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How to satisfy a Galaxy tool dependency on python-irodsclient
by Lawrence, Cris W 24 Jan '17

24 Jan '17

I am a Galaxy noob trying to write a Galaxy tool that needs to employ the python-irodsclient module. I can install it on my laptop via pip. But I am trying to make it available to Galaxy via planemo. Apparently, this module is not available in the conda channels. How else can I satisfy my dependency? Thanks for any and all help. - Cris

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Which "upstream" Ansible Playbook to use for local galaxy instance?
by Hendrickson, Curtis (Campus) 24 Jan '17

24 Jan '17

Dear Galatic Advisors, We're building a new set of machines to replace our current local galaxy instance (prod, dev and db VMs running CentOS against a local SLURM cluster with local storage, want to start using wsgi), and are planning to start using Ansible, instead of doing everything by hand. Looking through the wikis and postings, we see many difference points of departure. Can anyone outline the pros and cons of these various choices or provide any recommendations? Is it best to use an edited version of this: https://github.com/galaxyproject/usegalaxy-playbook Or this: https://github.com/galaxyproject/ansible-galaxy I also see a 3rd version that is linked from the "setting up your own galaxy" page (wiki) https://wiki.galaxyproject.org/Admin/GetGalaxy (Playbook) https://github.com/ARTbio/GalaxyKickStart Ideally, we'd like to benefit from updates to the upstream package. All three seem to be actively supported. Thanks Curtis @ UAB.edu PS - is it better to post this on galaxy-dev or on https://biostar.usegalaxy.org?

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display at UCSC does not work
by Hans-Rudolf Hotz 24 Jan '17

24 Jan '17

Hi I am trying to set up the possibility to display data sets with the UCSC genome browser for our new galaxy installation. After clicking on "display at UCSC main", I get the UCSC genome browser, opening in the right assembly, and at the correct location, but I get the following Error: Warning/Error(s): redirected to non-http(s): /login?redirect=%2Froot%2Fdisplay_as In galaxy.ini, I did uncomment the line: display_servers = hgw1.cse.ucsc.edu,hgw2.cse.ucsc.edu,hgw3.cse. ... We use the 'new' authentication method to connect to our LDAP server, with the following changes in galaxy.ini: require_login = True auth_config_file = config/auth_conf.xml Connection from UCSC to our galaxy server is working, since I can display the data, when I switch to require_login = False it works, independent of whether I am logged in or not. Is there a way to get it to work, even if I have "require_login = True"? Thank you very much for your help Regards, Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland

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Resource temporarily unavailable
by Durdevic, Marija 24 Jan '17

24 Jan '17

Dear developers, >From time to time I have issue on my Galaxy server. The problem is when job is done and results has to be written to the database something happened. The error message is: "/home/data/galaxy_database/files/024/dataset_24790.dat: Resource temporarily unavailable" where "/home/data/galaxy_database/files/024/dataset_24790.dat" is path to the output file. Although it produced reasonable output the job is shown as failed. I am running galaxy over Slurm and we use NFS for connection with storage. Do anyone have idea what can be possible reason for such error? Thanks in advance. Best, Marija

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Synnefo Storage Backend for Galaxy
by Stavros 0 Sachtouris 20 Jan '17

20 Jan '17

Hello, my name is Stavros Sachtouris and I'm developing an object storage backend for Synnefo [1] Object Store (aka Pithos+ [2]). In the context of the OpenMinTeD (Open MINing for TExt and Data) project [3], we are trying to use Galaxy as a workflow engine and we need to set it up on to use our Object Store (Pithos+). Therefore, we need a Pithos+ backend for Galaxy. Pithos+ API claims compatibility with OpenStack Swift API, but in practice this rarely works. That's why we have developed our own python API library (kamaki [5]). In order to provide Pithos+ access to Galaxy, I had to develop a Pithos+ backend using kamaki. We then deployed a testing Galaxy and patched it with our code and it seems to work well. I'm sending this message for two reasons: a. to let the Galaxy developers know about our interest in Galaxy and start a cooperation which is hopefully going to be beneficial for both parties. b. to ask for advice and guidelines on how to prepare my first patch and how to ship it for review. Although the patch seems to work, we feel like we are missing further testing. Bellow you can find more information on who we are, what cloud we are providing, what is OpenMinTeD and how is it related to Galaxy. Who are we ------------ I work for the Greek Research Network of Technology (GRNET S.A. [3]) as a software developer. The last few years I'm been involved in many cloud-related projects like Synnefo, ~okeanos and OpenMinTeD (more on them later). Synnefo, Pithos+, ~okeanos --------------------------- Synnefo [1] is an open source cloud software developed and supported by GRNET. It features an OpenStack REST API, many interesting features and it is around for more than 5 years already. Pithos+ is the object storage service of Synnefo, providing object storage with de-duplication, sharing and more. ~okeanos is the largest Synnefo deployment providing thousands of virtual machines and terabytes of storage to academic users in Greece and all over Europe. ~okeanos is also operated and supported by GRNET. OpenMinTeD ------------- OpenMinTeD is a collaborative project aiming in deploying text and data mining tools to academic communities. Galaxy ahs been selected as the main tool to support workflows. The plan is to run Galaxy on GRNET ~okeanos infrastructure, use Pithos+ object storage as a storage backend and make it collaborate with docker-oriented tools like Mesos/Marathon or Docker Swarm on ~okeanos provisioned VMs. [1] https://www.synnefo.org [2] https://www.synnefo.org/docs/synnefo/latest/pithos.html [3] https://www.openminted.eu [4] https://www.grnet.gr [5] https://www.synnefo.org/docs/kamaki/latest/ Stavros Sachtouris Software Engineer @ www.grnet.gr

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Making symlinks in "command" section of tool XML
by Peter Briggs 19 Jan '17

19 Jan '17

Dear Developers I'm currently looking at develop a tool for a local pipeline, and want to make symlinks as part of the script in the "command" section of the tool XML - something like e.g. <command interpreter="bash"><![CDATA[ ## Create links to input FASTQs and Final_names.txt file #for $fq_pair in $fastq_pairs ln -s "${fq_pair.fastq_r1}" && ... #end for ... But when I try running the tool I get a failure with the message: Fatal error: Exit code 127 () bash: /PATH/TO/TOOL/DIR/ln: No such file or directory (NB I've snipped out the real path above, but essentially it's the directory where the tool XML is installed.) I know that it's permissible to use 'cp' and 'mv' in this context, so is 'ln' treated differently? Is there an alternative way to make symlinks in the command? Thanks for your help! Best wishes Peter -- Peter Briggs peter.briggs(a)manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482

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Nominate the training topics you want to see at GCC2017
by Olivier Inizan 19 Jan '17

19 Jan '17

Hello all, Training Day topics are nominated by you, the Galaxy Community. Please take a minute to nominate a topic. Any topic of interest to the Galaxy Community can be nominated and you are encouraged to nominate more than one topic. If you are looking for ideas, see the topic nominated in - 2016 bit.ly/gcc2016noms, - 2015 bit.ly/gcc2015vote, - 2014 bit.ly/1s6NtMN, - 2013bit.ly/1i2j1gN, - and the Galaxy Events page (new.galaxyproject.org/events/) The 2017 Galaxy Community Conference (GCC2017, gcc2017.sciencesconf.org) will be held 26-30 in Montpellier, France. It will feature two days of training: the first day will be single track focused on introducing Galaxy for bioinformatics analysis; the second day will feature multiple tracks spanning the breadth of Galaxy usage, admin, deployment, and tools. Nominated topics will be published on the GCC2017 Training page as they come in (gcc2017.sciencesconf.org/) Topic Nominations close 20 January. Topics will be compiled into a uniform list by GCC2017 organizers, and then voted on by the Galaxy Community starting one week later. You can nominate a topic now: https://t.co/DkOmqELY6h Olivier Inizan, On behalf of the GCC2017 Organizing Committee Olivier Inizan ------------------------------------------------ Merci de noter ma nouvelle adresse: olivier.inizan(a)inra.fr Unité de Recherches en Génomique-Info (UR INRA 1164), INRA, Centre de recherche de Versailles, bat.18 RD10, route de Saint Cyr 78026 Versailles Cedex, FRANCE Tél: +33 1 30 83 38 25 Fax: +33 1 30 83 38 99 http://urgi.versailles.inra.fr [urgi.versailles.inra.fr] Twitter: @OlivierInizan

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Fwd: Fwd: Usegalaxy.org Data Rsync Connection refused
by Christopher Previti 17 Jan '17

17 Jan '17

Dear all, I was wondering if anybody was able to get the rsync server datacache.g2.bx.psu.edu to work? Have there been non-documented changes? We still get following messages: rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/phiX . rsync: failed to connect to datacache.g2.bx.psu.edu (128.118.250.10): Connection refused (111) rsync error: error in socket IO (code 10) at clientserver.c(128) [Receiver=3.1.1] My colleague Georgios Nikolis and I are working on a local Galaxy installation at the DKFZ and would really like to use the pre-built indices. Cheers, Christopher Previti -------- Weitergeleitete Nachricht -------- Betreff: Fwd: [galaxy-dev] Usegalaxy.org Data Rsync Connection refused Datum: Tue, 13 Dec 2016 13:46:48 +0100 Von: Georgios Nikolis <g.nikolis(a)dkfz-heidelberg.de> An: Christopher Previti <christopher.previti(a)dkfz-heidelberg.de> *Georgios Nikolis* Genomics and Proteomics Core Facility High Throughput Sequencing (W190) IT Management Genomics Proteomics German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany phone: +49 6221 42-4659 g.nikolis(a)dkfz.de <http://www.dkfz.de/> www.dkfz.de <http://www.dkfz.de/> logo <http://www.dkfz.de> Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta VAT-ID No.: DE143293537 -------- Forwarded Message -------- Subject: [galaxy-dev] Usegalaxy.org Data Rsync Connection refused Date: Fri, 28 Oct 2016 15:23:14 +0200 From: Georgios Nikolis <g.nikolis(a)dkfz-heidelberg.de> To: galaxy-dev(a)lists.galaxyproject.org <galaxy-dev(a)lists.galaxyproject.org> Dear all, we are currently working on setting up a new local Galaxy installation and I would like to obtain the genome reference data available on the public Galaxy instance. I am following the instructions on the Wiki page (https://wiki.galaxyproject.org/Admin/UseGalaxyRsync) but I can't seem to be able to access datacache.g2.bx.psu.edu via rsync. rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/phiX . rsync: failed to connect to datacache.g2.bx.psu.edu (128.118.250.10): Connection refused (111) rsync error: error in socket IO (code 10) at clientserver.c(128) [Receiver=3.1.1] Does anyone know if the URL has changed in the meantime? Is there any alternative way to access this data? Thanks in advance! Best regards, Georgios -- *Georgios Nikolis* Genomics and Proteomics Core Facility High Throughput Sequencing (W190) IT Management Genomics Proteomics German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany phone: +49 6221 42-4659 g.nikolis(a)dkfz.de <http://www.dkfz.de/> www.dkfz.de <http://www.dkfz.de/> logo <http://www.dkfz.de> Management Board: Prof. Dr. Michael Boutros (interim), Prof. Dr. Josef Puchta VAT-ID No.: DE143293537

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Python script can't can't import BioPython modules in Galaxy 16.01
by Makis Ladoukakis 17 Jan '17

17 Jan '17

Hello everyone, I've recently upgraded to Galaxy 16.01 and i have some issues with a python wrapper from a tool. When I run it via Galaxy I get the following error: Traceback (most recent call last): File "/home/galaxy_user/galaxy/tools/myTools/know_parser/know_parser.py", line 12, in <module> from Bio import SeqIO ImportError: No module named Bio However when I click on the "view details" icon to copy the command from the tool and run it on my command line the tool works perfectly. In addition this issue occurs while I already have installed BioPython. When I type Python and write "from Bio import SeqIO" I get no error. Can this be an issue related to the virtual environment that is initialized each time Galaxy starts? Thank you in advance, Makis Ladoukakis

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Update Galaxy from 15.10 to 16.10
by Jochen Bick 17 Jan '17

17 Jan '17

Hi, today we tried to update from 15.10 to 16.10 which included an update of your database from 129 to 131. Do we necessary run into problem if we update from an one year old instance? How is the galaxy.ini updated? Or galaxy.ini does not know any conda yet. Thanks in advance. Cheers Jochen

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