- galaxy-dev - lists.galaxyproject.org

Trying to understand python dependencies
by Tony Schreiner 28 Jul '16

28 Jul '16

I have galaxy server 15.10 running on Ubuntu 14.04, which has python 2.7.5. I was in the process of adding matplotlib from the toolchest. It has a dependency on package_python_2_7. Before proceeding, I'd like to understand a bit how that works. Does that install a whole new python, and how then does it get invoked? Tony Schreiner

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Password Parameter Opinions
by Katherine Beaulieu 28 Jul '16

28 Jul '16

Hi Everyone, I know this is sort of a controversial topic so I will try to tread lightly. It seems that for a couple of years the idea of a password parameter for Galaxy tools has come up a lot but has also been rejected a lot although I believe there is a lot of merit to it. I have found at least two other times where people have tried to implement this and it was rejected, but there must have been a reason why they needed that parameter. My situation currently is that I have created two tools in Galaxy which communicate with another software called iRODS which needs authentication from the user. In my own department, there is another tool that was created which needed authentication from the user but the developer had to create some other workaround for this problem. In terms of the work I have done for this so far, I have been working off the latest release version of Galaxy. I have implemented the field so that it is obfuscated in the tool form view as well as on the tool info page. I will next be looking into storing the parameter in an environment variable so it doesn't get passed through the command line and encrypting the password before it enters the database. Speaking with a co-worker of mine, we discussed the possibility of implementing two option, irreversible encryption of the password as it gets entered into the database but then making the tool not workflow compatible, or using regular encryption and making the tool workflow compatible. I look forward to hearing your opinions and ideas. Katherine

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TestToolShed down?
by Peter Cock 28 Jul '16

28 Jul '16

Hello all, The main Tool Shed seems fine, but the Test Tool Shed is not: https://testtoolshed.g2.bx.psu.edu/ > Galaxy > > The Tool Shed could not be reached > > You are seeing this message because a request to the > Tool Shed timed out or was refused. This may be a temporary > issue which could be resolved by retrying the operation you > were performing. If you receive this message repeatedly or > for an extended amount of time, please report it to the > Galaxy Team at galaxy-bugs(a)bx.psu.edu with details on > what you were trying to do and the URL in the address bar. > More information on the current state of Galaxy services > may be available on the Galaxy status page or the > @galaxyproject Twitter feed. The https://status.galaxyproject.org/ page reports it should be operational. It responds to ping (same server name and IP address as the main Tool Shed): $ ping -c 4 testtoolshed.g2.bx.psu.edu PING radegast.galaxyproject.org (128.118.250.5) 56(84) bytes of data. 64 bytes from radegast.galaxyproject.org (128.118.250.5): icmp_seq=1 ttl=45 time=130 ms 64 bytes from radegast.galaxyproject.org (128.118.250.5): icmp_seq=2 ttl=45 time=129 ms 64 bytes from radegast.galaxyproject.org (128.118.250.5): icmp_seq=3 ttl=45 time=129 ms 64 bytes from radegast.galaxyproject.org (128.118.250.5): icmp_seq=4 ttl=45 time=129 ms --- radegast.galaxyproject.org ping statistics --- 4 packets transmitted, 4 received, 0% packet loss, time 3133ms rtt min/avg/max/mdev = 129.744/129.955/130.358/0.348 ms $ ping -c 4 toolshed.g2.bx.psu.edu PING radegast.galaxyproject.org (128.118.250.5) 56(84) bytes of data. 64 bytes from radegast.galaxyproject.org (128.118.250.5): icmp_seq=1 ttl=45 time=130 ms 64 bytes from radegast.galaxyproject.org (128.118.250.5): icmp_seq=2 ttl=45 time=129 ms 64 bytes from radegast.galaxyproject.org (128.118.250.5): icmp_seq=3 ttl=45 time=129 ms 64 bytes from radegast.galaxyproject.org (128.118.250.5): icmp_seq=4 ttl=45 time=130 ms --- radegast.galaxyproject.org ping statistics --- 4 packets transmitted, 4 received, 0% packet loss, time 3135ms rtt min/avg/max/mdev = 129.785/129.977/130.196/0.179 ms Peter

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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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