- galaxy-dev - lists.galaxyproject.org

GMOD codefest registration now open
by Scott Cain 19 Nov '19

19 Nov '19

Hello, As announced last month, there will be a GMOD codefest held before the Plant and Animal Genome meeting in San Diego, January 9-10, 2020. The meeting will be held at the Handlery hotel (down the street from the Town and Country Hotel). Logistical and other information can be found at the GMOD wiki as the details become more solid: http://gmod.org/wiki/Codefest_2020 Several potential projects are described in this document: https://docs.google.com/document/d/1_CnUW_W4tNyl7lSlihCwZDKT45VQQxcI3I-Vgjn… We know for sure that there will be developers from the Tripal, Apollo, JBrowse, and Chado projects. Of course, other projects like Galaxy, InterMine, and MAKER are welcome too! See you in San Diego! Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research

1 0

Deleted Galaxy Account
by Horstmann, Cullen M 15 Nov '19

15 Nov '19

Good evening, Upon trying to log onto my galaxy profile I received this message: "This account has been marked deleted, contact your local Galaxy administrator to restore the account." I was hoping I could re-gain access to this account because I have a lot of differential gene expression data on my account. Please let me know what I need to do to re-gain access at your earliest convenience. Kind Regards, Cullen Horstmann Missouri State University Master's in Biology Graduate Researcher | Kim Lab Teaching Assistant | Biology Department

2 1

Invitation to join the Open Life Science Program
by Bérénice Batut 14 Nov '19

14 Nov '19

Dear members of the Galaxy community, Yo, Malvika and I are organizing the Open Life Science (https://openlifesci.org/ <https://openlifesci.org/>) program for mentoring and training early-stage researchers and potential academic leaders who want to become ambassadors for Life Science in their communities. The first cohort of this program will run from January to April 2020. Participants of this 15-week mentoring & training program will learn essential knowledge required to create, lead, and sustain an Open Science project, connect with members across different communities, backgrounds, and identities by sharing their experiences and expertise. The complete schedule and participation guidelines of the program are available at https://openlifesci.org/syllabus <https://openlifesci.org/syllabus>. This program gives a unique opportunity to develop an Open Science project that participants either already have been working on, or want to develop in the near future within life sciences. More information regarding the roles and benefits for our mentees <https://openlifesci.org/about#mentees> and eligibility of a proposed project <https://openlifesci.org/index#projects> can be found on our website. Applications can be submitted until 8 December 2019 (midnight in any part of the world) at https://easychair.org/cfp/ols-2020 <https://easychair.org/cfp/ols-2020>. To answer any questions related to this program, an online information session (webinar) will be held on 27 November 2019 at 16:00 GMT (Check your local time <https://arewemeetingyet.com/Berlin/2019-11-27/17:00/OpenLifeSci%20&%20eLife…>). Please find more details and sign up on this shared document <https://docs.google.com/document/d/1EIDzZi5mgRiWR7cJQl0up470C87GsbcoTR_6-cs…>. Please feel free to contact us for more information by emailing (hello(a)openlifesci.org <mailto:hello@openlifesci.org>) or connecting on Twitter @openlifesci <https://twitter.com/openlifesci>, and to forward this email to anyone who may be interested. Best regards, Bérénice, Malvika, Yo OpenLifeSci Organisers https://openlifesci.org <https://openlifesci.org/>

1 0

November Galaxy News
by Dave Clements 12 Nov '19

12 Nov '19

Hello all, The November 2019 Galactic News includes Galactic news under this or any other sun: * 19 Upcoming Events * 208 new publications * 2 new blog posts * Galaxy Platform News * Training material and doc updates * Openings with 5 organizations * Releases * Other news See https://galaxyproject.org/news/2019-11-galaxy-update/ for details. Thanks, Dave C -- https://galaxyproject.org/

1 0

IT Engineers for Break Fix Services
by fieldengineer77＠gmail.com 06 Nov '19

06 Nov '19

engineers are going to be a crucial part of making sure that your business stays up and running efficiently. You can hire engineers to complete break fix maintenance which means that that you pay them a fee for their services and only for the work that they have completed. This is an attractive prospect to business owners, and one that could save your business quite a fair bit of money. More Info : https://www.fieldengineer.com/c1/hire-freelance-it-engineers-for-break-fix-…

1 0

pbs-python issues
by Sandra Maksimovic 11 Oct '19

11 Oct '19

Hi all, As a galaxy newbie, I'm struggling to get the pbs-python module working on our galaxy instance. PBS is installed to a custom location on a shared filesystem mounted via NFS to our galaxy server, however, installing pbs-python using the git clone / python venv method in the documentation fails because it can't find PBS and there does not appear to be any way to define it for pbs-python (I could be wrong?). ... gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DTORQUE_4 -I/usr/include/torque -Isrc/C++ -I/usr/include/python2.7 -c src/C++/pbs_wrap.cxx -o build/temp.linux-x86_64-2.7/src/C++/pbs_wrap.o In file included from src/C++/pbs_wrap.cxx:2978:0: src/C++/pbs_ifl.h:90:32: fatal error: u_hash_map_structs.h: No such file or directory #include "u_hash_map_structs.h" ^ compilation terminated. error: command 'gcc' failed with exit status 1 So I went ahead and installed pbs_python from source (which does allow you define a PBS_PYTHON_INCLUDEDIR environment variable), however, galaxy does not seem to like this as evidenced by errors during startup. I suspect this has to do with pbs_python not being installed into the galaxy virtual environment. galaxy[97486]: Traceback (most recent call last): galaxy[97486]: File "<string>", line 1, in <module> galaxy[97486]: File "/hpc/software/installed/galaxy/19.05/lib/galaxy/dependencies/__init__.py", line 179, in optional galaxy[97486]: conditional = ConditionalDependencies(config_file) galaxy[97486]: File "/hpc/software/installed/galaxy/19.05/lib/galaxy/dependencies/__init__.py", line 32, in __init__ galaxy[97486]: self.parse_configs() galaxy[97486]: File "/hpc/software/installed/galaxy/19.05/lib/galaxy/dependencies/__init__.py", line 41, in parse_configs galaxy[97486]: for plugin in ElementTree.parse(job_conf_xml).find('plugins').findall('plugin'): galaxy[97486]: File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1182, in parse galaxy[97486]: tree.parse(source, parser) galaxy[97486]: File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 656, in parse galaxy[97486]: parser.feed(data) galaxy[97486]: File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1642, in feed galaxy[97486]: self._raiseerror(v) galaxy[97486]: File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1506, in _raiseerror galaxy[97486]: raise err galaxy[97486]: xml.etree.ElementTree.ParseError: junk after document element: line 4, column 0 I've attempted reinstalls of the git clone / python venv method with the PBS environment variable to no avail. I was wondering if someone might have any ideas about working around this roadblock, or may have encountered a similar module installation issue in the past? Also, I was hoping to get some ideas/examples of generic job_conf.xml definitions for PBS clusters? Things like best practices, caveats, etc. My understanding is that, unless configured otherwise, galaxy will submit jobs as the galaxy user and that configuring the server to run jobs as end users themselves is difficult/risky. Just wondering if you guys might have opinions/thoughts/recommendations about this? And finally, what would be a good way to test that galaxy is submitting jobs to the queue properly? Is there some generic test data/procedure to verify that the galaxy instance is working as expected? Thanks, Sandra Maksimovic Systems Administrator Information Technology Murdoch Children's Research Institute The Royal Children's Hospital, 50 Flemington Road Parkville, Victoria 3052 Australia T +61 3 8341 6498 E sandra.maksimovic(a)mcri.edu.au<mailto:sandra.maksimovic@mcri.edu.au> W mcri.edu.au<https://www.mcri.edu.au/> Disclaimer This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Children’s Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication.

3 8

GMOD codefest before PAG
by Scott Cain 10 Oct '19

10 Oct '19

I am pleased to announce there will be a GMOD codefest occurring before the Plant and Animal Genomes meeting in San Diego. The codefest will be at the Town and Country hotel on January 9 and 10. If you would like to suggest a problem or project to address, add it to this Google Doc <https://docs.google.com/document/d/1_CnUW_W4tNyl7lSlihCwZDKT45VQQxcI3I-Vgjn…>. The codefest is open to anyone who'd like to work on any GMOD project (or, better yet, any combination of GMOD projects), including but not limited to Tripal <http://gmod.org/wiki/Tripal>, Chado <http://gmod.org/wiki/Chado>, JBrowse <http://gmod.org/wiki/JBrowse> (1 and 2), Galaxy <http://gmod.org/wiki/Galaxy> and InterMine <http://gmod.org/wiki/InterMine>. We already know that there will be Tripal, Chado and JBrowse developers present. Registration information will be coming soon. You can follow the changes to this page: http://gmod.org/wiki/Codefest_2020 to keep up to date, or follow The Tweet of GMOD (@gmodproject) on Twitter. See you in San Diego, Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research

2 1

The entire page in the center panel after login
by Olivier Inizan 07 Oct '19

07 Oct '19

Hi there, We have a strange behaviour with our galaxy interface. If we use the login form in the center panel, the entire page (tool, history and center panel) is displayed in the center panel (see file in attachment). Our galaxy version is 19.05 (we do not had this behavior in the previous version), and our instance is connected to a LDAP. We have rebuild the client interface (make client-production) but the behaviour is still the same ... Any ideas ? Olivier [cid:BE367C74-73AF-4FAD-8F3A-26FCC219921E] Olivier INIZAN olivier.inizan(a)inra.fr<mailto:olivier.inizan@inra.fr> Unité Mathématiques & Informatique Appliquées du Génome à l'Environnement Domaine de Vilvert 78352 Jouy-en-Josas Tél: +33 (0)1 34 65 29 43

2 2

October Galaxy News: Events, pubs, platforms, jobs, training, and more
by Dave Clements 02 Oct '19

02 Oct '19

Hello all, The October 2019 Galactic News is out! https://galaxyproject.org/news/2019-10-galaxy-update/ There is, as always, a lot going on: - 20 Upcoming Events - 143 new publications - Galaxy Platform News - 6 Openings - Training material and doc updates - Other news too Check it out, Dave C and the Galaxy Community -- https://galaxyproject.org/

1 0

September Galaxy News: INCOB, Galaxy Africa, ACM BCB, GTN, QFAB, ...
by Dave Clements 30 Aug '19

30 Aug '19

Hello all, The September 2019 Galactic news has been published: There are a bunch of upcoming events, including Galaxy @ INCOB, Galaxy Africa, two Bioconda / ToolShed events, a GTN CoFest, QFAB training, a Galaxy Netherlands gathering, (plus more than 20 more). We are also highlighting the new Climate Science Workbench Galaxy server, three recent blog posts, six doc & training updates, and 6 (or 11, depending on how you count) open positions. Find information on all this and more on the Galaxy Community Hub: https://galaxyproject.org/news/2019-09-galaxy-update/ And it's all in a spiffy new format. Hope to see you in Jakarta, Niagara Falls, Ghana, Brisbane, Utrecht, Sri Lanka, Ireland, online, ... Dave C and the Galaxy Community -- https://galaxyproject.org/

1 0