- galaxy-dev - lists.galaxyproject.org

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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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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