject.org

8 participants
10 discussions

URL prefix doesn't work properly in Galaxy v18.09
by Ping Luo 20 May '19

20 May '19

I configured URL prefix in galaxy 18.09. It has problems of resolving some of the links, including: workflow visualize -> create visualization shared data -> workflows shared data -> visualizations I will use workflow as an example to illustrate what happens. When the mouse cursor is put on workflow, the URL shown in at the left bottom of the browser shows https://xxx.xxx.tamu.edu/galaxy/workflows/list But after I clicked 'workflow', the real URL shown in the address bar is actually https://xxx.xxxx.tamu.edu/galaxy/galaxy//workflows/list?__identifer=sk0xsyw… Of course, there is no such a page and the browser shows a blank page. If I manually remove one galaxy in the URL, the page is correctly shown. Beside the four mentioned above, other links work fine. If galaxy is configured without prefix, then there is no problem. I also tested v18.05. With all the configuration being the same, this version doesn't have the problem with prefix like v18.09 does. So I think this is a bug in v18.09 with URL prefix. Ping

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Nginx+Shibboleth+UCSC
by Martin Demko 18 Apr '19

18 Apr '19

Dear list, I have been trying to manage an access to UCSC genome browser from our Galaxy instance which uses Nginx as a proxy with external authentication via Shibboleth and IdP service. Not even the configuration of nginx+shibboleth was quite complicated to achieve (but I succeeded after a week or so) but now during a testing phase, we have found out that a cooperation with external UCSC servers is forbidden due to our auth. configuration. I have found a way how to do that but only for Apache (https://docs.galaxyproject.org/en/master/admin/special_topics/apache.html#d…) so I tried to do something similar in Nginx but only with IP addresses as Nginx doesn't support using of named domains and defined a location: location /display_as { satisfy any; deny all; allow 128.114.119.131; allow 128.114.119.132; allow 128.114.119.133; allow 128.114.119.134; allow 128.114.119.135; allow 128.114.119.136; } Used IP addresses should be the right ones for UCSC servers according to few sources such as (https://genome.soe.ucsc.narkive.com/sll2JSk2/ucsc-ip-address): hgw1.cse.ucsc.edu hgw2.cse.ucsc.edu hgw3.cse.ucsc.edu hgw4.cse.ucsc.edu hgw5.cse.ucsc.edu hgw6.cse.ucsc.edu I tried to change the location also to "/display_application" but didn't help (actually, I don't know why in the documentation there is used as the location that "/display_as" as I have never encountered such location in Galaxy which is my first question). In galaxy.ini I set: display_servers = hgw1.cse.ucsc.edu,hgw2.cse.ucsc.edu,hgw3.cse.ucsc.edu,hgw4.cse.ucsc.edu,hgw5.cse.ucsc.edu,hgw6.cse.ucsc.edu,hgw7.cse.ucsc.edu,hgw8.cse.ucsc.edu,lowepub.cse.ucsc.edu,128.114.119.131,128.114.119.132,128.114.119.133,128.114.119.134,128.114.119.135,128.114.119.136 Just for case I used both, the domains and also IP addresses. Also I have tried to use only the domains or only the addresses but nothing helped. Then I found out after reading of the following (https://www.switch.ch/aai/guides/sp/access-rules/) that the main obstacle should be actually shibboleth so I defined in /etc/shibboleth/shibboleth2.xml an unrestricted path: <RequestMapper type="XML"> <RequestMap> <Host name="our.galaxy.something" authType="shibboleth" requireSession="true" redirectToSSL="443" > <Path name="display_application" requireSession="false" redirectToSSL="443" />  </Host> </RequestMap> </RequestMapper> Again, I have tried to use both locations "display_as" and "display_application", but it haven't solved my problem entirely. I moved forward I suppose because now the requests should be going around the authentication but UCSC stil warns me that: Expected 200 https://our.galaxy.something/display_application/e1304269a2f56a52/ucsc_bigw…: 403 Forbidden Before that it was a different message containing the address of our idp server so I believe I'am on the right way here. The presence of attribute 'authType="shibboleth"' seams to be useless as 'requireSession="false"' is used. Then I tried to teach Nginx to use also the domain names with the using of 3rd party nginx-http-rdns module from (https://github.com/flant/nginx-http-rdns), so my nginx.conf looked like: ....only the part of nginx.conf.... ############## Shibboleth authentication conf ################# # FastCGI authorizer for Shibboleth Auth Request module location = /shibauthorizer { internal; include fastcgi_params; fastcgi_pass unix:/var/run/shibboleth/shibauthorizer.sock; } # FastCGI responder for SSO location /Shibboleth.sso { include fastcgi_params; fastcgi_pass unix:/var/run/shibboleth/shibresponder.sock; } ############### Entry point for Galaxy ############### # Location secured by Shibboleth location / { shib_request /shibauthorizer; more_clear_input_headers 'Variable-*' 'Shib-*' 'Remote-User' 'REMOTE_USER' 'Auth-Type' 'AUTH_TYPE' 'GX_SECRET'; include uwsgi_params; shib_request_set $shib_id $upstream_http_variable_eppn; uwsgi_param HTTP_REMOTE_USER $shib_id; uwsgi_param HTTP_GX_SECRET $our_secret; uwsgi_pass 127.0.0.1:4001; # resolver $correct_resolver_acc_to_resolv.conf; # rdns on; # satisfy any; # rdns_allow genome\.ucsc\.edu; # rdns_allow hgw1\.cse\.ucsc\.edu; # rdns_allow hgw2\.cse\.ucsc\.edu; # rdns_allow hgw3\.cse\.ucsc\.edu; # rdns_allow hgw4\.cse\.ucsc\.edu; # rdns_allow hgw5\.cse\.ucsc\.edu; # rdns_allow hgw6\.cse\.ucsc\.edu; # rdns_allow hgw7\.cse\.ucsc\.edu; # rdns_allow hgw8\.cse\.ucsc\.edu; } # location /display_as { # resolver $correct_resolver_acc_to_resolv.conf; # rdns on; # satisfy any; # rdns_allow genome\.ucsc\.edu; # rdns_allow hgw1\.cse\.ucsc\.edu; # rdns_allow hgw2\.cse\.ucsc\.edu; # rdns_allow hgw3\.cse\.ucsc\.edu; # rdns_allow hgw4\.cse\.ucsc\.edu; # rdns_allow hgw5\.cse\.ucsc\.edu; # rdns_allow hgw6\.cse\.ucsc\.edu; # rdns_allow hgw7\.cse\.ucsc\.edu; # rdns_allow hgw8\.cse\.ucsc\.edu; # } # location /display_application { # resolver $correct_resolver_acc_to_resolv.conf; # rdns on; # satisfy any; # rdns_allow genome\.ucsc\.edu; # rdns_allow hgw1\.cse\.ucsc\.edu; # rdns_allow hgw2\.cse\.ucsc\.edu; # rdns_allow hgw3\.cse\.ucsc\.edu; # rdns_allow hgw4\.cse\.ucsc\.edu; # rdns_allow hgw5\.cse\.ucsc\.edu; # rdns_allow hgw6\.cse\.ucsc\.edu; # rdns_allow hgw7\.cse\.ucsc\.edu; # rdns_allow hgw8\.cse\.ucsc\.edu; # } ....END of the part of nginx.conf.... Everything commented out, I tried to use together or one at the time but nothing helped. But there are differences: 1) when uncommented only location /display_application - I will get just a blank page with: 404 Not Found. 2) when uncommented only location /display_as - nothing changes. 3) when uncommented part inside the location "/" - I will get a new message: Error unexpected end of input reading http header on https://our.galaxy.something/display_application/e1304269a2f56a52/ucsc_bigw… And now I'm out of ideas. I would really appreciate any help. PS: I stil don't get why in the documentation for Apache configuration (https://docs.galaxyproject.org/en/master/admin/special_topics/apache.html#d…) there is used the /display_as location. Can somebody explain, please? Thank you in advance, Martin Demko

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tool installation problem
by Matthias Bernt 27 Mar '19

27 Mar '19

Dear list, I have a problem during installing a tool version that I previously uninstalled. I get the message: `Revision 0696db066a5b of repository deseq2 owned by iuc has already been installed.` It seems to be uninstalled on the file system. Are there any entries that might be left in the DB? Thanks in advance. 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 Helmholtz-Zentrum für Umweltforschung GmbH - UFZ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 1269, Fax +49 341 235 1468 (optional) max.mustermann(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. Georg Teutsch Administrative Geschäftsführerin/Administrative Managing Director: Dr. Sabine König

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GalaxyAdmins online meetup this Thursday
by Dave Clements 21 Mar '19

21 Mar '19

Hi All, The GalaxyAdmins group is back (thanks to a rejuvenation by Helena Rasche), and will have its first online meetup in over two year this Thursday. *When:* 21 March 2019, 15:00 GMT (see your local time <https://www.timeanddate.com/worldclock/fixedtime.html?msg=March+2019+Galaxy…> ) *Where: *On Zoom <https://zoom.us/>. If you don't already have the Zoom client installed, then you'll need to download it <https://support.zoom.us/hc/en-us/articles/207373866-Zoom-Installers> before the meetup. *We will publish the Zoom room link here <https://galaxyproject.org/community/galaxy-admins/meetups/2019-03-21/> and on Twitter <https://twitter.com/galaxyproject> before the meeting.* *What:* We will have a general discussion / give and take about Galaxy administration and a presentation by Pablo Moreno <https://galaxyproject.org/blog/2018-08-cotm-pablo-moreno/> on *Running Galaxy on Kubernetes.* - Interested? It would be great to have you join us. Thanks and hope to see you Thursday, Dave C (channeling Helena) -- https://galaxyproject.org/ https://usegalaxy.org/

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Serious issues with picard-tools after upgrade to Galaxy version 19.01
by Previti 20 Mar '19

20 Mar '19

Dear all, I'm having serious issues with picard tools (latest Galaxy version 2.18.2.1 by devteam) after upgrading our galaxy to version 19.01 I've been running fastqtoSam on paired-end data: _JAVA_OPTIONS=${_JAVA_OPTIONS:-'-Xmx200g -Xms256m'} && export _JAVA_OPTIONS && picard FastqToSam FASTQ="/opt/galaxy/galaxy/database/files/039/dataset_39081.dat" FASTQ2="/opt/galaxy/galaxy/database/files/039/dataset_39082.dat" QUALITY_FORMAT="Standard" OUTPUT="/opt/galaxy/galaxy/database/files/039/dataset_39441.dat" READ_GROUP_NAME="A" SAMPLE_NAME="sample-a" MIN_Q="0" MAX_Q="93" STRIP_UNPAIRED_MATE_NUMBER="false" ALLOW_AND_IGNORE_EMPTY_LINES="false" SORT_ORDER=coordinate VALIDATION_STRINGENCY="LENIENT" QUIET=true VERBOSITY=ERROR `if [ -n "$TMPDIR" ] ; then echo 'TMP_DIR=$TMPDIR' ; else if [ -n "$TEMP" ] ; then echo 'TMP_DIR=$TEMP' ; fi ; fi` But the bam file I get is not readable and I also get following message: Picked up _JAVA_OPTIONS: -Xmx200g -Xms256m 14:16:29.629 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/galaxy/galaxy/database/dependencies/_conda/envs/__picard@2.18.2/share/picard-2.18.2-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so does anybody know what's going on? The output "bam" file is the correct size (>20GB) but not readable... Thanks and best regards, Christopher Previti *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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GCC2019 Registration & Abstract Submission are Open
by Dave Clements 19 Mar '19

19 Mar '19

*We are pleased to announce that registration <https://galaxyproject.org/events/gcc2019/registration/> and abstract submission <https://galaxyproject.org/events/gcc2019/abstracts/> for the 2019 Galaxy Community Conference (GCC2019) <https://galaxyproject.org/events/gcc2019/> are now open.* GCC2019 will be held 1-8 July in Freiburg, Germany. The *tenth* GCC <https://galaxyproject.org/gcc/> will have many familiar features from earlier years, including accepted and lightning talks, posters and demos, birds-of-a-feather gatherings (BoFs), training, and a CollaborationFest. 2019 also brings the most significant conference program update <https://gcc2019.sched.com/> in several years: - some training will be integrated with the main conference, - three days of conference instead of two, - several parallel sessions, - and a strong emphasis on organizing content by domain. GCC2019, like every GCC before it, will be built around *community*. Training topics are nominated, selected, and presented by the community. Presentations will feature the full spectrum of Galaxy applications, enhancements and deployments from the community as well. If you are working in data intensive life science research then there will not be a better place to share your work, learn from others, and find new collaborators. *Registration* Early registration <https://galaxyproject.org/events/gcc2019/registration/> starts at €49/day for students and postdocs, and €79 / day for other academics and non-profit researchers. Early registration ends 17 May, *when rates go up by 60%. So, register early <https://galaxyproject.org/events/gcc2019/registration/>.* *Present your work!* Abstract submission <https://galaxyproject.org/events/gcc2019/abstracts/> for talks, lightning talks, demos and posters is now open. If you work in data-intensive life science (or in other fields using Galaxy) then please consider presenting your work at GCC2019. This is an ideal chance to present to 200+ researchers, all addressing common challenges in data intensive science. Review of oral presentations starts on 22 April, in a little over a month. *Submit an abstract (or two) now <https://galaxyproject.org/events/gcc2019/abstracts/>!* *We hope to see you in Freiburg!* GCC2019 Organizers <https://galaxyproject.org/events/gcc2019/organizers/> -- https://galaxyproject.org/ https://usegalaxy.org/

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Upload bigger 2GB
by Jochen Bick 13 Mar '19

13 Mar '19

Hi, since some months we have the problem that users are allowed to upload files bigger 2GB. Is there some kind of options in the galaxy config that can stop this? Our data storage is not able to handle such big data duplication, we used to use Shared Data->Data libraries to reduce data duplication. Thanks in advance. Cheers Jochen -- ETH Zurich *Jochen Bick* Animal Physiology Institute of Agricultural Sciences Postal address: Universitätstrasse 2 / LFW B 58.1 8092 Zurich, Switzerland Office: Eschikon 27 8315 Lindau, Switzerland Phone +41 52 354 92 06 jochen.bick(a)usys.ethz.ch <mailto:jochen.bick@usys.ethz.ch> www.ap.ethz.ch

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Gateways 2019 Call for Participation (Abstracts due April 29; Full submissions due May 6)
by Katherine Lawrence 08 Mar '19

08 Mar '19

* Call for Participation: Gateways 2019(September 23–25, San Diego, California) is now accepting submissions of papers, demos, tutorials, and panels (2–4 pages) on the topic of gateways for science, engineering, or other disciplines. Gateways are user-friendly interfaces to scientific computing, data, and other domain-specific resources to support research and education. Topics may include their design, use, impact, development processes, sustainability, best practices, or any other aspect that you think fellow gateway creators or users will find interesting to learn. We also welcome educational topics directed toward the next generation of gateway creators. In addition, this year Gateways 2019 is co-located with the eScience <https://escience2019.sdsc.edu/>conference. The two conferences will offer shared sessions and connected registration.Abstracts are due April 29, and full submissions are due May 6, 2019.A poster session deadline (open to all attendees) will be August 15. Read more details in the Call for Participation:http://sciencegateways.org/gateways2019/call*

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Bismark - Bug in Bismark Pretty Report ?
by Previti 08 Mar '19

08 Mar '19

Dear Galaxy Community, I just recently started testing the Bismark methylation tools, everything works fine until I try to make a "pretty report". Some information is not included in the report, instead you see placeholders I attached the output I get and shown below are the job parameters. Does anybody know where to fix this? Best regards, Christopher Bismark Pretty Report Dataset Information Number: 198 Name: Bismark Pretty Report on data 190, data 189, and others: Download pretty html report Created: Thu 07 Mar 2019 03:24:40 PM (UTC) Filesize: 2.7 MB Dbkey: ? Format: html Job Information Galaxy Tool ID: toolshed.g2.bx.psu.edu/repos/bgruening/bismark/bismark_pretty_report/0.20.0 Galaxy Tool Version: 0.20.0 Tool Version: Tool Standard Output: stdout <http://dkfzgalaxy/datasets/971c2f882eb14ac3/stdout> Tool Standard Error: stderr <http://dkfzgalaxy/datasets/971c2f882eb14ac3/stderr> Tool Exit Code: 0 History Content API ID: 971c2f882eb14ac3 (41433) Job API ID: 58816697357e736f (22051) History API ID: 5fccce9c1b3793da (807) UUID: 45bedd12-6ce5-4d63-a1e2-e05883b0c356 Full Path: /opt/galaxy/galaxy/database/files/038/dataset_38737.dat Tool Parameters Input Parameter Value Note for rerun Submit a Bismark mapping report 191: Bismark Meth. Extractor on data 60 and data 133: Genome-wide methylation report. <http://dkfzgalaxy/datasets/c53067deacfc4f28/show_params> additional_reports Submit the corresponding Bismark deduplication report 197: Bismark Deduplicate on data 133: deduplication report <http://dkfzgalaxy/datasets/622377f5e70addd2/show_params> Submit the corresponding Bismark splitting report 189: Bismark Meth. Extractor on data 60 and data 133: Splitting Report <http://dkfzgalaxy/datasets/aa40ffd063a4645f/show_params> Submit the corresponding Bismark M-bias report 190: Bismark Meth. Extractor on data 60 and data 133: Mbias Report <http://dkfzgalaxy/datasets/47db6b20871008b9/show_params> Submit the corresponding Bismark nucleotide report Create a separate logfile, otherwise logs are added to the dataset info. False Inheritance Chain Bismark Pretty Report on data 190, data 189, and others: Download pretty html report Command Line python '/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/bgruening/bismark/7bffcb6fc81d/bismark/bismark2report_wrapper.py' --alignment_report '/opt/galaxy/galaxy/database/files/038/dataset_38715.dat' --dedup_report '/opt/galaxy/galaxy/database/files/038/dataset_38736.dat' --splitting_report '/opt/galaxy/galaxy/database/files/038/dataset_38713.dat' --mbias_report '/opt/galaxy/galaxy/database/files/038/dataset_38714.dat' --output_html_report '/opt/galaxy/galaxy/database/files/038/dataset_38737.dat' Job Metrics core Cores Allocated 8 Job End Time 2019-03-07 16:49:58 Job Runtime (Wall Clock) 25 minutes Job Start Time 2019-03-07 16:24:43 Memory Allocated (MB) 510000 Job Dependencies Dependency Dependency Type Version bismark conda 0.20.0 -- *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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March 2019 Galaxy News: GCC2019 childcare sponsors, and more!
by Mo Heydarian 04 Mar '19

04 Mar '19

Hello All, The *March 2019 Galactic News <https://galaxyproject.org/news/2019-03-galaxy-update/>* is here! - Event News - eLife and F1000Research sponsor childcare at GCC2019 <https://github.com/galaxyproject/galaxy-hub/blob/master/src/news/2019-03-ga…> - The GalaxyAdmins <https://github.com/galaxyproject/galaxy-hub/blob/master/src/news/2019-03-ga…> meetup is back March 21! - 184 new publications <https://github.com/galaxyproject/galaxy-hub/blob/master/src/news/2019-03-ga…>, great resources lead to great insight. - Some most excellent Galaxy Platform News <https://github.com/galaxyproject/galaxy-hub/blob/master/src/news/2019-03-ga…>, including metagenomics, predictive model building, epigenome-wide association studies, immunogenomics, DNA methylation analysis, and more! - An interview on The Galactic Blog <https://github.com/galaxyproject/galaxy-hub/blob/master/src/news/2019-03-ga…> with Nate Coraor <https://github.com/galaxyproject/galaxy-hub/blob/master/src/people/nate/ind…> about CVMFS & Galaxy. - At least 15 Open positions <https://github.com/galaxyproject/galaxy-hub/blob/master/src/news/2019-03-ga…> in five countries on two continents. - A burst of Training Updates <https://github.com/galaxyproject/galaxy-hub/blob/master/src/news/2019-03-ga…> . - ToolShed contributions <https://github.com/galaxyproject/galaxy-hub/blob/master/src/news/2019-03-ga…> . - Galaxy 19.01 released <https://github.com/galaxyproject/galaxy-hub/blob/master/src/news/2019-03-ga…> ! - And a bunch of other news <https://github.com/galaxyproject/galaxy-hub/blob/master/src/news/2019-03-ga…> too. If you have anything to add to next month's newsletter, then please send it to outreach(a)galaxyproject.org. Cheers, Mo Heydarian, on behalf of everyone

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galaxy-dev March 2019