- galaxy-dev - lists.galaxyproject.org

Galaxy Job Error
by evan clark 14 Jun '17

14 Jun '17

Has anyone seen a similar error like this before. We are unsure if galaxy is causing the issue or it is being cuased by slurm as it seems galaxy is prematurely deleting a file. galaxy.jobs.runners DEBUG 2017-06-14 19:36:45,719 (3261/143577) Unable to cleanup /cm/shared/apps/galaxy/prod/galaxy/database/jobs_directory/003/3261/galaxy_3261.ec: [Errno 2] No such file or directory: '/cm/shared/apps/galaxy/prod/galaxy/database/jobs_directory/003/3261/galaxy_3261.ec' galaxy.jobs.output_checker DEBUG 2017-06-14 19:36:45,725 Tool produced standard error failing job - [slurmstepd: get_exit_code task 0 died by signal

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Release of Galaxy 17.05
by Jennifer Hillman-Jackson 12 Jun '17

12 Jun '17

Dear Galaxy Fans, We are pleased to announce the *release of Galaxy 17.05*. Thanks to the #usegalaxy committers and you, our community! Full release notes: https://docs.galaxyproject.org/en/master/releases/17.05_announce.html Highlights: *Tag your data with propagating hashtags* Large Galaxy histories used to be messy. Hashtags make it easy to track dataset (and collection) relationships. These two movies (both under a minute) explain how to use this with datasets <https://vimeo.com/216884518> and with collections <https://vimeo.com/216895965>. Learn more about Galaxy histories in our updated tutorial <https://galaxyproject.org/tutorials/histories/> *Drag & Drop datasets into tool inputs*Interface now allows dragging datasets from history panel into the content selectors of the tool form. Implemented in Pull Request 3871 <https://github.com/galaxyproject/galaxy/pull/3871>.*Upload directly to a collection* You can now bypass the history manipulation and upload your data straight into a collection for convenience. Learn more about collections and how to use them in a new tutorial <https://galaxyproject.org/tutorials/collections/>. We extend special thanks to the 64 New Contributors <https://docs.galaxyproject.org/en/master/releases/17.05_announce.html#new-c…> to Galaxy in the past year. *Thanks for using Galaxy!* *http://galaxyproject.org <http://galaxyproject.org>*

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AD Intergration
by John Chen 08 Jun '17

08 Jun '17

Hi, I am trying to integrate AD with Galaxy. My auth_config.xml look like the below, but galaxy won't start with those setting. If anyone has any other sample of a configuration that they don't mind sharing, it be great. The Python LDAP has been installed, RHEL7 alone with ldap-dev <auth> <authenticator> <type>activedirectory</type> <options> <allow-register>False</allow-register> <auto-register>True</auto-register> <server><a class="moz-txt-link-freetext" href="ldap://dc1.example.com">ldap://dc1.example.com</server> <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> <search-user>jsmith</search-user> <search-password>mysecret</search-password> <bind-user>{sAMAccountName}</bind-user> <bind-password>{password}</bind-password> <auto-register-username>{sAMAccountName}</auto-register-username> <auto-register-email>{mail}</auto-register-email> </options> </authenticator> </auth> Any suggestion ?? Thanks

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GCC2017: Talk schedule posted; Register by 16 June
by Dave Clements 08 Jun '17

08 Jun '17

Hello all, A few GCC2017 <https://gcc2017.sciencesconf.org/> things: 1) The presentation schedule <https://gcc2017.sched.com/> has been posted. 2) The poster and demo schedule will likely be posted later today 3) Lightning talk <https://gcc2017.sciencesconf.org/page/submit> and birds-of-a-feather <https://docs.google.com/forms/d/e/1FAIpQLSdRCs97OWt47qmMxWZAtSV3TTLJ24IhW0m…> submission are still open 4) There is still limited space available for late poster and computer demo submissions <https://gcc2017.sciencesconf.org/page/submit> 5) Register by 16 June <https://gcc2017.sciencesconf.org/page/registration> >From this point on most/all emails about GCC2017 will go only to those that have registered for it. The final announcement going out to non-Galaxy mailing lists is below. Please forward to anyone who you think might be interested. And, we do hope to see you in Montpellier! Dave C on behalf of the GCC2017 Organizing Committee -- 2017 Galaxy Community Conference (GCC2017) 26-30 June 2017 Montpellier, France https://gcc2017.sciencesconf.org/ https://gcc2017.sched.com/ -- The Galaxy Community Conference (GCC) <https://gcc2017.sciencesconf.org/> brings together researchers working in and supporting data intensive life science research. There is no better place to share your work and learn from others that are addressing diverse questions and facing common challenges in data intensive biology. GCC participants work across the tree of life, around the world, and represent universities, research organizations, industry, medical schools and research hospitals. GCC2017 will be in Montpellier, France, 26-30 June and features two days of presentations, discussions, poster sessions, lightning talks, computer demos, keynotes, and birds-of-a-feather meetups <https://gcc2017.sched.com/overview/type/Conference>, all about data-intensive biology and the tools that support it. GCC2017 also features data and coding hackathons <https://gcc2017.sciencesconf.org/page/hackathon>, and two days of training <https://gcc2017.sched.com/overview/type/Training> covering 16 different topics. GCC2017 will be held at Le Corum Conference Centre <http://www.montpellier-events.com/en/The-Corum/Presentation> in the heart of Montpellier <https://gcc2017.sciencesconf.org/resource/page/id/2>, just 10km from the Mediterranean. Registration closes 16 June <https://gcc2017.sciencesconf.org/page/registration>. Costs start at 75€ per day for postdocs and students. If you work in data intensive life science research then GCC2017 is an ideal opportunity to present your work. Lightning talk <https://gcc2017.sciencesconf.org/page/submit> and birds-of-a-feather <https://docs.google.com/forms/d/e/1FAIpQLSdRCs97OWt47qmMxWZAtSV3TTLJ24IhW0m…> submission are still open, and there is limited space available for late poster and computer demo submissions <https://gcc2017.sciencesconf.org/page/submit>. About Galaxy Galaxy <https://galaxyproject.org/> is an open, web-based platform for data-intensive biomedical analysis used by tens of thousands of researchers around the world. It supports ad hoc exploration and analysis through scalable and repeatable data analysis pipelines for large research studies. Galaxy is available in over 90 free and publicly accessible web servers, on public and national cloud infrastructures, and is locally installed at hundreds, if not thousands, of research organisations around the world. We hope to see you in Montpellier! Au revoir, The GCC2017 Organising Committee -- https://galaxyproject.org/ https://getgalaxy.org/ https://usegalaxy.org/ https://gcc2017.sciencesconf.org/

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Paste/Fetch data, indicate filename before download data (default = Pasted Entry)
by SAPET, Frederic 08 Jun '17

08 Jun '17

hello just like Floreline : http://dev.list.galaxyproject.org/Paste-Fetch-data-indicate-filename-before… some of my colleagues ask me if it could be possible to rename the uploaded ( from pasted data) file before the download. I would like to know if it could be added as an enhancement for a future release ? thank you Fred --- Frederic Sapet Bioinformatics Research Engineer BIOGEMMA - Upstream Genomics Group Centre de Recherche de Chappes CS 90126 63720 CHAPPES FRANCE Tel : +33 (0)4 73 67 88 54 Fax : +33 (0)4 73 67 88 99 E-mail : frederic.sapet(a)biogemma.com<mailto:frederic.sapet@biogemma.com>

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composite datatypes: uploading and optional files
by Peter van Heusden 06 Jun '17

06 Jun '17

Hi there We've got a composite datatype (neostore) for Neo4j databases. Currently the upload is disabled because to upload you need to select each individual file of the database directory (which is tedious). Is there a more efficient way to upload composite datatypes? E.g. as a tar.gz or zip file? If not, has anyone looked into supporting this? (I see @jmchilton was noted as working on a composite uploading for 17.05) Secondly, we're moving to support Neo4j 3.2.0. In this version there is a minor (1 file) change in the files used to store the database. Can composite datatypes have "optional files"? Thanks, Peter

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June 2017 News of the Galaxy
by Dave Clements 06 Jun '17

06 Jun '17

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galaxy & DFARS
by Eric Rasche 02 Jun '17

02 Jun '17

Has anyone dealt with DFARS requirements and data in Galaxy? Similar themes across other requirement sets might be: encryption of data at rest, DoD 32-pass secure deletion of data, providing access logs for datasets/histories/intermediate steps, providing logs of changes to access control policies for histories/datasets. Just wondering before we come under these regs and need to be doing all of this. Cheers, Eric

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bwa_mem and "-t" option
by David Kovalic 01 Jun '17

01 Jun '17

Hi, Is it possible, and if so how, to run the galaxy devteam (version546ada4a9f43) of bwa_mem with the "-t" option and a value >1? "-t INT number of threads [1]" This would be quite useful, and used, for accelerating single bwa mem jobs. Thanks, David

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Large Number of jobs Failing following error
by Evan 31 May '17

31 May '17

My galaxy instance has suddenly begun having jobs failing. The error below is what is produced by the log. galaxy.objectstore CRITICAL 2017-05-31 01:44:49,932 None delete error [Errno 39] Directory not empty:

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