January 2019 - galaxy-dev - lists.galaxyproject.org

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 19 Apr '19

19 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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[GSoC 2019] [Open Genome Informatics] Google Summer of Code 2019 Participation
by Robin Haw 11 Feb '19

11 Feb '19

Dear All, The Open Genome Informatics team serves as an “umbrella" organization to support the efforts of many open access open-source bioinformatics projects for Google Summer of Code (GSoC)<https://summerofcode.withgoogle.com/>. Among this list of projects are GMOD and its software projects -- GBrowse, JBrowse; Galaxy; Reactome; WormBase; DockStore; Bioconda; and others. Call for 2019 Project Ideas and Mentors: We are seeking project ideas to post and attract talented students to this year’s Summer of Code competition. If you have a project idea for which you would like to mentor a student, please contact Robin Haw, Marc Gillespie, Dave Clements, Dannon Baker, and Scott Cain (emails above). You can also submit your ideas here<http://gmod.org/wiki/GSOC_Project_Ideas_2019> or this online form<https://docs.google.com/forms/d/1uQlpsbPCnhNwO5OFKAB-IiY9DLWlmaHZATnaeP6KHhw>. For more information please refer to the Open Genome Informatics page<http://gmod.org/wiki/GSoC>. The mentoring organization application deadline with GSoC is February 6th, 2019 at 3 pm EST. So, if you are interested in taking part with the team please let us know as soon as possible. Please forward this to others who might be interested in taking part. If you have any questions please let us know. Thanks, Robin, Marc, Dave, Dannon, and Scott.

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Question using sftp to upload file to galaxy
by Rui Wang 06 Feb '19

06 Feb '19

Hey Folks, I'm looking at the instructions of using ftp with proftpd. There is a section talking about extending it to use sftp. However, the sample config isn't comprehensive. I'm wondering if anyone has a working config for reference? What's the setting of user and group? It says it should match the one in the SQLNamedQuery, what does it mean exactly? I start proftpd as root, but start galaxy as bioinfoadmin(normal user with sudo). Just fyi, my proftpd config module and config file are pasted below. I'm working it out on a trial and error fashion, please feel free to point out if anything is wrong! Cheers, Rui modules: $ sbin/proftpd -l Compiled-in modules: mod_core.c mod_xfer.c mod_rlimit.c mod_auth_unix.c mod_auth.c mod_ls.c mod_log.c mod_site.c mod_delay.c mod_facts.c mod_sql.c mod_sql_postgres.c mod_sql_passwd.c mod_sftp.c mod_cap.c etc/proftpd.conf ServerType standalone # You must put this in a virtual host if you want it to listen on its own port. VHost != Apache Vhost. <VirtualHost 10.3.17.42> Port 2222 SFTPEngine on AuthOrder mod_auth_unix.c mod_sql.c # If you don't do this you will get weird disconnects SFTPHostKey /etc/ssh/ssh_host_rsa_key RequireValidShell no MaxLoginAttempts 6 ServerName "Galaxy SFTP" DefaultServer on Umask 077 User bioinfoadmin Group bioinfoadmin UseFtpUsers off DefaultRoot ~ AllowOverwrite on AllowStoreRestart on SQLEngine on SQLGroupInfo sftp_groups name id members # Do not authenticate against real (system) users <IfModule mod_auth_pam.c> AuthPAM off </IfModule> # Common SQL authentication options SQLPasswordEngine on SQLBackend postgres SQLConnectInfo galaxy@galaxy.my.org:5432 bioinfoadmin dbpwd SQLAuthenticate users # Configuration that handles PBKDF2 encryption # Set up mod_sql to authenticate against the Galaxy database SQLAuthTypes PBKDF2 SQLPasswordPBKDF2 SHA256 10000 24 SQLPasswordEncoding base64 SQLPasswordUserSalt sql:/GetUserSalt # Define a custom query for lookup that returns a passwd-like entry. Replace 512s with the UID and GID of the user running the Galaxy server SQLUserInfo custom:/LookupGalaxyUser SQLNamedQuery LookupGalaxyUser SELECT "email, (CASE WHEN substring(password from 1 for 6) = 'PBKDF2' THEN substring(password from 38 for 69) ELSE password END) AS password2,512,512,'/media/galaxy/galaxy/database/ftp/%U','/bin/bash' FROM galaxy_user WHERE email='%U'" # Define custom query to fetch the password salt SQLNamedQuery GetUserSalt SELECT "(CASE WHEN SUBSTRING (password from 1 for 6) = 'PBKDF2' THEN SUBSTRING (password from 21 for 16) END) AS salt FROM galaxy_user WHERE email='%U'" </VirtualHost> # Don't use IPv6 support by default. UseIPv6 off MaxInstances 30 # To cause every FTP user to be "jailed" (chrooted) into their home # directory, uncomment this line. # Bar use of SITE CHMOD by default <Limit SITE_CHMOD> DenyAll </Limit> # Bar use of RETR (download) since this is not a public file drop <Limit RETR> DenyAll </Limit> ~

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Re: [galaxy-dev] [External] Copying files to FTP upload directory
by Keith Suderman 02 Feb '19

02 Feb '19

I have been creating directories for the users, but putting files in (for example) /home/galaxy/database/ftp/user(a)example.com <mailto:home/galaxy/database/ftp/user@example.com> does not make them available for the user(a)example.com <mailto:user@example.com> user in Galaxy. Also for the list admins... I never did see my message appear on the list and the message Cicada replied to appears to be from galaxy-dev-bounces(a)lists.galaxyproject.org <mailto:galaxy-dev-bounces@lists.galaxyproject.org>. Any ideas why my message(s) appear to be bouncing. I am pretty sure I am sending from the correct address. Cheers, Keith > On Jan 25, 2019, at 4:36 PM, Dennis, H. E. Cicada Brokaw <hbrokaw(a)iu.edu> wrote: > > I think you have to create the user's directories under /home/galaxy/database/ftp. I don't think Galaxy will create them if they are not there. > Cicada > > ________________________________________ > From: galaxy-dev <galaxy-dev-bounces(a)lists.galaxyproject.org> on behalf of Keith Suderman <suderman(a)cs.vassar.edu> > Sent: Friday, January 25, 2019 4:01 PM > To: Galaxy Dev List > Subject: [External] [galaxy-dev] Copying files to FTP upload directory > > Hello, > > I am trying to (ab)use the FTP file upload functionality to get data from an external service into Galaxy. From my reading of the docs I simply need to configure the ftp_upload_dir and ftp_upload_site in my galaxy.ini (haven't migrated to yaml yet) and Galaxy will expect to find subdirectories named after the user's account (email) in the ftp_upload_dir. > > I have configured the ftp_upload_dir (/home/galaxy/database/ftp in our case) and the "Choose FTP File" button is now available in the Upload dialog, however regardless of where I put files, or what I name them, Galaxy always reports that "Your FTP directory does not contain any files." For example, if I have the user account user(a)example.org I would expect to be able to place files in /home/galaxy/database/ftp/user(a)example.org and they will be available in the Upload dialog for the user(a)example.org user. However, this is not working; am I missing something? > > Thanks, > Keith > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/

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Bugfix for CollectRNAmetrics (Picardtools)
by Previti 29 Jan '19

29 Jan '19

Dear all, I just fixed a bug that prevented CollectRNAmetrics (a Picard-Tool, galaxy version 2.7.1) from working with GTF annotation files: The pre-processing step that converts gtf to the genepred format needs two extra parameters (marked red): gtfToGenePred -genePredExt -geneNameAsName2 'test.gtf' refFlat.tab.raw The format of my GTF is: Seqname Source Feature Start End Score Strand Frame Attributes 3R FlyBase gene 722370 722621 . - . gene_id "FBgn0085804"; gene_name "CR41571"; gene_source "FlyBase"; gene_biotype "pseudogene"; I'm assuming this is the "standard" GTF format (according to ensembl) How's the best way to make this type of thing known...? Cheers, 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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Vote Now: GCC2019 Training Topics
by Dave Clements 29 Jan '19

29 Jan '19

Hello all, The next 2019 Galaxy Community Conference (GCC2019) <https://galaxyproject.org/events/gcc2019/> will be in Freiburg (Germany) in July. This year the program is specifically aimed at drawing in more Galaxy end-users, including for training. We are really interested it what you would like to learn. *Please take a few minutes to decide <https://galaxyproject.org/events/gcc2019/training/#training-topic-votes> and then vote which training should be offered during GCC2019 <https://goo.gl/forms/iaY5AezdFpyJ0ETh2>! *If there is *any* chance that you will attend then we want to hear from you. *Topic voting closes 4 February.* The Training schedule, including instructors, will be published before early registration opens. GCC2019 <https://galaxyproject.org/events/gcc2019/> will be held 1-6 July in Freiburg, Germany. If you work in data-intensive biomedical research, there is no better place than GCC2019 to present your work and to learn from others. Thanks, and see you in Freiburg The GCC2019 Organizers <https://galaxyproject.org/events/gcc2019/organizers/> -- https://galaxyproject.org/ https://usegalaxy.org/

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Copying files to FTP upload directory
by Keith Suderman 26 Jan '19

26 Jan '19

Hello, I am trying to (ab)use the FTP file upload functionality to get data from an external service into Galaxy. From my reading of the docs I simply need to configure the ftp_upload_dir and ftp_upload_site in my galaxy.ini (haven't migrated to yaml yet) and Galaxy will expect to find subdirectories named after the user's account (email) in the ftp_upload_dir. I have configured the ftp_upload_dir (/home/galaxy/database/ftp in our case) and the "Choose FTP File" button is now available in the Upload dialog, however regardless of where I put files, or what I name them, Galaxy always reports that "Your FTP directory does not contain any files." For example, if I have the user account user(a)example.org I would expect to be able to place files in /home/galaxy/database/ftp/user(a)example.org and they will be available in the Upload dialog for the user(a)example.org user. However, this is not working; am I missing something? Thanks, Keith

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Input paired dataset collection in workflow
by Christopher Previti 24 Jan '19

24 Jan '19

Dear Galaxy Community, Is there a way to input a paired dataset collection into a workflow? I would like to build a workflow using cutadapt with a paired dataset collection but...I'm missing something. I have seen workflows (at usegalaxy.eu for example: 1_CLIPseq-Explorer_demulti_PEAKachu_iCLIP_hg19) where this is possible. But how is this done practically? Thanks and best regards, Christopher 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 42-4434 christopher.previti(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 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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usegalaxy.eu is hiring!
by Björn Grüning 13 Jan '19

13 Jan '19

Dear Friends, we have a wide variety of active projects and are searching for a software engineer (100%), system analysts/administrators (100%), data analyst (100%), and a community and/or research manager (100%). Read more at https://galaxyproject.eu/posts/2019/01/10/openpositions/ and join our team in Freiburg (Germany). Talk to you soon :) Björn, on behalf of the Freiburg Galaxy team

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Re: [galaxy-dev] Central German Galaxy User Group Meeting 2
by Matthias Bernt 09 Jan '19

09 Jan '19

Hi Kristian, > - Die <test>, <output tests> oder <assert_stdout> funktionieren nur für > ein einziges Tool? Genau. > Wenn man einen ganzen Workflow testen muss, dann kann > man das wie machen? Wir hatten dazu mal wft4galaxy benutzt, evtl. gibts > noch was besseres? Habe ich selber noch keine Erfahrung mit gemacht. Kannst zum Beispiel mal bei usegalaxy-eu schauen: https://github.com/usegalaxy-eu/workflow-testing/blob/master/.travis.yml https://github.com/usegalaxy-eu/workflow-testing/blob/master/run_galaxy_wor… die scheinen planemo zu nutzen. Waere mal eine passende Frage fuer galaxy-dev(a)lists.galaxyproject.org ... > - Erzeugt PLANEMO sowohl eine Galaxy-XML als auch CONDA-rules? Nein, nur das Galaxy xml. > - Wenn ich CONDA Regeln erzeuge, wie gelangt das automatisch nach > BIOCONTAINER? Wenn dein recipe in bioconda gemerged wurde wird automatisch ein container mit erzeugt .. soweit ich weiss. > - Hast du schon einmal von der Common Tool Description (CTD) gehört? > Damit kann man mit einer Tool-Beschreibung Tools für verschiedene > Workflow-Systeme erzeugen. Weißt du ob das mittlerweile gut funktioniert? Davon habe ich noch nichts gehoert. Kannst du mir mal einen link schicken - taete mich interessieren. Gruesse, Matthias > Viele Grüße, *Kristian > > >> On 7. Jan 2019, at 17:46 , Matthias Bernt <m.bernt(a)ufz.de >> <mailto:m.bernt@ufz.de>> wrote: >> >> Hi, >> >> wir werden versuchen zumindest den Vormittag per skype zu uebertragen. >> Am besten einfach mich (mbatle) ab ca 8:45 mal anschreiben. >> >> Gruesse, >> Matthias >> >> On 05.01.19 11:50, Peters, Kristian wrote: >>> Hallo Matthias, >>> Januar ist bei mir sehr gefüllt und es sind noch ein paar wichtige >>> Sachen oben drauf gekommen. Daher hatte ich mich vorsichtshalber >>> nicht in den Doodle eingetragen. Vielleicht ist es möglich, per >>> Telefonkonferenz (Hangout, Skype) remote teilzunehmen? Das würde mir >>> viel Zeit am Dienstag ersparen. >>> Viele Grüße, *Kristian >>>> On 4. Jan 2019, at 19:40 , Neumann, Steffen <sneumann(a)ipb-halle.de >>>> <mailto:sneumann@ipb-halle.de> <mailto:sneumann@ipb-halle.de>> wrote: >>>> >>>> Hi Matthias, >>>> >>>> ich habe die Koordination von einem grösseren Antrag geerbt, >>>> und werde daher am Dienstag nicht nach Leipzig kommen können :-( >>>> >>>> Kristian hat in den letzten Wochen ebenfalls >>>> an einem Workflow für MetFrag gearbeitet, >>>> zu dem wir bis jetzt PhenoMeNal packaging haben. >>>> >>>> Gruss, >>>> Steffen >>>> >>>> >>>> On Fri, 2019-01-04 at 18:46 +0100, Matthias Bernt wrote: >>>>> Dear all, >>>>> >>>>> our meeting (workshop on building Galaxy tools and conda packages) >>>>> will >>>>> take place next Tuesday (Feb 8th). Below we compiled the most >>>>> important >>>>> informations for you. Just write an email if you have any further >>>>> questions. >>>>> >>>>> We are currently expecting the eight participants who registered >>>>> here: >>>>> https://dudle.inf.tu-dresden.de/7yxdfay2/. Let me know if you >>>>> changed >>>>> you plans. >>>>> >>>>> The meeting will take place in the KUBUS (Tagungsbüro 131) at the >>>>> UFZ. >>>>> How to reach the UFZ is described here: >>>>> https://www.ufz.de/index.php?de=34272 The KUBUS is in front of the >>>>> UFZ. >>>>> So you don't need to enter through the main gate. >>>>> >>>>> Plan: >>>>> >>>>> - We will start at 9:00. >>>>> - For the morning we plan to introduce you to the basics of >>>>> - building tools for Galaxy with planemo and >>>>> - building conda packages >>>>> - For lunch there is a "Kantine" at the UFZ. >>>>> - In order to practice the learned topics we planned to use the >>>>> afternoon as a kind of hackaton where you can (start to) build >>>>> your own Galaxy tool or conda package. We will be there for >>>>> questions >>>>> and introduce advanced topics as needed. >>>>> >>>>> Therefore it would be great if you 'bring' a tool of your choice, >>>>> eg >>>>> your own tool for wrapping, this could be e.g. a shell, R, or >>>>> python >>>>> script or some software package that can be compiled. >>>>> >>>>> In case that you don't have an idea we have prepared one or two >>>>> examples. >>>>> >>>>> Important: >>>>> >>>>> Since some of the required software is quite large we would like to >>>>> ask you to prepare a few things if possible (at least the first >>>>> point). >>>>> >>>>> 1. You will need a linux command line >>>>> >>>>> If your laptop runs Windows you could install VirtualBox and install >>>>> a >>>>> linux in this box. Linux images for VirtualBox that are ready to use >>>>> are >>>>> available, eg. >>>>> https://www.osboxes.org/ubuntu/#ubuntu-1804-vbox >>>>> >>>>> 2. Download and prepare the bioconda recipes repository >>>>> >>>>> - optional: create a fork of >>>>> https://github.com/bioconda/bioconda-recipes >>>>> - clone your fork or the main repository, i.e. either `git clone >>>>> https://github.com/USERNAME/bioconda-recipes` (replace USERNAME) or >>>>> `git >>>>> clone https://github.com/bioconda/bioconda-recipes` >>>>> >>>>> (see >>>>> >>>> https://bioconda.github.io/contrib-setup.html#git-and-github-one-time-setup >>>>> ) >>>>> >>>>> In the bioconda-recipes root directory call: >>>>> >>>>> ``` >>>>> ./bootstrap.py TEMPORARY_PATH_TO_WHERE_MINICONDA_SHOULD_BE_INSTALLED >>>>> ``` >>>>> >>>>> Replace TEMPORARY_PATH_TO_WHERE_MINICONDA_SHOULD_BE_INSTALLED with >>>>> some >>>>> path where miniconda can be installed. >>>>> >>>>> (see https://bioconda.github.io/contribute-a-recipe.html#test-locally >>>>> ) >>>>> >>>>> 3. Prepare planemo and Galaxy >>>>> >>>>> Install `planemo` via pip or conda as described here: >>>>> >>>>> (see https://planemo.readthedocs.io/en/latest/installation.html) >>>>> >>>>> Get a copy of the Galaxy sources: >>>>> >>>>> ``` >>>>> git clone -b release_18.09 >>>>> https://github.com/galaxyproject/galaxy.git >>>>> ``` >>>>> >>>>> We are looking forward to see you on Tuesday. >>>>> >>>>> Best, >>>>> Joerg and Matthias >>>>> >>>>> >>>>> >>>>> On 04.12.18 10:31, Matthias Bernt wrote: >>>>>> Dear all, >>>>>> >>>>>> we will meet on 8th of January at the UFZ in Leipzig. I reserved a >>>>>> room >>>>>> for 10 people (Tagungsbüro 131 KUBUS). There are still some places >>>>>> free, >>>>>> if you want to come and did not fill the dudle yet (or if you were >>>>>> unsure) I would like to ask you to add yourself -- in order to >>>>>> keep >>>>>> track on the number of attendees. >>>>>> >>>>>> We will send directions and all necessary informations before the >>>>>> meeting. >>>>>> >>>>>> Looking forward to see you. >>>>>> >>>>>> Cheers, >>>>>> Matthias >>>>>> >>>>>> >>>>>> On 30.11.18 15:56, Matthias Bernt wrote: >>>>>>> Gentle reminder to fill the dudle :) Currently we have only >>>>>>> three >>>>>>> entries. >>>>>>> >>>>>>> Cheers, >>>>>>> Matthias >>>>>>> >>>>>>> On 26.11.18 13:44, Matthias Bernt wrote: >>>>>>>> Dear all, >>>>>>>> >>>>>>>> since there was only little feedback on the last survey I will >>>>>>>> start >>>>>>>> another try to schedule the 2nd CGGUG meeting. The idea is to >>>>>>>> have a >>>>>>>> workshop on building Galaxy tools and conda packages (of course >>>>>>>> there >>>>>>>> will be also sufficient time for other discussions on the >>>>>>>> administration or use of Galaxy). >>>>>>>> >>>>>>>> Please fill in here until the end of the November: >>>>>>>> >>>>>>>> https://dudle.inf.tu-dresden.de/7yxdfay2/ >>>>>>>> >>>>>>>> Our preference would be the 17th in December :) >>>>>>>> >>>>>>>> Best, >>>>>>>> Matthias >>>>>>>> >>>>>>>> >>>>>>>> On 30.08.18 12:53, Matthias Bernt wrote: >>>>>>>>> Dear all, >>>>>>>>> >>>>>>>>> Joerg Fallman and myself agreed on a week early in December >>>>>>>>> for the >>>>>>>>> next meeting that will take place in Leipzig (at UFZ or >>>>>>>>> Bioinformatics@Uni-Leipzig): >>>>>>>>> >>>>>>>>> Feel free to mark preferred dates here: >>>>>>>>> >>>>>>>>> https://dudle.inf.tu-dresden.de/cggug2-date/ >>>>>>>>> >>>>>>>>> We will keep you posted. >>>>>>>>> >>>>>>>>> Best, >>>>>>>>> Matthias >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> On 22.08.2018 14:32, Matthias Bernt wrote: >>>>>>>>>> Dear all, >>>>>>>>>> >>>>>>>>>> it has been a while since our last meeting in Halle and we >>>>>>>>>> have >>>>>>>>>> thought about reanimating the meeting here in Leipzig >>>>>>>>>> (hopefully in >>>>>>>>>> September). >>>>>>>>>> >>>>>>>>>> Since building Galaxy tools and conda packages seemed to be >>>>>>>>>> topics >>>>>>>>>> that are of interest for many of you Joerg Fallmann, >>>>>>>>>> Stephanie >>>>>>>>>> Kehr, and myself thought that we could give a little >>>>>>>>>> workshop on at >>>>>>>>>> least one of these topics. >>>>>>>>>> >>>>>>>>>> If you are interested then just check one of the options or >>>>>>>>>> leave a >>>>>>>>>> comment here: https://dudle.inf.tu-dresden.de/cggug2/ >>>>>>>>>> >>>>>>>>>> We will try to find a date and room as soon as we have an >>>>>>>>>> approximate number of participants (poll will close on 29th >>>>>>>>>> of >>>>>>>>>> September). >>>>>>>>>> >>>>>>>>>> Best, >>>>>>>>>> Matthias >>>>>>>>>> >>>>> >>>>> >>>> -- >>>> >>>> IPB Halle AG Massenspektrometrie & Bioinformatik >>>> Dr. Steffen Neumann http://www.IPB-Halle.DE >>>> Weinberg 3 Tel. +49 (0) 345 5582 - 1470 >>>> 06120 Halle +49 (0) 345 5582 - 0 >>>> sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 >>> Dr. Kristian Peters >>> IPB-Halle, AG Massenspektrometrie & Bioinformatik >>> Weinberg 3 >>> 06120 Halle (Saale) >>> kpeters[at]ipb-halle.de <http://ipb-halle.de> <http://ipb-halle.de> >>> Tel. +49 (0)345 5582 1475 >>> Fax. +49 (0)345 5582 1409 >> >> -- >> >> ------------------------------------------- >> 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 <mailto:m.bernt@ufz.de>, www.ufz.de <http://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. Dr. h.c. Georg Teutsch >> ------------------------------------------- > > Dr. Kristian Peters > IPB-Halle, AG Massenspektrometrie & Bioinformatik > Weinberg 3 > 06120 Halle (Saale) > kpeters[at]ipb-halle.de <http://ipb-halle.de> > Tel. +49 (0)345 5582 1475 > Fax. +49 (0)345 5582 1409 > > -- ------------------------------------------- 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 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. Dr. h.c. Georg Teutsch -------------------------------------------

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sorry
by Matthias Bernt 08 Jan '19

08 Jan '19

Dear all, sorry for the last post .. accident. But it actually contained an interesting question: What are currently good approaches for testing workflows? Cheers and sorry again :(, 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 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. Dr. h.c. Georg Teutsch -------------------------------------------

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run.sh problem
by Matthias Bernt 08 Jan '19

08 Jan '19

Dear all, a colleague tries to run.sh on a Manjaro Linux and got the following error: ``` yarn run v1.12.3 $ NODE_ENV=production gulp staging && concurrently "yarn run style" "yarn run webpack-production-maps" "yarn run gulp clean && yarn run gulp-production-maps" && yarn run save-build-hash gulp[12888]: ../src/node_contextify.cc:628:static void node::contextify::ContextifyScript::New(const v8::FunctionCallbackInfo<v8::Value>&): Assertion `args[1]->IsString()' failed. 1: 0x8daaa0 node::Abort() [gulp] 2: 0x8dab75 [gulp] 3: 0x90e2f7 node::contextify::ContextifyScript::New(v8::FunctionCallbackInfo<v8::Value> const&) [gulp] 4: 0xb5e71b [gulp] 5: 0xb606b2 v8::internal::Builtin_HandleApiCall(int, v8::internal::Object**, v8::internal::Isolate*) [gulp] 6: 0x6f20bcdbe1d /tmp/yarn--1546955496175-0.8677740791371564/node: line 3: 12888 Aborted (core dumped) "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/.venv/bin/node" "$@" error Command failed with exit code 134. info Visit https://yarnpkg.com/en/docs/cli/run for documentation about this command. ERROR: Galaxy client build failed. See ./client/README.md for more information, including how to get help. Problem running Galaxy command []. Traceback (most recent call last): File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/bin/planemo", line 11, in <module> sys.exit(planemo()) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py", line 764, in __call__ return self.main(*args, **kwargs) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py", line 717, in main rv = self.invoke(ctx) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py", line 1137, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py", line 956, in invoke return ctx.invoke(self.callback, **ctx.params) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py", line 555, in invoke return callback(*args, **kwargs) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/decorators.py", line 64, in new_func return ctx.invoke(f, obj, *args, **kwargs) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py", line 555, in invoke return callback(*args, **kwargs) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/planemo/cli.py", line 195, in handle_blended_options return f(*args, **kwds) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/planemo/commands/cmd_serve.py", line 43, in cli galaxy_serve(ctx, runnables, **kwds) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/planemo/galaxy/serve.py", line 22, in serve return _serve(ctx, runnables, **kwds) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/planemo/galaxy/serve.py", line 54, in _serve raise Exception(message) Exception: Problem running Galaxy command []. ``` Would be great to have a suggestion... 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 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. Dr. h.c. Georg Teutsch -------------------------------------------

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Forgotten password
by Dalibor Miklík 07 Jan '19

07 Jan '19

Hello, recently I tried to login to my Galaxy account but, obviously, I forgot my password and I can't reset it because I didn't receive any email from the webpage. Can you please help me? Best regards Dalibor Miklik

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January 2019 Galactic News: Events (Admin Training, PAG, GSOC, GCC, GalaxyAdmins), Platforms, Pubs, Jobs, COTM!, Doc, Training, Tools, Releases and more!
by Mo Heydarian 04 Jan '19

04 Jan '19

Hello All, Happy New Year! The *January 2019 Galactic News* is here! This is a summary of what is going on in the Galaxy community. Here's what's happening: - Event News <https://galaxyproject.org/news/2019-01-galaxy-update/#event-news> - 2019 Galaxy Admin Training: Registration is still open! <https://galaxyproject.org/news/2019-01-galaxy-update/#2019-galaxy-admin-tra…> - Training topic nomination for GCC2019 Training extended through 15 January! <https://galaxyproject.org/news/2019-01-galaxy-update/#gcc2019-training-topi…> - Galaxy will be at the 2019 Plant and Animal Genome (PAG) conference <https://galaxyproject.org/news/2019-01-galaxy-update/#galaxy-pag-2019> - Galaxy needs your Google Summer of Code Project suggestions <https://galaxyproject.org/news/2019-01-galaxy-update/#galaxy-needs-your-goo…> - And GalaxyAdmins needs your topic suggestions <https://galaxyproject.org/news/2019-01-galaxy-update/#galaxyadmins-needs-yo…> - 80 new publications <https://galaxyproject.org/news/2019-01-galaxy-update/#publications>, including several spectacular ones - Some most excellent Galaxy Platform News <https://galaxyproject.org/news/2019-01-galaxy-update/#galaxy-platforms-news>, including the *EGI Marketplace*. - The Contributor of the Month is ... Simon Gladman <https://galaxyproject.org/news/2019-01-galaxy-update/#new-galactic-blog-pos…> ! - 17 Open positions <https://galaxyproject.org/news/2019-01-galaxy-update/#whos-hiring> in 6 countries on 3 continents. - Doc, Hub, and Training Updates <https://galaxyproject.org/news/2019-01-galaxy-update/#doc-hub-and-training-…> covering RNA-Seq visualizations, BlockClust, cloud storage, cancer proteogenomics, and some introductory videos - ToolShed contributions <https://galaxyproject.org/news/2019-01-galaxy-update/#toolshed-contributions> - New releases <https://galaxyproject.org/news/2019-01-galaxy-update/#releases>: - Tripal Galaxy - connect Galaxy to your online database - BioBlend - a Python API for Galaxy and CloudMan - Planemo - utilities for building tools for Galaxy - And a bunch of other news <https://galaxyproject.org/news/2019-01-galaxy-update/#other-news> too See the newsletter for all of the details! Thanks for using Galaxy! Cheers, Mo Heydarian, on behalf of Galaxy

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