- galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] Running Galaxy through Apache
by Jeffrey Long 06 May '13

06 May '13

1) Any idea which proxy settings in the universe_wsgi file need to be set other than the ones on the website? Those are the only ones I changed. I scrolled down to the 'Advanced Proxy' settings but didn't see anything that looked relevant to me. Probably I should have sent this earlier, but this is the traceback I get; it looks like there's a url somewhere that's not getting passed along or re-assembled properly. Exception happened during processing of request from ('127.0.0.1', 47424) Traceback (most recent call last): File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 1053, in process_request_in_thread self.finish_request(request, client_address) File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request self.RequestHandlerClass(request, client_address, self) File "/usr/lib/python2.7/SocketServer.py", line 638, in __init__ self.handle() File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 432, in handle BaseHTTPRequestHandler.handle(self) File "/usr/lib/python2.7/BaseHTTPServer.py", line 340, in handle self.handle_one_request() File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 427, in handle_one_request self.wsgi_execute() File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 287, in wsgi_execute self.wsgi_start_response) File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/config.py", line 285, in __call__ return self.app(environ, start_response) File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/urlmap.py", line 193, in __call__ path_info = self.normalize_url(path_info, False)[1] File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/urlmap.py", line 117, in normalize_url or self.domain_url_re.search(url)), "URL fragments must start with / or http:// (you gave %r)" % url AssertionError: URL fragments must start with / or http:// (you gave '.') 2) Are the static subdirectories strictly necessary, or can I worry about one problem at a time? I've tried both commenting out the proxy lines (in apache2.conf) and leaving them in, and I get the same behaviour. Thanks, I'll try to remember to 'reply-all' here! -Jeff On Mon, Apr 29, 2013 at 1:23 PM, Adam Brenner <aebrenne(a)uci.edu> wrote: > Hia Jeff, > > I think this is related to the proxy settings in Galaxy (universe_wsgi.ini) > > What is happening is that if you look at the source code for your > galaxy website, it is trying to load css/images from: > http://trove.usask.ca/galaxy/static/style/base.css?v=1367254127 But if > you visit that link it offers you a 404 not found. Make sure the proxy > settings in your universe_wsgi.ini is set correctly. > > If it is, it could be that you need to setup proxies for the > subdirectories as well. If you look at the nginx guide here: > http://wiki.galaxyproject.org/Admin/Config/Performance/nginx%20Proxy > you will notice that we provide alias for /static/*. > > In terms of doing this in Apache, you may need to add more proxy pass > lines that correspond to the subdirectories in question. > > > Be sure to post back to the Galaxy listsrv so that future people may > benefit from this! > -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 > > > On Mon, Apr 29, 2013 at 9:51 AM, Jeffrey Long <jlong1(a)ualberta.ca> wrote: > > Hi Adam thanks for the response, > > I'm not using VirtualHosts. I just copied the lines shown into > > /etc/apache2/apache.conf (this is on Ubuntu Linux). > > > > I copied the lines you list (with appropriate modification) into this > same > > apache.conf. That seems to work - as far as Apache goes! However, when > I > > load galaxy in a browser now, I get a bunch of gobbledigook (it looks > like > > the frames aren't being built properly or something). You can take a > look; > > I've temporarily enabled the site to be world-viewable. > > > > http://trove.usask.ca/galaxy > > > > Thanks for your help! > > > > -Jeff > > > > > > On Fri, Apr 26, 2013 at 10:11 PM, Adam Brenner <aebrenne(a)uci.edu> wrote: > >> > >> Jeff, > >> > >> How / Where did you add the apache changes? Are you using VirutalHosts > >> or ... ? Quick glance, everything appears correct. Its been a while > >> since I used Apache (switched everything to nginx) however I believe > >> if you want to setup a Reverse Proxy, you need to add / use the proxy > >> pass lines which does not appear in the Galaxy Wiki. > >> > >> Something like this should work: (untested...) > >> > >> <IfModule mod_proxy.c> > >> ProxyRequests Off > >> <Proxy *> > >> AddDefaultCharset off > >> Order Deny,Allow > >> Deny from all > >> Allow from *.ualberta.ca # Change / Remove as needed > >> </Proxy> > >> > >> ProxyPass /galaxy http://localhost:8080/ > >> ProxyPassReverse /galaxy http://localhost:8080/ > >> # Line below is optional > >> Redirect permanent /galaxy http://mymachine.com/galaxy > >> > >> ProxyVia On > >> </IfModule> > >> > >> > >> Let us know, > >> -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 > >> > >> > >> On Fri, Apr 26, 2013 at 2:56 PM, Jeffrey Long <jlong1(a)ualberta.ca> > wrote: > >> > 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#prefix > >> > prefix = /galaxy > >> > > >> > [app:main] > >> > > >> > filter-with = proxy-prefix > >> > cookie_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 > >> > > >> > > >> > ___________________________________________________________ > >> > 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/ > >> > > > >

3 4

"Published Workflows" missing from "All Workflows"
by Peter Cock 06 May '13

06 May '13

Hello all, This is to report a usability bug with workflows - specifically the curiously separate handling of "Published Workflows" in the user interface. 1. Log into your Galaxy account, 2. On the top ribbon, click on "Shared Data", "Published Workflows", and make a note of the entries. 3. Return to the main screen via the top ribbon entry "Analyse Data" 4. On the bottom of the left hand tool column, under "Workflows" click on "All workflows". Observe results. 5. On the top ribbon, click on "Workflows". Observe results. Actual result (in 4 and 5): Two sections, "Your workflows" and "Workflows shared with you by others" Expected result (in 4 and 5): Three sections, "Your workflows", "Workflows shared with you by others", "Published Workflows". i.e. "Published Workflows" are hidden or separated away from the others. This appears to be a design choice (like shared datasets they must be "imported" before use), but if so this could be clarified as follows: Suggested result (in 4 and 5): Two sections, "Your workflows" and "Workflows shared with you by others", plus a footnote (with link) saying something about additional workflows are available to import from "Published Workflows". Regards, Peter

2 2

Taxonomy fetching not working
by Deepthi Thomas Kannanayakal 06 May '13

06 May '13

Hi Galaxy team, I am having problems with taxonomy information fetching.(Metagenomic Analysses->Fetch taxonomic representation). According to the following link http://dev.list.galaxyproject.org/quot-Fetch-taxonomic-representation-quot-… I have installed libraries from https://bitbucket.org/natefoo/taxonomy I have installed them in my local directory(not in /usr/local). But I am still having problem /bin/sh: taxBuilder: command not found What am I missing here? Thanks, Deeps *Deepthi Theresa Thomas Kannanayakal Bioinformatics Database Specialist Sun Visual Genomic Centre, Suite 1150, Health Science Centre 3330 Hospital Drive NW Department of Biochemistry and Molecular Biology Faculty of Medicine, University of Calgary T2N 4N1 Calgary, Alberta, Canada** * *Ph: (403) - 210 6661 Fax: (403) - 210 9538*

2 1

Conditional tool options based on input file format?
by Peter Cock 06 May '13

06 May '13

Dear all, I've looked over the wiki and as far as I can see, 'when' tags used inside 'conditional' tags only work on another input variable's values. I would like to be able to do is a conditional based on the file format of an input file. For instance, a tool might take XML or tabular files, and need to show additional parameters for one input type but not the other. Does this enhancement idea seem useful? Peter

4 6

LWR runner configuration for shared folder in cluster
by Krampis, Konstantinos 06 May '13

06 May '13

Hi all, I am trying to set up a Galaxy cluster using the LWR runner. The nodes have a shared filesystem and in universe.wsgi this parameter is set : job_working_directory = /mnt/shared ... clustalw = lwr://http://192.168.33.12:8913 .... this folder has been "chown-ed" to the galaxy user, and also is "a+w", while it has been verified that can been read / written by ssh-ing to each node of the cluster. The sticky bit is set. When I try to run jobs (I used clustalw as example) there seems to be confusion between where Galaxy puts files and where LWR tries to read them from. Here are two setups that error out: 1). When in server.ini for LWR the following is set as: staging_directory = /mnt/shared/000 galaxy error: galaxy.jobs DEBUG 2013-05-06 10:21:22,320 (128) Working directory for job is: /mnt/shared/000/128 galaxy.jobs.handler DEBUG 2013-05-06 10:21:22,320 dispatching job 128 to lwr runner galaxy.jobs.handler INFO 2013-05-06 10:21:22,427 (128) Job dispatched galaxy.datatypes.metadata DEBUG 2013-05-06 10:21:22,875 Cleaning up external metadata files galaxy.jobs.runners.lwr ERROR 2013-05-06 10:21:22,902 failure running job 128 lwr error (on the cluster node): File "/home/vagrant/jmchilton-lwr-5213f6dce32d/lwr/app.py", line 81, in setup manager.setup_job_directory(job_id) File "/home/vagrant/jmchilton-lwr-5213f6dce32d/lwr/manager.py", line 101, in setup_job_directory os.mkdir(job_directory) OSError: [Errno 17] File exists: '/mnt/shared/000/128' 2). When in server.ini for LWR the following is set as: staging_directory = /mnt/shared galaxy error: galaxy.jobs DEBUG 2013-05-06 10:28:46,872 (129) Working directory for job is: /mnt/shared/000/129 galaxy.jobs.handler DEBUG 2013-05-06 10:28:46,872 dispatching job 129 to lwr runner galaxy.jobs.handler INFO 2013-05-06 10:28:46,967 (129) Job dispatched 192.168.33.1 - - [06/May/2013:10:28:48 -0200] "GET /api/histories/2a56795cad3c7db3 HTTP/1.1" 200 - "http://192.168.33.11:8080/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.31 (KHTML, like Gecko) Chrome/26.0.1410.65 Safari/537.31" galaxy.jobs.runners.lwr DEBUG 2013-05-06 10:28:50,653 run_results {'status': 'status', 'returncode': 0, 'complete': 'true', 'stderr': '', 'stdout': ''} galaxy.datatypes.metadata DEBUG 2013-05-06 10:28:50,970 Cleaning up external metadata files galaxy.jobs.runners.lwr ERROR 2013-05-06 10:28:51,050 failure running job 129 lwr error (on the cluster node): resp.app_iter = FileIterator(result) File "/home/vagrant/jmchilton-lwr-5213f6dce32d/lwr/framework.py", line 111, in __init__ self.input = open(path, 'rb') IOError: [Errno 2] No such file or directory: u'/mnt/shared/129/outputs/dataset_170.dat' The full error stacks are at the end of this email. It might be something very simple that I am missing, but any feedback would be greatly appreciated. Thanks ! Ntino -- Konstantinos (Ntino) Krampis, Ph.D. Asst. Professor, Informatics J.Craig Venter Institute kkrampis(a)jcvi.org agbiotec(a)gmail.com +1-540-200-8277 Web: http://bit.ly/cloud-research http://cloudbiolinux.org/ http://twitter.com/agbiotec ---- GALAXY ERROR galaxy.jobs DEBUG 2013-05-06 10:21:22,320 (128) Working directory for job is: /mnt/shared/000/128 galaxy.jobs.handler DEBUG 2013-05-06 10:21:22,320 dispatching job 128 to lwr runner galaxy.jobs.handler INFO 2013-05-06 10:21:22,427 (128) Job dispatched galaxy.datatypes.metadata DEBUG 2013-05-06 10:21:22,875 Cleaning up external metadata files galaxy.jobs.runners.lwr ERROR 2013-05-06 10:21:22,902 failure running job 128 Traceback (most recent call last): File "/home/vagrant/galaxy-dist/lib/galaxy/jobs/runners/lwr.py", line 286, in run_job file_stager = FileStager(client, command_line, job_wrapper.extra_filenames, input_files, output_files, job_wrapper.tool.tool_dir) File "/home/vagrant/galaxy-dist/lib/galaxy/jobs/runners/lwr.py", line 40, in __init__ job_config = client.setup() File "/home/vagrant/galaxy-dist/lib/galaxy/jobs/runners/lwr.py", line 212, in setup return self.__raw_execute_and_parse("setup", { "job_id" : self.job_id }) File "/home/vagrant/galaxy-dist/lib/galaxy/jobs/runners/lwr.py", line 150, in __raw_execute_and_parse response = self.__raw_execute(command, args, data) File "/home/vagrant/galaxy-dist/lib/galaxy/jobs/runners/lwr.py", line 146, in __raw_execute response = self.url_open(request, data) File "/home/vagrant/galaxy-dist/lib/galaxy/jobs/runners/lwr.py", line 134, in url_open return urllib2.urlopen(request, data) File "/usr/lib/python2.7/urllib2.py", line 126, in urlopen return _opener.open(url, data, timeout) File "/usr/lib/python2.7/urllib2.py", line 406, in open response = meth(req, response) File "/usr/lib/python2.7/urllib2.py", line 519, in http_response 'http', request, response, code, msg, hdrs) File "/usr/lib/python2.7/urllib2.py", line 444, in error return self._call_chain(*args) File "/usr/lib/python2.7/urllib2.py", line 378, in _call_chain result = func(*args) File "/usr/lib/python2.7/urllib2.py", line 527, in http_error_default raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) HTTPError: HTTP Error 500: Internal Server Error ---- LWR ERROR Exception happened during processing of request from ('192.168.33.11', 44802) Traceback (most recent call last): File "/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread self.finish_request(request, client_address) File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request self.RequestHandlerClass(request, client_address, self) File "/usr/lib/python2.7/SocketServer.py", line 638, in __init__ self.handle() File "/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 442, in handle BaseHTTPRequestHandler.handle(self) File "/usr/lib/python2.7/BaseHTTPServer.py", line 340, in handle self.handle_one_request() File "/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 437, in handle_one_request self.wsgi_execute() File "/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 287, in wsgi_execute self.wsgi_start_response) File "/home/vagrant/jmchilton-lwr-5213f6dce32d/lwr/framework.py", line 35, in __call__ return controller(environ, start_response, **request_args) File "/home/vagrant/jmchilton-lwr-5213f6dce32d/lwr/framework.py", line 90, in controller_replacement result = func(**args) File "/home/vagrant/jmchilton-lwr-5213f6dce32d/lwr/app.py", line 81, in setup manager.setup_job_directory(job_id) File "/home/vagrant/jmchilton-lwr-5213f6dce32d/lwr/manager.py", line 101, in setup_job_directory os.mkdir(job_directory) OSError: [Errno 17] File exists: '/mnt/shared/000/128'

2 4

galaxysession cookie secure flag
by Vipin TS 06 May '13

06 May '13

Hi dev-team, We have placed our galaxy instance ssl and I need to make sure that the secure flag is set on the cookie (commonly represented by the word “secure” under the Security column) but I am not able to do the same. something like below: [image: Inline image 2] when I checked on my instance I saw as below: [image: Inline image 3] I have made necessary changes to my ssl.conf to put the flag as secure, but it seems not appearing here. Header edit Set-Cookie ^(.*)$ $1;Secure;HttpOnly does anybody have an experience in setting up the same. thanks in advance, --/Vipin

1 1

Any hint on how to use Galaxy within virtualenv?
by Jean-Francois Payotte 06 May '13

06 May '13

Dear Galaxy mailing list, We ran into the same issue described in this post: http://dev.list.galaxyproject.org/markupsafe-module-conflicts-tc4656214.html The exact error message we are getting, with a few different tools is: /Galaxy/galaxy_dist/lib/galaxy/__init__.py:79: UserWarning: Module markupsafe was already imported from /usr/lib64/python2.6/site-packages/markupsafe/__init__.pyc, but /Galaxy/galaxy_dist/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg is being added to sys.path self.check_version_conflict() >From the solution given in the above-mentioned post, I guess we would have to run Galaxy inside virtualenv. (Details of the procedure to install virtualenv, are given here: http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer) However, I am not sure to understand completely how it works. Can we use our already existing Galaxy instance with virtualenv? And how can we achieve this? For the installation of "virtualenv" part, I think we are ok. It is the next step: how to tell Galaxy to run in this virtualenv, that I am not sure about. Thank you in advance for your help! Jean-Francois

2 4

May 2013 Galaxy Update
by Dave Clements 06 May '13

06 May '13

1 0

user creation using API
by Hagai Cohen 06 May '13

06 May '13

Hi, I would like to auto create users on my local Galaxy instance. I saw that in the "create user" on the API, I should enable use_remote_user (which as I understand means that I have to use Apache or nginx). Is there another way besides using Apache to create users automatically? Thanks, Hagai

3 3

(no subject)
by sridhar srinivasan 06 May '13

06 May '13

Dear All, i am installing galaxy first time. i face problem while installing the python eggs. while running the Run.sh command it gives as /home/sbsuser/.python-eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg-tmp/csamtools.so:6: RuntimeWarning: __builtin__.file size changed, may indicate binary incompatibility �b�n 640�c��?��U�#k�!\jZo�[&��[<��9-��ra#��8n��C�U�;B�SlK(p��U�&�P w 5 ≠ ' H è π ø * ─ ␋ Ð Ä @ ê i couldn't read the message and also i couldn't open the galaxy page http://localhost:8080 Could you please suggest tth epossibilities to install. Thanks in advance Regards Sridhar

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