- galaxy-dev - lists.galaxyproject.org

"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

2 2

Running galaxy using Apache as proxy
by Michael Place 04 May '13

04 May '13

Hello, I am trying to run galaxy using Apache as the proxy server. This is intended to be internal to our lab. I have galaxy running and working. The problem is that the pages load slowly and then seem to time out after 10 min or so. If I login and click get data then go away for a few minutes , then I come back and click a tool I get: The connection to the server was reset while the page was loading. If I retry the page loads. This makes the page very clunky. httpd.conf changes: <IfModule mod_proxy.c> ProxyRequests On <Proxy * > Order deny,allow Deny from all Allow from * </Proxy> <VirtualHost *:8080> ServerName 192.168.0.240 RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /opt/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /opt/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /opt/galaxy-dist/galaxy-dist/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /opt/galaxy-dist/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /opt/galaxy-dist/static/robots.txt [L] RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P] </VirtualHost> I have attached the universe_wsgi.ini and my httpd.conf I am running CentOS. Thank you, Mike

2 1