- galaxy-dev - lists.galaxyproject.org

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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Re: [galaxy-dev] list of names, variables that cannot be used inside XML
by Jochen Bick 20 Feb '17

20 Feb '17

Ok ur right.... I cannot reproduce this error any more... must be a typo or I don't know, sorry guys. Cheers Jochen On 20.02.2017 14:44, John Chilton wrote: > Really, that doesn't sounds correct. Why is pmode not allowed? > > -John > > On Mon, Feb 20, 2017 at 5:22 AM, Jochen Bick <jochen.bick(a)usys.ethz.ch> wrote: >> Hi all, >> >> is there any list available of names that are not allowed to use inside >> xml code? I just found out that "pmode" is one of them. >> >> Cheers Jochen >> >> >> -- >> ETH Zurich >> *Jochen Bick* >> Animal Physiology >> Institute of Agricultural Sciences >> Postal address: Universitätstrasse 2 / LFW B 58.1 >> Office: Tannenstrasse 1 / TAN D 6.2 >> 8092 Zurich, Switzerland >> >> Phone +41 44 632 28 25 >> jochen.bick(a)usys.ethz.ch <mailto:jochen.bick@usys.ethz.ch> >> www.ap.ethz.ch >> ___________________________________________________________ >> 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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list of names, variables that cannot be used inside XML
by Jochen Bick 20 Feb '17

20 Feb '17

Hi all, is there any list available of names that are not allowed to use inside xml code? I just found out that "pmode" is one of them. Cheers Jochen -- ETH Zurich *Jochen Bick* Animal Physiology Institute of Agricultural Sciences Postal address: Universitätstrasse 2 / LFW B 58.1 Office: Tannenstrasse 1 / TAN D 6.2 8092 Zurich, Switzerland Phone +41 44 632 28 25 jochen.bick(a)usys.ethz.ch <mailto:jochen.bick@usys.ethz.ch> www.ap.ethz.ch

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Problem with dataset_permissions and roles
by Lemley, Rob 17 Feb '17

17 Feb '17

Hi all, This may or may not be an actual problem, it's just something we ran into on our Galaxy instance in the past few days. The symptom was that when a user clicked the "Edit attributes" button on an item in their history, they would get an "Internal server error" message. After that their history would completely disappear from the interface. Any attempts to reload it with the "Refresh history" button would result in an error. The only way to get it back was to restart Galaxy. The error from uwsgi.log is below. After some digging in the database, I found that the "role_id" column on every entry in "dataset_permissions" had no value. Additionally, the two users who have datasets on the system had no private roles in the "roles" table. I fixed the issue by creating new private roles for those users, then manually setting "role_id" in the "dataset_permissions" table. Unfortunately my Postgres backups only go back a few days, so I can't tell if something happened to those tables somewhere along the line. We're running the release_17.01 branch plus some customizations, nothing that affects those tables though. Has anyone else seen anything like this? Thanks, -Rob galaxy.web.framework.decorators ERROR 2017-02-17 10:32:36,574 Uncaught exception in exposed API method: Traceback (most recent call last): File "/software/galaxy/app/galaxy/lib/galaxy/web/framework/decorators.py", line 295, in decorator rval = func( self, trans, *args, **kwargs ) File "/software/galaxy/app/galaxy/lib/galaxy/webapps/galaxy/api/history_contents.py", line 72, in index return self.__index_v2( trans, history_id, **kwd ) File "/software/galaxy/app/galaxy/lib/galaxy/webapps/galaxy/api/history_contents.py", line 582, in __index_v2 user=trans.user, trans=trans, view='detailed', **serialization_params ) ) File "/software/galaxy/app/galaxy/lib/galaxy/managers/base.py", line 719, in serialize_to_view return self.serialize( item, all_keys, **context ) File "/software/galaxy/app/galaxy/lib/galaxy/managers/hdas.py", line 362, in serialize return super( HDASerializer, self ).serialize( hda, keys, user=user, **context ) File "/software/galaxy/app/galaxy/lib/galaxy/managers/datasets.py", line 534, in serialize serialized = super( DatasetAssociationSerializer, self ).serialize( dataset_assoc, keys, **context ) File "/software/galaxy/app/galaxy/lib/galaxy/managers/base.py", line 632, in serialize returned[ key ] = self.serializers[ key ]( item, key, **context ) File "/software/galaxy/app/galaxy/lib/galaxy/managers/datasets.py", line 438, in <lambda> return lambda i, k, **c: serializer( i.dataset, key or k, **c ) File "/software/galaxy/app/galaxy/lib/galaxy/managers/datasets.py", line 213, in serialize_permissions 'manage' : [ self.app.security.encode_id( perm.role.id ) for perm in management_permissions ], AttributeError: 'NoneType' object has no attribute 'id' -- Rob Lemley Systems Administrator - CIRC University of Rochester

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Re: [galaxy-dev] regarding tool dependencies
by Martin Čech 17 Feb '17

17 Feb '17

Hi Nir, there is very well maintained Docker image with fully configured Galaxy available here: http://bgruening.github.io/docker-galaxy-stable/ The documentation for Galaxy administration is linked from here: https://new.galaxyproject.org/docs/#administration - most notably the recent slide decks for administration training are available here: https://gvlproject.github.io/dagobah-training/ If you encounter any problems come to chat with us here: https://gitter.im/galaxyproject/Lobby Please let us know if you are interested in more. Martin On Fri, Feb 17, 2017 at 12:14 PM Nir Shachaf <nir.shachaf(a)weizmann.ac.il> wrote: > Dear Martin, > > I appreciate your detailed reply. On zero order, my tool, along with other > existing Galaxy "metabolomics" tools should work in-house, and therefore I > can rely on system dependencies, which might mater be resolved through some > help from the community. > > However, I would like to raise a slightly bigger issue, as at least for > me, setting up the Galaxy framework is a very intricate job, evolving > editing several configuration files which goes much beyond the setting of > package dependencies. In my opinion it would be very useful to have some > "quick start recipes", or a predefined VM which can work out of the box, > including, e.g. a per-configured demo users' DB and a linked FTP server for > uploading files, etc. At least, a tutorial on how to setup such a system on > several popular Linux configurations would be greatly appreciated! At the > moment, I have abandoned the idea of setting up Galaxy in my lab, due to > time-consuming configuration problems... hopefully, we can re-try in the > future. > > Many thanks once more, > Nir. > > ------------------------------ > *From:* Martin Čech [marten(a)bx.psu.edu] > *Sent:* Thursday, February 09, 2017 6:46 PM > *To:* Nir Shachaf; galaxy-dev(a)bx.psu.edu > *Subject:* Re: [galaxy-dev] regarding tool dependencies > > Hello Nir, > > the tool publishing process looks like this: tools for Galaxy are > contributed by developers like you to the Tool Shed > https://toolshed.g2.bx.psu.edu/ which serves as an 'appstore' for > Galaxies worldwide. Any Galaxy administrator can then instal the tool. Some > tools have dependencies, yours seem to depend on R. The recommended way to > have Galaxy installed these dependencies for you is to use Conda (list of > some available R packages here: https://anaconda.org/r/repo?type=conda) > To learn more about Conda please visit > https://docs.galaxyproject.org/en/master/admin/conda_faq.html > > Alternatively, when you do not care about sharing your tool, and you do > not need to track reproducibility you can add any tool to Galaxy locally > (add the .xml wrapper and point tool_conf.xml at it and restart Galaxy). > When the tool is executed and no dependencies are found Galaxy will look > for its executable and if it is on the $PATH it will just use it. > > Please let us know if you have more questions. > > Thanks for using Galaxy, > > Martin > > > On Thu, Feb 9, 2017 at 11:01 AM Nir Shachaf <nir.shachaf(a)weizmann.ac.il> > wrote: > > Dear Galaxy-dev team, > > As a research scientist in the dept. of Plant Sciences I would like to > contribute a tool to the 'Metabolomics' tool-box under Galaxy. The tool is > principally written in R, with some dependencies (namely: R>=3.x, and > several R packages). Following the documentation in: > > https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies > > https://wiki.galaxyproject.org/Admin/Config/ToolDependencies > > I admit I get confused by the numerous possibilities offered by the > framework. My main concern is to be able to link the Galaxy server to tools > already installed on my development environment, and NOT to depend on the > tools available in the tool-shed repository (as many are not there, and > there are specific versions requirements). > > Could you kindly direct me to the relevant solution, or a user's-list > post, if applicable? > > Many thanks in advance, > Nir Shachaf, > Plant Sciences Dept., > Weizmann Inst. of Science, > Rehovot, Israel. > ___________________________________________________________ > 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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