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Command Line Tool for Creating New Users
by Neil.Burdett＠csiro.au 30 Apr '13

30 Apr '13

Hi, I'm trying to use the tool, however, when I run it I get: python create_galaxy_users.py Traceback (most recent call last): File "create_galaxy_users.py", line 2, in <module> from scripts.db_shell import * ImportError: No module named scripts.db_shell I've set my PYTHONPATH to be ~/galaxy-dist/lib. What else do I need to do? I'm running the script from ~/galaxy-dist/ directory, but I get the same error if I copy it into the scripts directory. I've checked and I can see that the scripts.db_shell.py script exists If I comment out the line then the next error I get is: python create_galaxy_users.py Traceback (most recent call last): File "create_galaxy_users.py", line 7, in <module> from galaxy.security import GalaxyRBACAgent File "/home/galaxy/galaxy-dist/lib/galaxy/security/__init__.py", line 9, in <module> from galaxy.model.orm import * File "/home/galaxy/galaxy-dist/lib/galaxy/model/__init__.py", line 15, in <module> from galaxy.security import RBACAgent, get_permitted_actions ImportError: cannot import name RBACAgent Any help much appreciated Neil ---------------------------------------------------------------------- Message: 1 Date: Sat, 27 Apr 2013 14:07:49 -0500 From: John Chilton <chilton(a)msi.umn.edu> To: Adam Brenner <aebrenne(a)uci.edu> Cc: "galaxy-dev(a)lists.bx.psu.edu" <galaxy-dev(a)lists.bx.psu.edu> Subject: Re: [galaxy-dev] Command Line Tool for Creating New Users Message-ID: <CANwbokctvXO-DFmamr77FU6BbDHGR1STG7mpH_LP+fE2nMcnag(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 I put together a script to do this. It is described in the galaxy-dev thread titled: "[galaxy-dev] user creation using API". It doesn't actually use the API, it uses the db_shell.py script. Hope this helps. -John On Thu, Apr 25, 2013 at 7:11 PM, Adam Brenner <aebrenne(a)uci.edu> wrote: > Howdy All, > > I was wondering if anyone has created a command line tool that will > add users to the Galaxy user database? > > I did look into switching to external user authentication via nginx, > however, this will result in us using the campus wide kerberos system > and allowing ~30,000 people access to Galaxy... and thus offering us > less fine grain control to Galaxy. > > Anything anyone has to share would be much appreciated, -Adam > > -- > Adam Brenner > Computer Science, Undergraduate Student Donald Bren School of > Information and Computer Sciences > > Research Computing Support > Office of Information Technology > http://www.oit.uci.edu/rcs/ > > University of California, Irvine > www.ics.uci.edu/~aebrenne/ > aebrenne(a)uci.edu > ___________________________________________________________ > 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: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ------------------------------ _______________________________________________ galaxy-dev mailing list galaxy-dev(a)lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ End of galaxy-dev Digest, Vol 82, Issue 28 ******************************************

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Galaxy Workflow Input Problem
by Amanda Dupuy 29 Apr '13

29 Apr '13

Dear Galaxy Team, I'm using the psu public galaxy software and cannot get my workflows to use the input files I'm selecting. Everytime I try to run the workflow, I enter all of the input files that I want to use, but after I hit run, the operations are performed only using my most recent Galaxy file as an input, instead of the ones that I selected. I realize that sometimes you have to wait for the page to refresh before executing if a new file is applied, but it doesn't seem that the page is trying to refresh. Do you have any tips for me? Thanks for your help, Amanda~ -- Amanda Dupuy PhD Student in Genetics and Genomics Department of Molecular and Cell Biology Center for Applied Genetics and Technology 354 Mansfield Road U-2131 Room 346 Storrs, CT 06269 Lab: 860-486-1896

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Galaxy hg repository problem "abort: path ... traverses symbolic link"
by Peter Cock 29 Apr '13

29 Apr '13

Hi all, I've got an hg puzzle, can anyone on the Galaxy team explain the cause of this and what action I can take to avoid it? Starting with a clean checkout, $ hg clone https://bitbucket.org/galaxy/galaxy-central warning: bitbucket.org certificate with fingerprint 24:9c:45:8b:9c:aa:ba:55:4e:01:6d:58:ff:e4:28:7d:2a:14:ae:3b not verified (check hostfingerprints or web.cacerts config setting) destination directory: galaxy-central requesting all changes adding changesets adding manifests adding file changes added 8886 changesets with 33822 changes to 6914 files (+1 heads) updating to branch default 4019 files updated, 0 files merged, 0 files removed, 0 files unresolved $ cd galaxy-central $ hg branch default $ hg branches default 8885:9852dd712f5c stable 8880:8da37d3985ab $ hg checkout stable abort: path 'static/june_2007_style/Makefile' traverses symbolic link 'static/june_2007_style' I was actually trying to checkout one of my own branches, having setup the .hg/hgrc to include a link to my own fork on bitbucket. Thanks! Peter

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Blast Errors
by Ganote, Carrie L 29 Apr '13

29 Apr '13

Hi list, I have a newly installed Galaxy instance (security_2013.04.08) and I am testing out NCBI Blast+ on it. I'm having trouble getting it to run. I'm using the following tools from the Galaxy Main Toolshed: blast_datatypes b3a3ba0c1d47 ncbi_blast_plus 1f546099212f Looks like blast is being called fine, but I get this: Fatal error: Matched on Error: Error: NCBI C++ Exception: "/N/soft/rhel6/ncbi-blast+/ncbi-blast-2.2.28+-src/c++/src/corelib/ncbiobj.cpp", line 925: Critical: ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL pointer. WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'asn1': 'module' object has no attribute 'GenericAsn1' WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'asn1-binary': 'module' object has no attribute 'GenericAsn1Binary' Anyone seen this? Thanks! Carrie Ganote

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Galaxy, CloudMan & nginx 1.4.0
by John Chilton 28 Apr '13

28 Apr '13

I wanted to update CloudMan to use nginx 1.4.0 for web socket proxy support, but I hit a problem. nginx-upload-module does not work with nginx 1.4.0 and the author has no intention of continuing work on the module. https://github.com/vkholodkov/nginx-upload-module/issues/41 There is a patch that based on the comments in the above thread doesn't work: http://paste.davromaniak.eu/index.php?show=110 And there are some related projects but I don't understand enough about how Galaxy is interacting with nginx upload to know if they are a promising replacement. https://github.com/pgaertig/nginx-big-upload https://github.com/agentzh/lua-resty-upload It also kind of seems like nginx might provide some support for handling uploads directly without that module, here is the example from that thread: location /upload { limit_except POST { deny all; } client_body_temp_path /tmp/; client_body_in_file_only on; client_body_buffer_size 128K; client_max_body_size 50M; proxy_pass_request_headers on; proxy_set_body $request_body_file; proxy_pass http://upstream; # will receive file_name only proxy_redirect off; } Can the galaxy solution be adapted for this client_body_xxx style? If not, has anyone looked at something like nginx-big-upload and gotten it to work? I suppose this is not likely since nginx 1.4 just came out, but it is worth asking. If someone does figure it out someday, let me know and I can test and update the CloudBioLinux/CloudMan stuff for whatever you figure out. Thanks, -John

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Command Line Tool for Creating New Users
by Adam Brenner 27 Apr '13

27 Apr '13

Howdy All, I was wondering if anyone has created a command line tool that will add users to the Galaxy user database? I did look into switching to external user authentication via nginx, however, this will result in us using the campus wide kerberos system and allowing ~30,000 people access to Galaxy... and thus offering us less fine grain control to Galaxy. Anything anyone has to share would be much appreciated, -Adam -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/ University of California, Irvine www.ics.uci.edu/~aebrenne/ aebrenne(a)uci.edu

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Running Galaxy through Apache
by Jeffrey Long 27 Apr '13

27 Apr '13

Hi folks, I am wanting to run a galaxy instance and serve it at a location other than the webserver root, i.e. at http://mymachine.com/galaxy rather than just at http://mymachine. To do this, I've followed the instructions about proxying Galaxy through Apache at http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy. I'm pretty sure I've followed the instructions exactly. I enabled the necessary apache proxy modules and then I added these lines to my apache.conf file: RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule^/galaxy/static/style/(.*) /myplace/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule^/galaxy/static/scripts/(.*) /myplace/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule^/galaxy/static/(.*) /myplace/galaxy-dist/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /myplace/galaxy-dist/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /myplace/galaxy-dist/static/robots.txt [L] RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P] ...and re-started the apache server without a problem (note: I also tried it commenting out everything but the first, second and last line in case there was an issue with the static stuff). I then made sure the following lines were present and uncommented in my universe_wsgi.ini file [filter:proxy-prefix]use = egg:PasteDeploy#prefixprefix = /galaxy[app:main] filter-with = proxy-prefixcookie_path = /galaxy I start up Galaxy. And still, I can only reach it on http://mymachine:8080, not at http://mymachine/galaxy as I intend. Any help would be appreciated! Thanks! -Jeff

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Environment variables
by Matthias Zytnicki 26 Apr '13

26 Apr '13

Dear everyone, I have spent hours trying to set environment variable in Galaxy. I am managing the "s_mart" repos (you can check it if you wish), and I created the simple files "test.xml" which prints the environment variables: --- <tool id="test" name="test"> <description>This is a test.</description> <requirements> <requirement type="set_environment">PYTHONPATH</requirement> </requirements> <command>env > $outputFile</command> <outputs> <data name="outputFile" format="txt" label="output test file"/> </outputs> <help>This is a test.</help> </tool> --- and "tool_dependencies.xml", which appends something to the PYTHONPATH variable.: --- <?xml version="1.0"?> <tool_dependency> <set_environment version="1.0"> <environment_variable name="PYTHONPATH" action="append_to">$REPOSITORY_INSTALL_DIR</environment_variable> </set_environment> </tool_dependency> --- As you guess, I cannot see anything added in the PYTHONPATH variable. I have tried to append INSTALL_DIR and even "/tmp". None worked. Do you have any suggestion for me? Many thanks to you all, Matthias.

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/bin/sh: 1: filename: not found
by Ramon Tiburski 25 Apr '13

25 Apr '13

I created a new tool in c++, and the "filename" is the name of my executable file. I have the xml and the executable file in the same directory, but I get this error when I try to run the tool. Someone can help me with this error? Thank you

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Speed up the galaxy
by 泽蔡 25 Apr '13

25 Apr '13

Hi all, How can I speed up the galaxy? Like how to use more cores and memeries.

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