galaxy-dev February 2017

galaxy-dev@lists.galaxyproject.org

40 participants
52 discussions

Shared Data Library, large number of files
by D K 01 Mar '17

01 Mar '17

Hi, I've noticed that the more files / folders (think hundreds of folders each with 20+ fastq files) I add to a Shared Data Library, the longer and longer it takes to initially navigate the folder structure (after clicking on the specific Shared Data Library). Just opening up the Shared Data Library can take several minutes and often the browser times out. Is there a way to speed this up? If it's relevant, when I add shared data, it's linked rather than copied into Galaxy. Any suggestions would be greatly appreciated Thanks!

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Galaxy and Torque
by Yip, Miu ki 28 Feb '17

28 Feb '17

Hi all, Is Torque still supported as a resource manager? This page ( https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster ) mentioned the usage of Torque and how to set it up. However, the setup instructions refer to a /script/scramble.py file which I assume interfaces with eggs. If I recall correctly, eggs were upgraded to wheels. Does this mean there are upgraded scripts in place of scramble.py and the eggs.ini? I saw this page ( https://biostar.usegalaxy.org/p/20470/ ) and it looks like nobody has a solution to this. Thanks!

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Re: [galaxy-dev] Execute command once job has completed
by Peter Cock 28 Feb '17

28 Feb '17

I do not believe that is possible (nor desirable in general, not everyone will need or want the converted file and the overhead that comes with creating and storing it). What do you want to do with the bigwig file, and is the automatic conversion working for you? i.e. If you have tool X in Galaxy which wants an bigwig input file, does Galaxy offer an automated conversion of your bedgraph file as an input in the drop down file list? Peter On Tue, Feb 28, 2017 at 5:27 PM, evan clark <eclark28(a)fau.edu> wrote: > By automatic I mean that once any bedgraph file is finished writing it will > automatically run the convert to bigwig command > > > Peter Cock > February 28, 2017 12:21 PM > It depends on what you mean by automatic. You could > create a Galaxy Workflow where a tool is run which > generates the bedgraph file, and then as the next > step it is converted to bigwig. > > For this specific task, it might be possible to exploit > the Galaxy datatype definition for bedgraph to allow > automatic conversion to bigwig - is this working for you? > > https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/conve… > > Peter > evan clark > February 28, 2017 11:47 AM > Is there a method to setup a command to run depending on the filetype of a > job. Essentially I want to setup a task where everytime a bedgraph file is > generated it will either automatically start a new job and convert it to > bigwig or, within the same job file it will convert the bedgraph to bigwig. > >

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Execute command once job has completed
by evan clark 28 Feb '17

28 Feb '17

Is there a method to setup a command to run depending on the filetype of a job. Essentially I want to setup a task where everytime a bedgraph file is generated it will either automatically start a new job and convert it to bigwig or, within the same job file it will convert the bedgraph to bigwig.

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Issue when using xsendfile with galaxy release_16.07
by SAPET, Frederic 28 Feb '17

28 Feb '17

Hello I'm trying the latest Galaxy (git status gives me : # On branch release_16.07) I've set the xsend option in galaxy.ini (in order to run Galaxy behind a web server proxy, and apply all methods described here : https://wiki.galaxyproject.org/Admin/Config/ApacheProxy) apache_xsendfile = True HTML, gff3,tabular files are just fine but the preview of some other files (txt, csv) is broken on the interface. When I want to preview a txt file : Not Found The requested URL /datasets/fd1df6a9052810d5/display/ was not found on this server. And apache says : [Thu Aug 18 15:33:48 2016] [error] [client 192.168.29.12] (13)Permission denied: xsendfile: cannot open file: /softs/bioinfo/galaxy-prod/database/files/000/dataset_19.dat, referer: http: But it looks like this is not really a problem related to access. Indeed, from the same file, I switch it from txt to tabular (edit attributes), the preview works. Are you able to reproduce the behavior ? The same problem occurs on release_16.01. It's fine with the release v15.05 which is my production server right now. Fred

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migratting to Galaxy new realease error
by Mohamed Kassam 24 Feb '17

24 Feb '17

Dear all, I have migrate my old version of Galaxy to the new release V17.01, And I am facing this error when I am running run.sh, any clue ? Installing collected packages: python-ldap Found existing installation: python-ldap 2.4.17 DEPRECATION: Uninstalling a distutils installed project (python-ldap) has been deprecated and will be removed in a future version. This is due to the fact that uninstalling a distutils project will only partially uninstall the project. Can't uninstall 'python-ldap'. No files were found to uninstall. Can't roll back python-ldap; was not uninstalled Exception: Traceback (most recent call last): File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/basecommand.py", line 215, in main status = self.run(options, args) File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/commands/install.py", line 342, in run prefix=options.prefix_path, File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/req/req_set.py", line 784, in install **kwargs File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/req/req_install.py", line 851, in install self.move_wheel_files(self.source_dir, root=root, prefix=prefix) File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/req/req_install.py", line 1064, in move_wheel_files isolated=self.isolated, File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/wheel.py", line 345, in move_wheel_files clobber(source, lib_dir, True) File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/wheel.py", line 329, in clobber os.utime(destfile, (st.st_atime, st.st_mtime)) OSError: [Errno 1] Operation not permitted: '/home/galaxy/galaxy-dist/.venv/lib64/python2.7/site-packages/dsml.pyo' Thanks, Mohamed

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The January 2017 (17.01) Galaxy release is out. Now with Conda 🐍 for everybody!
by Jennifer Hillman-Jackson 24 Feb '17

24 Feb '17

Dear Community, *The Galaxy Committers team <https://github.com/galaxyproject/galaxy/blob/dev/doc/source/project/organiz…> is pleased to announce the January 2017 (17.01) <https://docs.galaxyproject.org/en/master/releases/17.01_announce.html> release of Galaxy.* *Thanks for using Galaxy!* *[image: Inline image 1]*

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Re: [galaxy-dev] The January 2017 (17.01) Galaxy release is out. Now with Conda 🐍 for everybody!
by Jennifer Hillman-Jackson 23 Feb '17

23 Feb '17

Hi Rezaul, The 17.01 image is available here: https://github.com/bgruening/docker-galaxy-stable/tree/release_17.01 I don't see the tweet about this being formally finalized/announced yet, so watch for that and update as needed. https://twitter.com/galaxyproject Thanks! Jen -- Jennifer Hillman-Jackson Galaxy Application Support http://usegalaxy.org http://galaxyproject.org http://biostar.usegalaxy.org On Thu, Feb 23, 2017 at 1:56 PM, Md. Rezaul Karim < rezaul.karim(a)insight-centre.org> wrote: > Hi, > > How could I use the latest version of Galaxy with Docker? > > I mean is there any Docker image of Galaxy in the Docker hub already? > > > > On Feb 23, 2017 9:27 PM, "Jennifer Hillman-Jackson" <jen(a)galaxyproject.org> > wrote: > >> Dear Community, >> >> *The Galaxy Committers team >> <https://github.com/galaxyproject/galaxy/blob/dev/doc/source/project/organiz…> is >> pleased to announce the January 2017 (17.01) >> <https://docs.galaxyproject.org/en/master/releases/17.01_announce.html> release of Galaxy.* >> >> *Thanks for using Galaxy!* >> >> >> >> *[image: Inline image 1]* >> >> >> >> ___________________________________________________________ >> 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/mailinglists/ >> >

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Blast db permission
by Mohamed Kassam 22 Feb '17

22 Feb '17

Dear all, I would like to know if it is possible to put permission on the macro.xml for ncbi-blast + database. For example if I want to show the db to one user and not to all. Best reagards, Mohamed

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Re: [galaxy-dev] nginx x-accel
by Briand, Sheldon (NRC/CNRC) 21 Feb '17

21 Feb '17

Hi, My problem was due to an old configuration in my galaxy.ini file. I had the following setting in my .ini but the correct setting earlier in the .ini file. nginx_x_accel_redirect_base = true I also had: location /_x_accel_redirect/ { internal; root /; } Instead of: location /_x_accel_redirect/ { internal; alias /; } In my nginx.conf file. The alias directive needs to be there or the value in nginx_x_accel_redirect_base gets placed in front of the download directory. Hopefully this helps someone else. Thanks, -Sheldon From: Briand, Sheldon (NRC/CNRC) Sent: Wednesday, February 15, 2017 2:01 PM To: 'galaxy-dev(a)lists.galaxyproject.org' <galaxy-dev(a)lists.galaxyproject.org> Subject: nginx x-accel Hi, I have galaxy 16.10. Whenever I try to download a file now nothing happens. I have followed the configuration guide for nginx to allow it to handle file downloads. However the nginx logs show that the file path has /etc/nginx/htmlTrue in front of the correct path. Obviously I have a misconfiguration somewhere but I am not sure what the problem is. Could someone point me in the right direction? Thanks, -Sheldon Sheldon Briand Computer Systems and Applications Analyst National Research Council/Government of Canada Sheldon.briand(a)canada.ca/<mailto:Sheldon.briand@canada.ca/> Tel: (902) 426-1677

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galaxy-dev February 2017