galaxy-dev January 2013

galaxy-dev@lists.galaxyproject.org

105 participants
195 discussions

Still seeing this CRITICAL message in the logs when its trying to delete the working directories
by Anthonius deBoer 13 Feb '13

13 Feb '13

Hi, I continue to see this error in the logs, every time a jobs finishes: galaxy.objectstore CRITICAL 2013-01-30 11:42:14,161 /mnt/ngs/analysis/svcgalaxy/DATA/job_working_directory/000/327 delete error [Errno 39] Directory not empty: '/mnt/ngs/analysis/svcgalaxy/DATA/job_working_directory/000/327' When I check the directory, it is of course empty: $ls -la /mnt/ngs/analysis/svcgalaxy/DATA/job_working_directory/000/327 total 68 drwxrwsr-x 2 svcgalaxy Domain Linux Users 0 Jan 30 11:42 . drwxrwsr-x 283 svcgalaxy Domain Linux Users 5793 Jan 30 11:45 .. Any ideas why this keeps happening? I end up with thousands of directories in the working directories which I need to clean out manually now... Thanks Thon

2 1

Nice 'citable' URLs for Galaxy Tool Shed repositories
by Peter Cock 11 Feb '13

11 Feb '13

Dear all, Something I am conscious of every time I have directed someone to a tool or wrapper on the Galaxy Tool Shed is the lack of nice stable URLs. The current frame based design hinders this - and as a result I usually just have to give the ToolShed URL and tell them what to search for. This problem is particularly acute for citing a tool shed entry, where a nice URL would be far better. I appreciate moving away from the current frame interface is a lot of work - although what Jeremy Goecks wrote last week suggests that is a long term goal: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-January/012792.html I would like something similar to the repository URL, but for the ToolShed interface. e.g. The repository view for my MIRA wrapper: http://toolshed.g2.bx.psu.edu/repos/peterjc/mira_assembler Perhaps is the short-term what could be done is to enhance the repository view, and include links between this and the current "Tool Shed" frame based page? That way we can share a nice URL like http://toolshed.g2.bx.psu.edu/repos/peterjc/mira_assembler to direct someone to a resource in the Tool Shed? e.g. (1) When viewing an entry on the "Tool Shed", include a prominent link to the repository URL (perhaps even with social media links like tweet or share this to emphasise this is the best URL to share). (2) In the header for each repo (perhaps in place of the current Mercuiral logo?) have a link to the "Tool Shed" frameset for the tool being viewed. Thanks, Peter

5 22

run_functional_tests.sh -sid option
by Peter 11 Feb '13

11 Feb '13

Hi, I'm trying to use run_functional_tests.sh to run all the tests for a section (group of tools). I've read the output from: ./run_functional_tests.sh help For example, from the tools_conf.xml.sample we have <section name="ENCODE Tools" id="EncodeTools"> <tool file="encode/gencode_partition.xml" /> <tool file="encode/random_intervals.xml" /> </section> And looking at these tools' XML files, <tool id="gencode_partition1" name="Gencode Partition"> and: <tool id="random_intervals1" name="Random Intervals"> I'd like to run the functional tests for the ENCODE tools, Using the switch for an individual tool id (-id) works, ./run_functional_tests.sh -id gencode_partition1 ... Ran 1 test in 22.302s ... and so does this (well, it say the tool doesn't have any tests which is true in this example): ./run_functional_tests.sh -id random_intervals1 ... Ran 1 test in 0.027s ... However, I also tried using the section id switch (-sid), ./run_functional_tests.sh -sid EncodeTools ... Ran 0 tests in 0.000s ... I also tried using the section name, /run_functional_tests.sh -sid "ENCODE Tools" Is this (-sid not working) a known issue, or am I using it wrong? Thanks, Peter

4 5

Job handler : crash
by Christophe Caron 07 Feb '13

07 Feb '13

Hello, We run Galaxy (2013 January version) with load balancing mode (5 x web manager, 5 job handler) with Apache/Sun Grid Engine 6.0u4/CentOS 6.3 - Since 2 weeks, some handler job process crash during the Galaxy startup with this error message in handlerx.log ..... Starting server in PID 13634. serving on http://127.0.0.1:8091 galaxy.jobs.handler DEBUG 2013-01-29 20:06:48,902 Stopping job 22842: galaxy.jobs.handler DEBUG 2013-01-29 20:06:48,902 stopping job 22842 in drmaa runner - The system log files report a segfault with libdrmaa kernel: python[13977]: segfault at 0 ip 00007f2811805dc5 sp 00007f27f4aac0a0 error 4 in libdrmaa.so.1.0[7f28116dd000+185000] Thanks for your help ! Christophe -- Christophe Caron Station Biologique / Service Informatique et Bio-informatique Place Georges Teissier - CS 90074 29688 Roscoff Cedex Analysis and Bioinformatics for Marine Science http://abims.sb-roscoff.fr/ christophe.caron(a)sb-roscoff.fr tél: +33 (0)2 98 29 25 43 / +33 (0)6 07 83 54 77

2 2

Problem referencing EMBOSS tools in universe_wsgi.ini
by Guest, Simon 07 Feb '13

07 Feb '13

We have set up our local Galaxy installation to submit jobs by default through HTCondor, using the drmaa tool runner. We override this on a tool-by-tool basis in universe_wsgi.ini, to specify certain tools we always want to run locally. The problem is that EMBOSS tools have a tool id like 'emboss: infoseq46', and it's not possible to reference a tool with an id containing a colon in the universe_wsgi.ini file (because colon is the character which separates a configuration item name from its value). It seems to me there are two possible solutions: 1. Implement some form of escape character processing in the config file parser (on top of Python's ConfigParser) so we can write tool ids in that file like 'emboss%3a infoseq46' 2. Change all the EMBOSS tools to have ids like 'emboss-infoseq46' rather than using a colon and space. For now, we are modifying our XML files locally (with a script) to do 2. Are there any comments from Galaxy developers on which of these solutions they prefer, or any reason why (2) shouldn't be incorporated in the Galaxy mainline? cheers, Simon ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. =======================================================================

2 2

Question regarding frequency of pbs_mom authentications
by Daniel Patrick Sullivan 06 Feb '13

06 Feb '13

Hi, Galaxy Developers, I have a couple of hopefully quick questions regarding PBS integration with Galaxy; I noticed (based on taking a look at the PBS log data) that Galaxy authenticates rather frequently to the pbs_mom server (please see the log data at the end of this email). Is the frequency of these connections common (i.e. sometimes several times per second). Is there any way to throttle this? Has anybody seen a problem resulting from the large number of authentication request from the Galaxy server to the pbs_mom server? It is suspected that the frequency of these connections is causing a problem on our scheduler node. Thank-you so much for taking the time to answer my questions. [a.cri.dsullivan@sc01 server_logs]$ tail -f 20130130 01/30/2013 10:30:50;0100;PBS_Server;Req;;Type AuthenticateUser request received from s.cri.galaxy(a)crigalaxy.uchicago.edu, sock=9 01/30/2013 10:30:50;0100;PBS_Server;Req;;Type StatusJob request received from s.cri.galaxy(a)crigalaxy.uchicago.edu, sock=12 01/30/2013 10:30:51;0100;PBS_Server;Req;;Type AuthenticateUser request received from s.cri.galaxy(a)crigalaxy.uchicago.edu, sock=10 01/30/2013 10:30:51;0100;PBS_Server;Req;;Type StatusJob request received from s.cri.galaxy(a)crigalaxy.uchicago.edu, sock=9 01/30/2013 10:30:52;0100;PBS_Server;Req;;Type AuthenticateUser request received from s.cri.galaxy(a)crigalaxy.uchicago.edu, sock=10 01/30/2013 10:30:52;0100;PBS_Server;Req;;Type StatusJob request received from s.cri.galaxy(a)crigalaxy.uchicago.edu, sock=9 01/30/2013 10:30:53;0100;PBS_Server;Req;;Type AuthenticateUser request received from s.cri.galaxy(a)crigalaxy.uchicago.edu, sock=10 01/30/2013 10:30:53;0100;PBS_Server;Req;;Type StatusJob request received from s.cri.galaxy(a)crigalaxy.uchicago.edu, sock=9 01/30/2013 10:30:54;0100;PBS_Server;Req;;Type AuthenticateUser request received from s.cri.galaxy(a)crigalaxy.uchicago.edu, sock=10 01/30/2013 10:30:54;0100;PBS_Server;Req;;Type StatusJob request received from s.cri.galaxy(a)crigalaxy.uchicago.edu, sock=9 01/30/2013 10:30:55;0100;PBS_Server;Req;;Type AuthenticateUser request received from s.cri.galaxy(a)crigalaxy.uchicago.edu, sock=10 01/30/2013 10:30:55;0100;PBS_Server;Req;;Type StatusJob request received from s.cri.galaxy(a)crigalaxy.uchicago.edu, sock=9 01/30/2013 10:30:56;0100;PBS_Server;Req;;Type AuthenticateUser request received from s.cri.galaxy(a)crigalaxy.uchicago.edu, sock=9 01/30/2013 10:30:56;0100;PBS_Server;Req;;Type StatusJob request received from s.cri.galaxy(a)crigalaxy.uchicago.edu, sock=12 01/30/2013 10:30:57;0100;PBS_Server;Req;;Type AuthenticateUser request received from s.cri.galaxy(a)crigalaxy.uchicago.edu, sock=9 01/30/2013 10:30:57;0100;PBS_Server;Req;;Type StatusJob request received from s.cri.galaxy(a)crigalaxy.uchicago.edu, sock=10 01/30/2013 10:30:58;0100;PBS_Server;Req;;Type AuthenticateUser request received from s.cri.galaxy(a)crigalaxy.uchicago.edu, sock=9 01/30/2013 10:30:58;0100;PBS_Server;Req;;Type StatusJob request received from s.cri.galaxy(a)crigalaxy.uchicago.edu, sock=12 Thank-you, Dan Sullivan

2 1

Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()
by Carl Eberhard 05 Feb '13

05 Feb '13

galaxy.jobs.handler DEBUG 2013-01-29 09:43:52,107 Loaded job runner: galaxy.jobs.runners.local:LocalJobRunner galaxy.jobs.handler ERROR 2013-01-29 09:43:52,111 Job runner is not loadable: galaxy.jobs.runners.lwr Traceback (most recent call last): File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/handler.py", line 447, in _load_plugin module = __import__( module_name ) File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/runners/lwr.py", line 232 worker = threading.Thread( ( name="LwrJobRunner.thread-%d" % i ), target=self.run_next ) ^ SyntaxError: invalid syntax It is significant - and not normal behavior. Good catch! (You can disregard the 'Error: this request returned None from get_history()' message; it records the lack of a current history which is normal when you access those pages but haven't logged in yet) On Tue, Jan 29, 2013 at 12:49 PM, Dan Tenenbaum <dtenenba(a)fhcrc.org> wrote: > Hi Carl, > > > > On Tue, Jan 29, 2013 at 9:30 AM, Carl Eberhard <carlfeberhard(a)gmail.com> > wrote: > > Those are both fine then. > > > > You've got us (temporarily) stumped - even the old timers here. > > > > Can you give some rough information on your system - what OS you're > using, > > what your network set up would be? > > > > Thanks again for looking into this. It's Mac OS X 10.8.2 with Chrome > 24.0.1312.56, though I have the same problems with Safari 6.0.2 > (8536.26.17) and Firefox 17.0. > Python 2.7.2. > > > Also - if it's not too problematic - can you do a fresh clone of Galaxy > onto > > your system and see if that installation has the same problem? > > > > I did this and it seems to have pretty much the same problem but a > slightly different manifestation. Now I am now getting the error > message "Error: this request returned None from get_history(): > http://localhost:8080/" when I try and upload a file; instead, no > error messages show up in the console, but the upload still fails. I > do however get that error message when I try and log in as a user > after registering that user. > > Another thing I notice, in the output immediately after starting run.sh: > > galaxy.jobs.handler DEBUG 2013-01-29 09:43:52,107 Loaded job runner: > galaxy.jobs.runners.local:LocalJobRunner > galaxy.jobs.handler ERROR 2013-01-29 09:43:52,111 Job runner is not > loadable: galaxy.jobs.runners.lwr > Traceback (most recent call last): > File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/handler.py", > line 447, in _load_plugin > module = __import__( module_name ) > File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/runners/lwr.py", > line 232 > worker = threading.Thread( ( name="LwrJobRunner.thread-%d" % i ), > target=self.run_next ) > ^ > SyntaxError: invalid syntax > > Maybe that is significant? > > Switching back to my previous distribution I get the identical behavior... > > Thanks, > Dan > > > > C > > > > > > > > > > On Mon, Jan 28, 2013 at 5:03 PM, Dan Tenenbaum <dtenenba(a)fhcrc.org> > wrote: > >> > >> On Mon, Jan 28, 2013 at 1:59 PM, Carl Eberhard <carlfeberhard(a)gmail.com > > > >> wrote: > >> > If you go to your galaxy root in a terminal and then cd to eggs, what > is > >> > the > >> > version listed for SQLAlchemy? > >> > > >> > >> SQLAlchemy-0.5.6_dev_r6498-py2.7.egg > >> > >> > >> > Do you have SQLAlchemy installed already on that machine (apart from > the > >> > one > >> > in Galaxy's eggs)? > >> > > >> > >> I don't think so. I never knowingly installed it and in a fresh python > >> session, 'import sqlalchemy' returns an error that there is no such > >> module. > >> > >> Thanks, > >> Dan > >> > >> > >> > > >> > > >> > On Mon, Jan 28, 2013 at 4:50 PM, Dan Tenenbaum <dtenenba(a)fhcrc.org> > >> > wrote: > >> >> > >> >> On Mon, Jan 28, 2013 at 1:40 PM, Carl Eberhard > >> >> <carlfeberhard(a)gmail.com> > >> >> wrote: > >> >> > I was incorrect in stating that the changes in the next galaxy-dist > >> >> > will > >> >> > help in this case, unfortunately. From the stack trace you posted, > >> >> > there > >> >> > is > >> >> > a deeper error with your instance that the client-side changes > won't > >> >> > help. > >> >> > > >> >> > Can you post the size, type, and name of the file you're trying to > >> >> > upload? > >> >> > > >> >> > >> >> I can reproduce this by just typing "hello, world" into the > >> >> "URL/Text:" box on the "Upload File" page. Any file of any type seems > >> >> to trigger this problem. > >> >> > >> >> Thanks, > >> >> Dan > >> >> > >> >> > >> >> > > >> >> > On Thu, Jan 24, 2013 at 6:12 PM, Dan Tenenbaum <dtenenba(a)fhcrc.org > > > >> >> > wrote: > >> >> >> > >> >> >> On Wed, Jan 23, 2013 at 3:19 PM, Carl Eberhard > >> >> >> <carlfeberhard(a)gmail.com> > >> >> >> wrote: > >> >> >> > Another thing you might try is to upload the file to our test > >> >> >> > server: > >> >> >> > https://test.g2.bx.psu.edu/ and see if that works. > >> >> >> > > >> >> >> > >> >> >> Thanks, that does work. > >> >> >> > >> >> >> Setting up an FTP server on my local installation seems pretty > >> >> >> complex. All I really want to do is work around this issue and > fool > >> >> >> Galaxy into thinking that I have uploaded a file using the > >> >> >> uploader...since this is a local installation I can put a file > >> >> >> anywhere on my system, I don't have to actually upload it, just > >> >> >> place > >> >> >> it in a directory. > >> >> >> > >> >> >> If there is no such workaround, I'll wait for the fix, I guess. > >> >> >> Thanks > >> >> >> very much for working on this! > >> >> >> Dan > >> >> >> > >> >> >> > >> >> >> > > >> >> >> > On Wed, Jan 23, 2013 at 6:06 PM, Carl Eberhard > >> >> >> > <carlfeberhard(a)gmail.com> > >> >> >> > wrote: > >> >> >> >> > >> >> >> >> If this is happening consistently and a refresh on the history > >> >> >> >> isn't > >> >> >> >> doing > >> >> >> >> anything, you might try ftp upload: > >> >> >> >> http://wiki.galaxyproject.org/FTPUpload > >> >> >> >> or if you have permissions or are an admin you can try > uploading > >> >> >> >> to > >> >> >> >> a > >> >> >> >> data > >> >> >> >> library: > >> >> >> >> > >> >> >> >> > >> >> >> >> > http://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles > >> >> >> >> > >> >> >> >> > >> >> >> >> > >> >> >> >> On Wed, Jan 23, 2013 at 5:44 PM, Dan Tenenbaum > >> >> >> >> <dtenenba(a)fhcrc.org> > >> >> >> >> wrote: > >> >> >> >>> > >> >> >> >>> On Wed, Jan 23, 2013 at 2:42 PM, Carl Eberhard > >> >> >> >>> <carlfeberhard(a)gmail.com> > >> >> >> >>> wrote: > >> >> >> >>> > What sort of database are you using on your local instance? > >> >> >> >>> > > >> >> >> >>> > >> >> >> >>> The default (sqlite I guess). It's a completely vanilla > >> >> >> >>> instance, I > >> >> >> >>> have not touched the config files. > >> >> >> >>> Dan > >> >> >> >>> > >> >> >> >>> > >> >> >> >>> > > >> >> >> >>> > On Wed, Jan 23, 2013 at 5:37 PM, Dan Tenenbaum > >> >> >> >>> > <dtenenba(a)fhcrc.org> > >> >> >> >>> > wrote: > >> >> >> >>> >> > >> >> >> >>> >> On Wed, Jan 23, 2013 at 2:35 PM, Carl Eberhard > >> >> >> >>> >> <carlfeberhard(a)gmail.com> > >> >> >> >>> >> wrote: > >> >> >> >>> >> > Thanks, Dan. That helps and I'll start looking into this. > >> >> >> >>> >> > > >> >> >> >>> >> > We will be pushing out a new galaxy-dist revision > sometime > >> >> >> >>> >> > this > >> >> >> >>> >> > week > >> >> >> >>> >> > if > >> >> >> >>> >> > all > >> >> >> >>> >> > goes well. This revision includes some code for the > history > >> >> >> >>> >> > panel > >> >> >> >>> >> > that > >> >> >> >>> >> > may > >> >> >> >>> >> > help handle this situation a bit better. I'd recommend > >> >> >> >>> >> > updating > >> >> >> >>> >> > to > >> >> >> >>> >> > that > >> >> >> >>> >> > revision when it comes out. > >> >> >> >>> >> > > >> >> >> >>> >> > >> >> >> >>> >> Thanks! Is there a workaround to upload a file or add it to > >> >> >> >>> >> my > >> >> >> >>> >> history > >> >> >> >>> >> in the meantime? Command-line is ok. If there isn't one, > >> >> >> >>> >> that's > >> >> >> >>> >> ok > >> >> >> >>> >> too.... > >> >> >> >>> >> Dan > >> >> >> >>> >> > >> >> >> >>> >> > >> >> >> >>> >> > >> >> >> >>> >> > I'll let you know what I can find. > >> >> >> >>> >> > Carl > >> >> >> >>> >> > > >> >> >> >>> >> > > >> >> >> >>> >> > > >> >> >> >>> >> > On Wed, Jan 23, 2013 at 5:18 PM, Dan Tenenbaum > >> >> >> >>> >> > <dtenenba(a)fhcrc.org> > >> >> >> >>> >> > wrote: > >> >> >> >>> >> >> > >> >> >> >>> >> >> Hi Carl, > >> >> >> >>> >> >> > >> >> >> >>> >> >> On Wed, Jan 23, 2013 at 2:14 PM, Carl Eberhard > >> >> >> >>> >> >> <carlfeberhard(a)gmail.com> > >> >> >> >>> >> >> wrote: > >> >> >> >>> >> >> > Heya, Dan. > >> >> >> >>> >> >> > > >> >> >> >>> >> >> > Sorry for the trouble. > >> >> >> >>> >> >> > When you get that error again look for a line like you > >> >> >> >>> >> >> > have > >> >> >> >>> >> >> > above: > >> >> >> >>> >> >> > Debug at: > http://localhost:8080/_debug/view/1358978130 > >> >> >> >>> >> >> > > >> >> >> >>> >> >> > If you open a new tab or window in your browser and go > >> >> >> >>> >> >> > to > >> >> >> >>> >> >> > the > >> >> >> >>> >> >> > address > >> >> >> >>> >> >> > ('http://localhost:8080/_debug ...'), you should see > a > >> >> >> >>> >> >> > more > >> >> >> >>> >> >> > informative > >> >> >> >>> >> >> > error message - complete with a list of function calls > >> >> >> >>> >> >> > that > >> >> >> >>> >> >> > led > >> >> >> >>> >> >> > to > >> >> >> >>> >> >> > the > >> >> >> >>> >> >> > error > >> >> >> >>> >> >> > (a stack trace). > >> >> >> >>> >> >> > > >> >> >> >>> >> >> > Can you post that stack trace when you see it? > >> >> >> >>> >> >> > > >> >> >> >>> >> >> > >> >> >> >>> >> >> Thanks for the quick response. Here it is: > >> >> >> >>> >> >> > >> >> >> >>> >> >> URL: > http://localhost:8080/tool_runner/upload_async_create > >> >> >> >>> >> >> File > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > '/Users/dtenenba/dev/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py', > >> >> >> >>> >> >> line 364 in respond > >> >> >> >>> >> >> app_iter = self.application(environ, > >> >> >> >>> >> >> detect_start_response) > >> >> >> >>> >> >> File > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > '/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py', > >> >> >> >>> >> >> line 98 in __call__ > >> >> >> >>> >> >> environ, self.app) > >> >> >> >>> >> >> File > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > '/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py', > >> >> >> >>> >> >> line 539 in intercept_output > >> >> >> >>> >> >> app_iter = application(environ, > >> >> >> >>> >> >> replacement_start_response) > >> >> >> >>> >> >> File > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > '/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', > >> >> >> >>> >> >> line 80 in __call__ > >> >> >> >>> >> >> return self.application(environ, start_response) > >> >> >> >>> >> >> File > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > '/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', > >> >> >> >>> >> >> line 632 in __call__ > >> >> >> >>> >> >> return self.application(environ, start_response) > >> >> >> >>> >> >> File > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > '/Users/dtenenba/dev/galaxy-dist/lib/galaxy/web/framework/base.py', > >> >> >> >>> >> >> line 160 in __call__ > >> >> >> >>> >> >> body = method( trans, **kwargs ) > >> >> >> >>> >> >> File > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > '/Users/dtenenba/dev/galaxy-dist/lib/galaxy/web/framework/__init__.py', > >> >> >> >>> >> >> line 73 in decorator > >> >> >> >>> >> >> return simplejson.dumps( func( self, trans, *args, > >> >> >> >>> >> >> **kwargs > >> >> >> >>> >> >> ) > >> >> >> >>> >> >> ) > >> >> >> >>> >> >> File > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > '/Users/dtenenba/dev/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py', > >> >> >> >>> >> >> line 317 in upload_async_create > >> >> >> >>> >> >> datasets.append( create_dataset( name ) ) > >> >> >> >>> >> >> File > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > '/Users/dtenenba/dev/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py', > >> >> >> >>> >> >> line 287 in create_dataset > >> >> >> >>> >> >> return upload_common.new_upload( trans, cntrller, ud, > >> >> >> >>> >> >> library_bunch=library_bunch, > >> >> >> >>> >> >> > >> >> >> >>> >> >> > state=trans.app.model.HistoryDatasetAssociation.states.UPLOAD > >> >> >> >>> >> >> ) > >> >> >> >>> >> >> File > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > '/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/actions/upload_common.py', > >> >> >> >>> >> >> line 213 in new_upload > >> >> >> >>> >> >> return new_history_upload( trans, uploaded_dataset, > >> >> >> >>> >> >> state ) > >> >> >> >>> >> >> File > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > '/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/actions/upload_common.py', > >> >> >> >>> >> >> line 118 in new_history_upload > >> >> >> >>> >> >> hda.state = state > >> >> >> >>> >> >> File > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > '/Users/dtenenba/dev/galaxy-dist/lib/galaxy/model/__init__.py', > >> >> >> >>> >> >> line 1048 in set_dataset_state > >> >> >> >>> >> >> object_session( self ).add( self.dataset ) > >> >> >> >>> >> >> AttributeError: 'NoneType' object has no attribute 'add' > >> >> >> >>> >> >> > >> >> >> >>> >> >> Dan > >> >> >> >>> >> >> > >> >> >> >>> >> >> > >> >> >> >>> >> >> > We can take it from there and thanks, > >> >> >> >>> >> >> > Carl > >> >> >> >>> >> >> > > >> >> >> >>> >> >> > > >> >> >> >>> >> >> > On Wed, Jan 23, 2013 at 5:04 PM, Dan Tenenbaum > >> >> >> >>> >> >> > <dtenenba(a)fhcrc.org> > >> >> >> >>> >> >> > wrote: > >> >> >> >>> >> >> >> > >> >> >> >>> >> >> >> Hi, > >> >> >> >>> >> >> >> > >> >> >> >>> >> >> >> I installed galaxy completely from scratch: > >> >> >> >>> >> >> >> > >> >> >> >>> >> >> >> rm -rf galaxy-dist && hg clone > >> >> >> >>> >> >> >> https://bitbucket.org/galaxy/galaxy-dist/ > >> >> >> >>> >> >> >> > >> >> >> >>> >> >> >> I'm not a mercurial expert but I think I have > changeset > >> >> >> >>> >> >> >> 8530:a4113cc1cb5e; at least that's the first entry in > >> >> >> >>> >> >> >> "hg > >> >> >> >>> >> >> >> log". > >> >> >> >>> >> >> >> > >> >> >> >>> >> >> >> Then started galaxy like this: > >> >> >> >>> >> >> >> cd galaxy-dist > >> >> >> >>> >> >> >> ./run.sh > >> >> >> >>> >> >> >> > >> >> >> >>> >> >> >> I went to http://localhost:8080 and tried to upload > a > >> >> >> >>> >> >> >> file. I > >> >> >> >>> >> >> >> never > >> >> >> >>> >> >> >> saw the file in my history, and this is what printed > >> >> >> >>> >> >> >> out > >> >> >> >>> >> >> >> in > >> >> >> >>> >> >> >> the > >> >> >> >>> >> >> >> console after I clicked "Execute" on the "Upload > File" > >> >> >> >>> >> >> >> page: > >> >> >> >>> >> >> >> > >> >> >> >>> >> >> >> galaxy.web.framework DEBUG 2013-01-23 13:56:11,573 > >> >> >> >>> >> >> >> Error: > >> >> >> >>> >> >> >> this > >> >> >> >>> >> >> >> request > >> >> >> >>> >> >> >> returned None from get_history(): > >> >> >> >>> >> >> >> > http://localhost:8080/tool_runner/upload_async_create > >> >> >> >>> >> >> >> galaxy.web.framework DEBUG 2013-01-23 13:56:11,573 > >> >> >> >>> >> >> >> Error: > >> >> >> >>> >> >> >> this > >> >> >> >>> >> >> >> request > >> >> >> >>> >> >> >> returned None from get_history(): > >> >> >> >>> >> >> >> > http://localhost:8080/tool_runner/upload_async_create > >> >> >> >>> >> >> >> galaxy.web.framework DEBUG 2013-01-23 13:56:11,573 > >> >> >> >>> >> >> >> Error: > >> >> >> >>> >> >> >> this > >> >> >> >>> >> >> >> request > >> >> >> >>> >> >> >> returned None from get_history(): > >> >> >> >>> >> >> >> > http://localhost:8080/tool_runner/upload_async_create > >> >> >> >>> >> >> >> galaxy.web.framework DEBUG 2013-01-23 13:56:11,573 > >> >> >> >>> >> >> >> Error: > >> >> >> >>> >> >> >> this > >> >> >> >>> >> >> >> request > >> >> >> >>> >> >> >> returned None from get_history(): > >> >> >> >>> >> >> >> > http://localhost:8080/tool_runner/upload_async_create > >> >> >> >>> >> >> >> galaxy.web.framework DEBUG 2013-01-23 13:56:11,573 > >> >> >> >>> >> >> >> Error: > >> >> >> >>> >> >> >> this > >> >> >> >>> >> >> >> request > >> >> >> >>> >> >> >> returned None from get_history(): > >> >> >> >>> >> >> >> > http://localhost:8080/tool_runner/upload_async_create > >> >> >> >>> >> >> >> galaxy.web.framework DEBUG 2013-01-23 13:56:11,573 > >> >> >> >>> >> >> >> Error: > >> >> >> >>> >> >> >> this > >> >> >> >>> >> >> >> request > >> >> >> >>> >> >> >> returned None from get_history(): > >> >> >> >>> >> >> >> > http://localhost:8080/tool_runner/upload_async_create > >> >> >> >>> >> >> >> galaxy.web.framework DEBUG 2013-01-23 13:56:11,573 > >> >> >> >>> >> >> >> Error: > >> >> >> >>> >> >> >> this > >> >> >> >>> >> >> >> request > >> >> >> >>> >> >> >> returned None from get_history(): > >> >> >> >>> >> >> >> > http://localhost:8080/tool_runner/upload_async_create > >> >> >> >>> >> >> >> galaxy.web.framework DEBUG 2013-01-23 13:56:11,574 > >> >> >> >>> >> >> >> Error: > >> >> >> >>> >> >> >> this > >> >> >> >>> >> >> >> request > >> >> >> >>> >> >> >> returned None from get_history(): > >> >> >> >>> >> >> >> > http://localhost:8080/tool_runner/upload_async_create > >> >> >> >>> >> >> >> galaxy.web.framework DEBUG 2013-01-23 13:56:11,574 > >> >> >> >>> >> >> >> Error: > >> >> >> >>> >> >> >> this > >> >> >> >>> >> >> >> request > >> >> >> >>> >> >> >> returned None from get_history(): > >> >> >> >>> >> >> >> > http://localhost:8080/tool_runner/upload_async_create > >> >> >> >>> >> >> >> 127.0.0.1 - - [23/Jan/2013:13:56:11 -0700] "POST > >> >> >> >>> >> >> >> /tool_runner/upload_async_create HTTP/1.1" 500 - > >> >> >> >>> >> >> >> "http://localhost:8080/" "Mozilla/5.0 (Macintosh; > Intel > >> >> >> >>> >> >> >> Mac > >> >> >> >>> >> >> >> OS X > >> >> >> >>> >> >> >> 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) > >> >> >> >>> >> >> >> Chrome/24.0.1312.56 > >> >> >> >>> >> >> >> Safari/537.17" > >> >> >> >>> >> >> >> Debug at: > http://localhost:8080/_debug/view/1358978130 > >> >> >> >>> >> >> >> 127.0.0.1 - - [23/Jan/2013:13:56:11 -0700] "GET > >> >> >> >>> >> >> >> /tool_runner/upload_async_message HTTP/1.1" 200 - > >> >> >> >>> >> >> >> "http://localhost:8080/" "Mozilla/5.0 (Macintosh; > Intel > >> >> >> >>> >> >> >> Mac > >> >> >> >>> >> >> >> OS X > >> >> >> >>> >> >> >> 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) > >> >> >> >>> >> >> >> Chrome/24.0.1312.56 > >> >> >> >>> >> >> >> Safari/537.17" > >> >> >> >>> >> >> >> 127.0.0.1 - - [23/Jan/2013:13:56:11 -0700] "GET > >> >> >> >>> >> >> >> /history > >> >> >> >>> >> >> >> HTTP/1.1" > >> >> >> >>> >> >> >> 200 > >> >> >> >>> >> >> >> - > >> >> >> >>> >> >> >> " > http://localhost:8080/tool_runner/upload_async_message" > >> >> >> >>> >> >> >> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) > >> >> >> >>> >> >> >> AppleWebKit/537.17 > >> >> >> >>> >> >> >> (KHTML, like Gecko) Chrome/24.0.1312.56 > Safari/537.17" > >> >> >> >>> >> >> >> > >> >> >> >>> >> >> >> Hope someone can help. > >> >> >> >>> >> >> >> Thanks, > >> >> >> >>> >> >> >> Dan > >> >> >> >>> >> >> >> > >> >> >> >>> >> >> >> > >> >> >> >>> >> >> >> > ___________________________________________________________ > >> >> >> >>> >> >> >> 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/ > >> >> >> >>> >> >> > > >> >> >> >>> >> >> > > >> >> >> >>> >> > > >> >> >> >>> >> > > >> >> >> >>> > > >> >> >> >>> > > >> >> >> >> > >> >> >> >> > >> >> >> > > >> >> > > >> >> > > >> > > >> > > > > > >

3 18

Behaviour of download_by_url with tar.gz during tool dependency installation
by Jean-Frédéric Berthelot 04 Feb '13

04 Feb '13

Hi list, When working to get a tool wrapper Toolshed-ready, I have explored how tool dependencies installation works, especially the download_by_url feature. I have summarised my understanding on the Wiki (hope this is clear and accurate): <http://wiki.galaxyproject.org/ToolShedToolFeatures?action=diff&rev1=33&rev2…> The difference of behaviour when dealing with a Tar and a Zip file lies in the methods tar_extraction_directory() and zip_extraction_directory() (in [1]), which try to locate the deflated files: * zip_extraction_directory() counts the number of non- .zip “files” in the current directory. If more than one, the current path is returned ; if one, this “file” is assumed to be the deflated directory, and the full path to this directory is returned. The file_name variable (set to the name of the downloaded file) is not used. * tar_extraction_directory() which takes the name of the downloaded_file and removes the extension. If a subdirectory of that name exists, it is returned . Otherwise, if the full path to the downloaded file exists, the current path is returned. Otherwise, an exception is raised. This difference of behaviour can be very confusing. My wrapper local installations kept failing because for my tool, the deflated directory name did not match the tar.gz name. I was confused because I was using the bowtie wrapper [2] as an example, where it is not an issue. The obvious workaround is to use the target_filename attribute to have the downloaded archive name match the subdirectory name (which I have done, and it works perfectly now). But I was wondering if it would be a good idea to harmonize both methods behaviour? (P.S. As I am not very familiar yet with the Galaxy development process, I believe posting here is appropriate ; but I’d be happy to open an issue − on the Trello if I am not mistaken? − if needed. ) [1] <https://bitbucket.org/galaxy/galaxy-central/src/f49ce2c1883e/lib/galaxy/too…> [2] <http://toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/file/0c7e4eadfb…> Cheers, -- Jean-Frédéric Bonsai Bioinformatics group

2 1

History not updating automatically
by Sajoscha Sauer 02 Feb '13

02 Feb '13

Hi list, I have a weird problem after updating to the latest version. After doing the update as usual, the history panel is not updating automatically anymore. And when I press refresh, I get an javascript popup saying: Error getting history updates from the server. Forbidden Also, in the log I see the following: galaxy.web.framework WARNING 2013-01-28 12:30:01,673 User logged in as '(null)' externally, but has a cookie as 'sauer(a)embl.de' invalidating session We are using LDAP to connect to Galaxy, but I don't know if this has something to do with the problem. As I said, it was working perfectly fine before the update. Does someone know the problem or has any ideas? Thanks for your help, Sajoscha

5 6

How to use the API when using a proxy server
by Anthonius deBoer 02 Feb '13

02 Feb '13

Hi, I am trying to use the API with my galaxy server running behind a proxy server. How do I pass username/password information to the API so it can actually run? If I use the regular API calls I get a access denied... Thanks Thon

3 4

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galaxy-dev January 2013