February 2013 - galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] Velvet program files
by Thyssen, Gregory - ARS 05 Feb '13

05 Feb '13

I partially answered my own questions by reading the Tool Dependencies wiki page. I installed velvet to my workstation. When I open the shell to start galaxy, I modify $PATH to include the velvet directory. Now the error I get in Velvet suggests it found the program, but something else is wrong. My new error is: No reads found The reads are fastq files that appear in my history and are data libraries housed in an external harddrive. I have used these same data before on the public server. Please advise, Thanks, Greg From: Thyssen, Gregory - ARS Sent: Tuesday, February 05, 2013 10:38 AM To: 'galaxy-dev(a)bx.psu.edu' Subject: Velvet program files So I am setting up my local Galaxy on a workstation for my own use. I have installed several programs from the Assembly Main Tool Shed. None works. Are these just the wrappers? Do I need to install, say, Velvet somewhere outside of Galaxy? How do I do this? My errors: 6: velveth on data 2 error An error occurred running this job:Unable to run velveth: No such file or directory 7: Abyss on data 5 error An error occurred running this job: ERROR: Expected exactly 3 arguments; got: 67 /media/My Passport/IM-Data2Bio-10262012/IM-mut1/Im-mutant-bulk_1.fastq /home/galaxy/galaxy-dist/database/files/000/dataset_9.dat 8: MIRA contigs (FASTA) error An error occurred running this job: Traceback (most recent call last): File "/home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/peterjc/mira_assembler/3e7eca1f5d04/mira_assembler/tools/sr_assembly/mira.py", line 33, in mira_ver = get_version() File "/home/galaxy/shed_tool 15: Singleton reads reads for velvet error An error occurred running this job: Error running preppereads.sh /bin/sh: /users/galaxy/galaxyscripts/prepare_pe_reads_for_velvet.sh: No such file or directory Thanks, Greg This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.

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Re: [galaxy-dev] install Galaxy in Windows (URGENT)
by Nate Coraor 05 Feb '13

05 Feb '13

On Feb 2, 2013, at 1:02 AM, Prasun Dutta wrote: > Hi Nate, > > Thanks for the reply. I have already installed VM and downloading Ubuntu now. I had some other queries: Hi Prasun, It's best to keep replies on the list, to ensure access to a wide audience of people who may be able to provide better answers than the original respondent. > Can I add my own tools in the main public galaxy? For example, I have some perl scripts that I have to connect together in a workflow. I know, its better to have a local instance for these kind of personal jobs, but still, I would be grateful if you could throw some light on it. And do we have to create our own xml code of the perl program I have written or galaxy can convert it on its own? It's not possible to install your own tools on Galaxy servers that you don't administrate due to the implications on security and resource usage. You do need to write your own XML, although for simple tools it is not very difficult and there are a plethora of tutorials and examples available. An automated alternative would be to use the Galaxy Tool Factory: http://www.ncbi.nlm.nih.gov/pubmed/23024011 --nate > > Regards, > Prasun Dutta > MSc (Bioinformatics) > School of Biological Sciences > University of Edinburgh, UK > > From: Nate Coraor <nate(a)bx.psu.edu> > To: Peter Cock <p.j.a.cock(a)googlemail.com> > Cc: Prasun Dutta <prasundutta87(a)yahoo.co.in>; "galaxy-dev(a)bx.psu.edu" <galaxy-dev(a)bx.psu.edu> > Sent: Saturday, 2 February 2013 3:11 AM > Subject: Re: [galaxy-dev] install Galaxy in Windows (URGENT) > > On Feb 1, 2013, at 11:12 AM, Peter Cock wrote: > > > On Fri, Feb 1, 2013 at 3:48 PM, Prasun Dutta <prasundutta87(a)yahoo.co.in> wrote: > >> Hi Peter, > >> > >> Unfortunately, I am not an advanced developer in python. Although, I have > >> 'Cygwin' in my system. Any heads up on that will be greatly appreciated? > >> > > > > Cygwin is a useful system for running Unix/Linux tools under Windows, > > and according to this old email from Nate you would need to use it: > > http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003671.html > > > > More recently a couple of people tried this and ran into problems: > > http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-October/007132.html > > http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-October/007180.html > > http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-October/007182.html > > > > For the simplest install and maintenance, choose what the Galaxy team > > use: Linux > > Even if you can get the framework to run, many tools with C dependencies are going to be a nightmare to use since the dependencies will almost certainly not compile. The easiest solution these days if you really have no access to a Linux system (the cloud is a good choice here) is probably to install Linux in a VM on your Windows system. This can be done for free with a VM platform like VirtualBox. > > --nate > > > > > Regards, > > > > Peter > > ___________________________________________________________ > > 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/ > > >

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Question regarding frequency of pbs_mom authentications
by Daniel Patrick Sullivan 05 Feb '13

05 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

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Error! Sam-to-bam samtools command not found
by Hakeem Almabrazi 05 Feb '13

05 Feb '13

Hi, I installed a local galaxy on Centos 6 and I followed the instructions on how to install samtools/bwa/bowtie found here http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup. I setup the correct env. for these programs correctly. Since I have no issues with the bwa and bowtie so I assumed I got everything correctly but that was not true since I keep getting the following error when I try Sam-To-Bam... ............. galaxy.jobs.runners.local DEBUG 2013-02-05 10:37:36,053 execution of external set_meta for job 62 finished galaxy.jobs DEBUG 2013-02-05 10:37:36,070 Tool did not define exit code or stdio handling; checking stderr for success galaxy.datatypes.metadata DEBUG 2013-02-05 10:37:36,101 setting metadata externally failed for HistoryDatasetAssociation 76: Error Setting BAM Metadata: /bin/sh: samtools: command not found galaxy.jobs.runners.local ERROR 2013-02-05 10:37:36,134 Job wrapper finish method failed Traceback (most recent call last): File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 156, in run_job job_wrapper.finish( stdout, stderr, exit_code ) File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 412, in finish dataset.datatype.set_meta( dataset, overwrite = False ) #call datatype.set_meta directly for the initial set_meta call during dataset creation File "/usr/local/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 213, in set_meta raise Exception, "Error Setting BAM Metadata: %s" % stderr Exception: Error Setting BAM Metadata: /bin/sh: samtools: command not found galaxy.datatypes.metadata DEBUG 2013-02-05 10:37:36,239 Cleaning up external metadata files ............ * Samtools is in the path: >echo $PATH /usr/local/galaxy/galaxy_env/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/usr/java/latest/bin:/usr/local/scripts:/usr/local/galaxy/software/samtools/0.1.16/bin/:/usr/local/galaxy/software/bwa/0.2.6/bin/:/usr/local/galaxy/software/bowtie/0.12.7/bin/:/usr/local/galaxy/software/fastx/0.0.13/bin/:/usr/local/galaxy/software/ncbi-blast/2.2.27/bin/:/usr/local/galaxy/software/lastz-distrib/1.02.00/bin/ * I setup the env.sh as recommended. >more //usr/local/galaxy/software/samtools/0.1.16/env.sh #Configure PATH to Samtools binaries PATH="/usr/local/galaxy/software/samtools/0.1.16/bin/:$PATH" export PATH * And here what I have in the bin:> ls -lh /usr/local/galaxy/software/samtools/0.1.16/bin/ total 1.5M -rwxr-xr-x 1 galaxy galaxy 2.4K Jan 29 12:53 blast2sam.pl -rwxr-xr-x 1 galaxy galaxy 2.1K Jan 29 12:53 bowtie2sam.pl -rwxr-xr-x 1 galaxy galaxy 19K Jan 29 12:53 export2sam.pl -rwxr-xr-x 1 galaxy galaxy 4.9K Jan 29 12:53 interpolate_sam.pl -rwxr-xr-x 1 galaxy galaxy 5.9K Jan 29 12:53 novo2sam.pl -rwxr-xr-x 1 galaxy galaxy 2.0K Jan 29 12:53 psl2sam.pl -rwxr-xr-x 1 galaxy galaxy 7.7K Jan 29 12:53 sam2vcf.pl -rwxrwxr-x 1 galaxy galaxy 1.4M Jan 29 12:53 samtools -rwxr-xr-x 1 galaxy galaxy 14K Jan 29 12:53 samtools.pl -rwxr-xr-x 1 galaxy galaxy 2.7K Jan 29 12:53 soap2sam.pl -rwxr-xr-x 1 galaxy galaxy 2.7K Jan 29 12:53 wgsim_eval.pl -rwxr-xr-x 1 galaxy galaxy 2.4K Jan 29 12:53 zoom2sam.pl * I could ran the samtools from anywhere in the system including from "galaxy" account. * I looked at this thread which the guy has similar problem but he was trying to set it up in a cluster and installing it on Ubunto. I read the whole thing and tried everything in there but no luck.... http://gmod.827538.n3.nabble.com/Exception-Error-Setting-BAM-Metadata-bin-s… * I have installed R and Python/rpy and set their env. as required (I THINK) assuming this might be a cause but I do not see anything in the error log that will indicate that... Can anyone help in debugging this issue please? Thanks hakeem

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permissions on library contents
by Olivia Doppelt 05 Feb '13

05 Feb '13

Hello, I'm looking for a way to change library permissions using galaxy API. When I look at the API documentation at the url > https://galaxy-dist.readthedocs.org/en/latest/_modules/galaxy/webapps/galax… There is supposed to be a way to do that but when I try to access my local galaxy url library permissions, the route isn't valid (http://localhost:8080/api/libraries/f2db41e1fa331b3e/permissions) Could you please help me with that ? Best regards, -- Olivia Doppelt-Azeroual, PhD CIB - Institut Pasteur, PARIS

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Fwd: Running galaxy from eclipse running PyDev
by Eric Kuyt 05 Feb '13

05 Feb '13

Hi All, I am Running my local galaxy instance in Eclipse - pydev to make debugging somewhat easier, but now I run into loads of Code errors. It seems that pydev doesn't understand the Bunch() Class frequently used in Galaxy. But also code errors that maybe could be fixed. such as: lib/galaxy/jobs/runner/lwr.py:232 #worker = threading.Thread( ( name="LwrJobRunner.thread-%d" % i ), # target=self.run_next ) --> #worker = threading.Thread( name="LwrJobRunner.thread-%d" % i , #target=self.run_next ) Are these real errors or am I doing something wrong. Is there anyone with more experience in running Galaxy from within Eclipse? Thanks, Eric

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File Upload doesn't generate any activity
by Stephen Groenewold 04 Feb '13

04 Feb '13

We've installed a local instance of Galaxy and are having trouble with the first step of uploading files. The only thing that will currently upload is text pasted into the URL/Text box. Any attempt to upload a file using the Browse File box not only fails, it never even starts. It's as if the Execute button is disabled. I've tried changing the ajax-upload parameter to "false" in tools/data_source/upload.xml (as mentioned in a workaround posted to the list by Daniel Blankenburg in Aug 2012). I've also tried using different browsers (including Internet Explorer) and going the route of Adding Data Libraries as Admin. None of those attempts have worked. Am I missing a configuration setup? Could there be permissions issues on the Galaxy machine? Thanks. Steve

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Why "upload" to Local Instance rather than "import"?
by Thyssen, Gregory - ARS 04 Feb '13

04 Feb '13

I have a local instance of Galaxy running on my workstation. I have external hard drives full of fastq sequencing files. I want to make them available to myself as data libraries. I am the Admin and sole user at this point. The "upload" data libraries seems to pass the data through the (slow) network, even though my workstation and external hard drives are linked by USB. What is the fastest way to import my files into my galaxy instance? Can I copy them into some folder on the workstation's hard drive? Since everything is physically connected, I don't think I should be limited by my network speed. Thanks, Greg Thyssen Gregory Thyssen, PhD Molecular Biologist Cotton Fiber Bioscience USDA-ARS-Southern Regional Research Center 1100 Robert E Lee Blvd New Orleans, LA 70124 gregory.thyssen(a)ars.usda.gov 504-286-4280 This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.

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Local toolshed not working "HTTPError: HTTP Error 400: Bad Request"
by Carlos Borroto 04 Feb '13

04 Feb '13

Hi, I interested in hosting a local toolshed. I was able to install it and add a tool to it. I have configured my local galaxy instance to pull tools from this local toolshed. As far as I can tell everything is working in the toolshed side of things, but when I try to install the tool I added I get this error: URL: http://galaxydev.bfx.brel.local/admin_toolshed/prepare_for_install?tool_she… File '/local/opt/galaxy/galaxy-dist.dev/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/local/opt/galaxy/galaxy-dist.dev/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/local/opt/galaxy/galaxy-dist.dev/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/local/opt/galaxy/galaxy-dist.dev/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/local/opt/galaxy/galaxy-dist.dev/lib/galaxy/web/framework/middleware/remoteuser.py', line 91 in __call__ return self.app( environ, start_response ) File '/local/opt/galaxy/galaxy-dist.dev/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/local/opt/galaxy/galaxy-dist.dev/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/local/opt/galaxy/galaxy-dist.dev/lib/galaxy/web/framework/__init__.py', line 208 in decorator return func( self, trans, *args, **kwargs ) File '/local/opt/galaxy/galaxy-dist.dev/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 1177 in prepare_for_install response = urllib2.urlopen( url ) File '/usr/lib64/python2.6/urllib2.py', line 126 in urlopen return _opener.open(url, data, timeout) File '/usr/lib64/python2.6/urllib2.py', line 397 in open response = meth(req, response) File '/usr/lib64/python2.6/urllib2.py', line 510 in http_response 'http', request, response, code, msg, hdrs) File '/usr/lib64/python2.6/urllib2.py', line 435 in error return self._call_chain(*args) File '/usr/lib64/python2.6/urllib2.py', line 369 in _call_chain result = func(*args) File '/usr/lib64/python2.6/urllib2.py', line 518 in http_error_default raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) HTTPError: HTTP Error 400: Bad Request I can manually confirm this URL is incorrect: tool_shed_url=http://toolsheddev.bfx.brel.local:9009/&repository_ids=ee9b707789bf4714&changeset_revisions=71b062907e0d When I try to directly access it I get this error: Not Found The resource could not be found. No action for /&repository_ids=ee9b707789bf4714&changeset_revisions=71b062907e0d I don't think is related but maybe I should mention it. I have to use a http proxy to access the web, so I have http_proxy environment variable set. This was causing issues with the local toolshed as my institution proxy won't respond for requests to local hostnames. The tool files would get uploaded but resetting the metadata would fail with: galaxy.util.shed_util_common DEBUG 2013-02-04 13:02:38,221 Resetting all metadata on repository: annotab galaxy.util.shed_util_common DEBUG 2013-02-04 13:02:38,271 Cloning repository revision: 0 galaxy.util.shed_util_common DEBUG 2013-02-04 13:02:38,276 Error cloning repository: HTTP Error 400: Bad Request galaxy.util.shed_util_common DEBUG 2013-02-04 13:02:38,326 Cloning repository revision: 1 galaxy.util.shed_util_common DEBUG 2013-02-04 13:02:38,329 Error cloning repository: HTTP Error 400: Bad Request galaxy.util.shed_util_common DEBUG 2013-02-04 13:02:38,377 Cloning repository revision: 2 galaxy.util.shed_util_common DEBUG 2013-02-04 13:02:38,380 Error cloning repository: HTTP Error 400: Bad Request I was able to fix this issue by editing ~/.hgrc and adding: [http_proxy] no = toolshed.bfx.brel.local,toolsheddev.bfx.brel.local I mention it just in case for some reason my issue could be related, although as I said I don't think so. Any help would be most welcomed, Thanks, Carlos

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Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()
by Carl Eberhard 04 Feb '13

04 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/ > >> >> >> >>> >> >> > > >> >> >> >>> >> >> > > >> >> >> >>> >> > > >> >> >> >>> >> > > >> >> >> >>> > > >> >> >> >>> > > >> >> >> >> > >> >> >> >> > >> >> >> > > >> >> > > >> >> > > >> > > >> > > > > > >

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