galaxy-dev July 2016

galaxy-dev@lists.galaxyproject.org

49 participants
69 discussions

workflow problems
by Cristel Thomas 28 Jul '16

28 Jul '16

Hi all, I ran into a weird behavior on my local instance of galaxy and I was wondering if anyone had the same experience (and if so what did you do to fix it?). When trying to run a workflow by clicking on the workflow name, it works. When trying to run the workflow by clicking on the arrow next to the name and then 'run', or by clicking on run from the workflow editor, it takes me to the interactive tour page. Anyone else? Thanks, Cris

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Info Page after tool execution
by Katherine Beaulieu 27 Jul '16

27 Jul '16

Hello Galaxy Community, Does anyone know what file would be responsible for creating the info page after the execution of a tool? This is the page you access after output has been created in the history, by clicking on the little 'i' icon. Thanks!

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Papers that cite Galaxy workflows
by Steve Cassidy 26 Jul '16

26 Jul '16

Hi all, I’m writing a paper that will include some evangelism for Galaxy in language sciences and I’d like to be able to cite examples of papers in the Bio field that cite Galaxy workflows. Even better would be the re-use of a Galaxy workflow cited in another paper. Does anyone have any good example papers they could refer me to. Thanks, Steve — Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy

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DOS attack launched from our Galaxy instance
by Suderman Keith 26 Jul '16

26 Jul '16

We are in the process of installing a Galaxy instance to Amazon EC2 and this morning I received an email from ec2-abuse(a)amazon.com saying that our EC2 instance has been flooding 45.64.64.40 with data in what looks like a DOS attack. A whois shows that the IP belongs to Incapsula, which appears to be a load balancing proxy server. Does anyone here recognize the IP or use Incapsula? My first thought is that something in Galaxy might be trying to "phone home". The Galaxy instance we are using is based on the galaxy-stable:16.04 Docker image from Björn with a few of our tools installed for testing. I've locked down access to the instance until I figure out what happened and I wanted to check in here first to see if I’ve been DOS’ing the Galaxy infrastructure or if anyone recognizes the IP address. Keith ------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY

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Fwd: Immersive Approaches to Biological Data Visualization CSHL Course December 2016
by James Taylor 26 Jul '16

26 Jul '16

Hello all, As many of you are interested in visualization I wanted to draw your attention to this NEW course on biological data visualization at Cold Spring Harbor, which is being led by some of our colleagues at the Texas Advanced Computing Center (who provide substantial support for Galaxy main). It will be very interesting to think about how immersive visualizations can be implemented in Galaxy in the future. -- jt ---------- Forwarded message ---------- From: Cold Spring Harbor Laboratory <meetmail(a)cshl.edu> Date: Tue, Jul 12, 2016 at 9:02 AM Subject: Immersive Approaches to Biological Data Visualization CSHL Course December 2016 To: james(a)jamestaylor.org <http://r20.rs6.net/tn.jsp?f=001KDLtFLPEpFJ3qaBaXgqiU3PiLHpGUgM6M05LbOYM3ePe…> <http://r20.rs6.net/tn.jsp?f=001KDLtFLPEpFJ3qaBaXgqiU3PiLHpGUgM6M05LbOYM3ePe…> Immersive Approaches to Biological Data Visualization <http://r20.rs6.net/tn.jsp?f=001KDLtFLPEpFJ3qaBaXgqiU3PiLHpGUgM6M05LbOYM3ePe…> December 1 - 10, 2016 *Applications due: August 15* *Instructors* *Kelly Gaither,* Texas Advanced Computing Center *Matthew Vaughn,* Texas Advanced Computing Center This course will explore the new frontier of immersive, interactive scientific visualization. It is aimed at researchers who wish to design and implement innovative visualization tools to help address biological or biomedical research questions. As part of their research programs, course participants will ideally have a need to visualize genomic or systems biology data, anatomical structures and models, scientific simulations, and/or other domains that generate complex, multidimensional, and often very large data sets. Through a combination of detailed lectures and intensive hands-on computing exercises led by course instructors, students will learn the principles of information and scientific visualization. However, rather than relying on simplified representations of complex data, students will learn these visualization principles within the newly emerging context of immersive augmented and virtual reality. They will work with tools such as Unity 3D and Blender, as well as scripting environments such as Bash and Python, to craft data visualizations using the Oculus Rift <http://r20.rs6.net/tn.jsp?f=001KDLtFLPEpFJ3qaBaXgqiU3PiLHpGUgM6M05LbOYM3ePe…> virtual reality headset and Leap Motion <http://r20.rs6.net/tn.jsp?f=001KDLtFLPEpFJ3qaBaXgqiU3PiLHpGUgM6M05LbOYM3ePe…> gesture sensor. Students will apply the concepts and techniques covered in class exercises to create an independent virtual reality data visualization project. Additionally, the hands-on training will be supplemented by guest lectures from some of the leading experts working in data visualization today. *Selected Major Topics* - Overview of Scientific Visualization - Perception & Color - Information Visualization - Scientific Visualization - Importing Scientific Data into an Immersive Visualization Framework - Tool Development Using Oculus and Leap Motion *Invited Speakers* *Min Chen,* Oxford University, U.K. *David Ebert,* Purdue University School of Electrical & Computer Engineering *Robert Kosara,* Tableau Software, Inc. *Brian McCann,* Texas Advanced Computing Center *Mariah Meyer,* University of Utah *Hanspeter Pfister,* Harvard University School of Engineering & Applied Sciences *Amitabh Varshney,* University of Maryland College Park Please click this link to go to the Immersive Approaches to Biological Data Visualization course website for more info. <http://r20.rs6.net/tn.jsp?f=001KDLtFLPEpFJ3qaBaXgqiU3PiLHpGUgM6M05LbOYM3ePe…> www.cshl.edu/meetings <http://r20.rs6.net/tn.jsp?f=001KDLtFLPEpFJ3qaBaXgqiU3PiLHpGUgM6M05LbOYM3ePe…> Cold Spring Harbor Laboratory Meetings & Courses | 1 Bungtown Road Cold Spring Harbor, 11724 Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11743 SafeUnsubscribe™ james(a)jamestaylor.org <http://visitor.constantcontact.com/do?p=un&m=001S3f9XM7Br7nKhcnZ-APDwA%3D%3…> Forward this email <http://ui.constantcontact.com/sa/fwtf.jsp?llr=6zadfgnab&m=1113676940093&ea=…> | Update Profile <http://visitor.constantcontact.com/do?p=oo&m=001S3f9XM7Br7nKhcnZ-APDwA%3D%3…> | About our service provider <http://www.constantcontact.com/legal/service-provider?cc=about-service-prov…> Sent by meetmail(a)cshl.edu

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Problem with samtools dependencies
by Raymond Wan 26 Jul '16

26 Jul '16

Dear all, I've been having some problems with some tool dependencies. With most of them, after a few iterations of uninstall and install, the problem seems to go away. (I'm not too sure about the reason as I didn't take good notes while working out the problem to determine what I finally did right.) However, I'm having a problem with samtools that differs from the samtools problem I had a few months ago (about the system's version of samtools being out of date). Both package_samtools_1_1 and package_samtools_1_2 seem to have the similar problem. For example, with package_samtools_1_2, I see this: ----- Missing repository dependencies: package_ncurses_5_9 5e1760c773ba iuc Uninstalled, missing tool dependencies Installed repository dependencies: package_zlib_1_2_8 63a4a902cda2 iuc Installed package_ncurses_5_9 335ebf512407 iuc Installed ----- I don't quite understand why package_ncurses_5_9 appears twice with two different versions. Is this a problem with something I did on my system? For package_samtools_1_1, package_ncurses_5_9 (5e1760c773ba) is also missing. But under "Installed tool dependencies", ncurses 5.9 is Installed. Does anyone have an idea of what I could do to resolve this? As an aside, can someone explain the difference between the owner "iuc" and "devteam"? I did find https://wiki.galaxyproject.org/IUC, but couldn't find a description of devtools. I have two versions of package_samtools_0_1_19 installed -- one from iuc and the other from devteam. Is it fine to leave this alone? Thank you! Ray

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This job failed for reasons that could not be determined.
by Ulf Schaefer 26 Jul '16

26 Jul '16

Hi all Certain jobs fail on my cloud Galaxy instance with the error message in the subject line. No stderr or stdout is produced by the tool, at least it's not accessible from Galaxy. However the data seems to be there, in so far that I can view it (clicking on the eye) and download it using the floppy disk icon. The only thing I see (repeatedly) in my Galaxy logs is this: ---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 46619) Traceback (most recent call last): File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 1085, in process_request_in_thread self.finish_request(request, client_address) File "/usr/lib/python2.7/SocketServer.py", line 334, in finish_request self.RequestHandlerClass(request, client_address, self) File "/usr/lib/python2.7/SocketServer.py", line 657, in __init__ self.finish() File "/usr/lib/python2.7/SocketServer.py", line 716, in finish self.wfile.close() File "/usr/lib/python2.7/socket.py", line 283, in close self.flush() File "/usr/lib/python2.7/socket.py", line 307, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe ---------------------------------------- Does this look familiar to anyone? Thanks very much for any input Ulf ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE **************************************************************************

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cannot extract genomic dna
by Alexandre Maucuer 25 Jul '16

25 Jul '16

Hi, I've installed a Galaxy instance on a local machine under ubuntu 16.04. I am trying to fetch sequences from hg19.2bit I downloaded from ucsc as ~/galaxy/depot/data2/galaxy/hg19$hg19.bit I added: hg19 /depot/data2/galaxy/hg19/hg19.2bit to my twobit.loc file in tool-data directory When running the extract genomic dna, I get the error: "No sequences are available for 'hg19', request them by reporting this error." see also attached screenshot Thanks in advance for your help -- Alexandre Maucuer, Ph.D., INSERM, France

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switching from Apache to "auth_conf" to handle external user authentication via LDAP
by Hans-Rudolf Hotz 25 Jul '16

25 Jul '16

Dear all Our production server uses Apache to handle external user authentication. I have now set up a new test server (16.04) which handles external user authentication via LDAP using the auth_conf file. This works nicely when using an empty database (I have managed to solve all last weeks problems). I have now connected my test server to a copy of the PostgreSQL database used on our production server. I try to log in, and I get: "This account was created for use with an external authentication method, contact...) and the login fails. If I now set external = 'f' in the galaxy_user table, it works Since manually modifying the database is a bad thing, I just want to double check, whether this is the right way to do it? If so, I will add a line or two to the wiki Many thanks for your help Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland

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activate authentication through LDAP using the auth_conf file
by Hans-Rudolf Hotz 22 Jul '16

22 Jul '16

Dear all I am looking into authentication through LDAP using the auth_conf file (we are currently using Apache to handle this). And it looks like, I am stuck at a very early step: I have started with a fresh checkout of release 16.04 (git clone -b master https://github.com/galaxyproject/galaxy.git) some modifications in galaxy.ini (host, port) and: auth_config_file = config/auth_conf.xml I start galaxy, and I try to login. In the log file I get: galaxy.webapps.galaxy.controllers.user DEBUG 2016-07-22 12:41:50,741 trans.app.config.auth_config_file: ./config/auth_conf.xml galaxy.auth.providers.ldap_ad DEBUG 2016-07-22 12:41:50,741 LDAP authenticate: email is hansrudolf.hotz(a)fmi.ch galaxy.auth.providers.ldap_ad DEBUG 2016-07-22 12:41:50,741 LDAP authenticate: .... This is what I expect...so far so good but further down, I get: galaxy.auth.providers.ldap_ad DEBUG 2016-07-22 12:41:50,742 LDAP authenticate: could not load ldap module According to our sysadmin, "python-ldap" is installed on the machine (running Red Hat 7.2). But I assume, it has to be within the galaxy created virtual env, hasn't-it? Hence I have tried the following cd <galaxy-root> . .venv/bin/activate pip install python-ldap Is this the right way to do it? Doing this, I have been running into the following error: Modules/errors.h:8:18: fatal error: lber.h: No such file or directory #include "lber.h" So I guess I have to tell my sysadmin to install "openldap-devel in order to have 'lber.h' on the system? Or do I have to do something else? Thank you very much for your help Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland

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galaxy-dev July 2016