October 2016 - galaxy-dev - lists.galaxyproject.org

Pulsar - running as real DRMAA user problems
by Poole, Richard 13 May '17

13 May '17

Hey John, So I’ve been happily using Pulsar to send all my Galaxy server jobs to our cluster here at UCL for several months now (I love it!). I am now exploring the ‘run-as-real-user’ option for DRMAA submissions and have run into a problem. The files are correctly staged, correctly chowned, successfully submitted to the queue and the job runs. However, at job end (collection?) fails with the following error message in Pulsar: Exception happened during processing of request from (‘*.*.*.*', 54321) Traceback (most recent call last): File "/opt/rocks/lib/python2.6/site-packages/Paste-2.0.1-py2.6.egg/paste/httpserver.py", line 1072, in process_request_in_thread self.finish_request(request, client_address) File "/opt/rocks/lib/python2.6/SocketServer.py", line 322, in finish_request self.RequestHandlerClass(request, client_address, self) File "/opt/rocks/lib/python2.6/SocketServer.py", line 617, in __init__ self.handle() File "/opt/rocks/lib/python2.6/site-packages/Paste-2.0.1-py2.6.egg/paste/httpserver.py", line 446, in handle BaseHTTPRequestHandler.handle(self) File "/opt/rocks/lib/python2.6/BaseHTTPServer.py", line 329, in handle self.handle_one_request() File "/opt/rocks/lib/python2.6/site-packages/Paste-2.0.1-py2.6.egg/paste/httpserver.py", line 441, in handle_one_request self.wsgi_execute() File "/opt/rocks/lib/python2.6/site-packages/Paste-2.0.1-py2.6.egg/paste/httpserver.py", line 291, in wsgi_execute self.wsgi_start_response) File "/cluster/galaxy/pulsar/pulsar/web/framework.py", line 39, in __call__ return controller(environ, start_response, **request_args) File "/cluster/galaxy/pulsar/pulsar/web/framework.py", line 144, in controller_replacement result = self.__execute_request(func, args, req, environ) File "/cluster/galaxy/pulsar/pulsar/web/framework.py", line 124, in __execute_request result = func(**args) File "/cluster/galaxy/pulsar/pulsar/web/routes.py", line 82, in status return status_dict(manager, job_id) File "/cluster/galaxy/pulsar/pulsar/manager_endpoint_util.py", line 12, in status_dict job_status = manager.get_status(job_id) File "/cluster/galaxy/pulsar/pulsar/managers/stateful.py", line 95, in get_status proxy_status, state_change = self.__proxy_status(job_directory, job_id) File "/cluster/galaxy/pulsar/pulsar/managers/stateful.py", line 115, in __proxy_status proxy_status = self._proxied_manager.get_status(job_id) File "/cluster/galaxy/pulsar/pulsar/managers/queued_external_drmaa_original.py", line 62, in get_status external_status = super(ExternalDrmaaQueueManager, self)._get_status_external(external_id) File "/cluster/galaxy/pulsar/pulsar/managers/base/base_drmaa.py", line 31, in _get_status_external drmaa_state = self.drmaa_session.job_status(external_id) File "/cluster/galaxy/pulsar/pulsar/managers/util/drmaa/__init__.py", line 50, in job_status return self.session.jobStatus(str(external_job_id)) File "build/bdist.linux-x86_64/egg/drmaa/session.py", line 518, in jobStatus c(drmaa_job_ps, jobId, byref(status)) File "build/bdist.linux-x86_64/egg/drmaa/helpers.py", line 299, in c return f(*(args + (error_buffer, sizeof(error_buffer)))) File "build/bdist.linux-x86_64/egg/drmaa/errors.py", line 151, in error_check raise _ERRORS[code - 1](error_string) InvalidJobException: code 18: The job specified by the 'jobid' does not exist. With this corresponding error from my Galaxy server: galaxy.tools.actions INFO 2016-10-13 18:47:51,851 Handled output (279.421 ms) galaxy.tools.actions INFO 2016-10-13 18:47:52,093 Verified access to datasets (5.271 ms) galaxy.tools.execute DEBUG 2016-10-13 18:47:52,118 Tool [toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4] created job [25008<http://toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4]%20…>] (560.404 ms) galaxy.jobs DEBUG 2016-10-13 18:47:52,579 (25008) Working directory for job is: /Users/galaxy/galaxy-dist/database/job_working_directory/025/25008 galaxy.jobs.handler DEBUG 2016-10-13 18:47:52,591 (25008) Dispatching to pulsar runner galaxy.jobs DEBUG 2016-10-13 18:47:52,677 (25008) Persisting job destination (destination id: hpc_low) galaxy.jobs.runners DEBUG 2016-10-13 18:47:52,681 Job [25008] queued (90.231 ms) galaxy.jobs.handler INFO 2016-10-13 18:47:52,699 (25008) Job dispatched galaxy.tools.deps DEBUG 2016-10-13 18:47:53,138 Building dependency shell command for dependency 'samtools' galaxy.jobs.runners.pulsar INFO 2016-10-13 18:47:53,233 Pulsar job submitted with job_id 25008 galaxy.jobs DEBUG 2016-10-13 18:47:53,257 (25008) Persisting job destination (destination id: hpc_low) galaxy.datatypes.metadata DEBUG 2016-10-13 18:51:03,922 Cleaning up external metadata files galaxy.jobs.runners.pulsar ERROR 2016-10-13 18:51:03,945 failure finishing job 25008 Traceback (most recent call last): File "/Users/galaxy/galaxy-dist/lib/galaxy/jobs/runners/pulsar.py", line 386, in finish_job run_results = client.full_status() File "/Users/galaxy/galaxy-dist/lib/pulsar/client/client.py", line 132, in full_status return self.raw_check_complete() File "/Users/galaxy/galaxy-dist/lib/pulsar/client/decorators.py", line 28, in replacement return func(*args, **kwargs) File "/Users/galaxy/galaxy-dist/lib/pulsar/client/decorators.py", line 13, in replacement response = func(*args, **kwargs) File "/Users/galaxy/galaxy-dist/lib/pulsar/client/client.py", line 146, in raw_check_complete check_complete_response = self._raw_execute("status", {"job_id": self.job_id}) File "/Users/galaxy/galaxy-dist/lib/pulsar/client/client.py", line 215, in _raw_execute return self.job_manager_interface.execute(command, args, data, input_path, output_path) File "/Users/galaxy/galaxy-dist/lib/pulsar/client/interface.py", line 96, in execute response = self.transport.execute(url, method=method, data=data, input_path=input_path, output_path=output_path) File "/Users/galaxy/galaxy-dist/lib/pulsar/client/transport/standard.py", line 34, in execute response = self._url_open(request, data) File "/Users/galaxy/galaxy-dist/lib/pulsar/client/transport/standard.py", line 20, in _url_open return urlopen(request, data) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 154, in urlopen return opener.open(url, data, timeout) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 437, in open response = meth(req, response) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 550, in http_response 'http', request, response, code, msg, hdrs) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 475, in error return self._call_chain(*args) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 409, in _call_chain result = func(*args) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 558, in http_error_default raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) HTTPError: HTTP Error 500: Internal Server Error I am running 15.10 and Python 2.7.10 on my iMac for the server and the cluster submission node is running Pulsar 0.5.0 and Python 2.7.12 For these tests I run Pulsar in an interactive window so I have not set the sudoers file up, but rather enter sudo password when requested by Pulsar (at the first step of chowning the staging directory). Also have rewrites set up in Galaxy’s pulsar_actions.yml and I am using remote_scp for the file transfers rather than http - although I have also tried switching back to http (as I noticed caching, which I am also testing, does not work with scp transfers) but get an identical set of error messages. As I say, I have no troubles using a regular queued_drmaa manager in pulsar. Any ideas what the problem may be? Cheers, Rich Richard J Poole PhD Wellcome Trust Fellow Department of Cell and Developmental Biology University College London 518 Rockefeller 21 University Street, London WC1E 6DE Office (518 Rockefeller): +44 20 7679 6577 (int. 46577) Lab (529 Rockefeller): +44 20 7679 6133 (int. 46133) https://www.ucl.ac.uk/cdb/academics/poole

2 5

Running jobs as real user and extra_file_path
by Louise-Amélie Schmitt 28 Apr '17

28 Apr '17

Hi everyone, I just wanted to ask how the extra_file_path is handled in case of job running as the real user since the file_path is only writable by the galaxy user. Any clue? Thanks, L-A

3 3

Issue when using xsendfile with galaxy release_16.07
by SAPET, Frederic 28 Feb '17

28 Feb '17

Hello I'm trying the latest Galaxy (git status gives me : # On branch release_16.07) I've set the xsend option in galaxy.ini (in order to run Galaxy behind a web server proxy, and apply all methods described here : https://wiki.galaxyproject.org/Admin/Config/ApacheProxy) apache_xsendfile = True HTML, gff3,tabular files are just fine but the preview of some other files (txt, csv) is broken on the interface. When I want to preview a txt file : Not Found The requested URL /datasets/fd1df6a9052810d5/display/ was not found on this server. And apache says : [Thu Aug 18 15:33:48 2016] [error] [client 192.168.29.12] (13)Permission denied: xsendfile: cannot open file: /softs/bioinfo/galaxy-prod/database/files/000/dataset_19.dat, referer: http: But it looks like this is not really a problem related to access. Indeed, from the same file, I switch it from txt to tabular (edit attributes), the preview works. Are you able to reproduce the behavior ? The same problem occurs on release_16.01. It's fine with the release v15.05 which is my production server right now. Fred

2 4

display at UCSC does not work
by Hans-Rudolf Hotz 24 Jan '17

24 Jan '17

Hi I am trying to set up the possibility to display data sets with the UCSC genome browser for our new galaxy installation. After clicking on "display at UCSC main", I get the UCSC genome browser, opening in the right assembly, and at the correct location, but I get the following Error: Warning/Error(s): redirected to non-http(s): /login?redirect=%2Froot%2Fdisplay_as In galaxy.ini, I did uncomment the line: display_servers = hgw1.cse.ucsc.edu,hgw2.cse.ucsc.edu,hgw3.cse. ... We use the 'new' authentication method to connect to our LDAP server, with the following changes in galaxy.ini: require_login = True auth_config_file = config/auth_conf.xml Connection from UCSC to our galaxy server is working, since I can display the data, when I switch to require_login = False it works, independent of whether I am logged in or not. Is there a way to get it to work, even if I have "require_login = True"? Thank you very much for your help Regards, Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland

1 1

Python script can't can't import BioPython modules in Galaxy 16.01
by Makis Ladoukakis 17 Jan '17

17 Jan '17

Hello everyone, I've recently upgraded to Galaxy 16.01 and i have some issues with a python wrapper from a tool. When I run it via Galaxy I get the following error: Traceback (most recent call last): File "/home/galaxy_user/galaxy/tools/myTools/know_parser/know_parser.py", line 12, in <module> from Bio import SeqIO ImportError: No module named Bio However when I click on the "view details" icon to copy the command from the tool and run it on my command line the tool works perfectly. In addition this issue occurs while I already have installed BioPython. When I type Python and write "from Bio import SeqIO" I get no error. Can this be an issue related to the virtual environment that is initialized each time Galaxy starts? Thank you in advance, Makis Ladoukakis

5 8

conda management of tools dependent on python3
by Wolfgang Maier 10 Nov '16

10 Nov '16

Dear all, I'm still pretty new to conda tool dependencies management and there is one thing I cannot find documented anywhere: How can I let conda manage tool dependencies that involve python3? If I let Galaxy install conda for me, it creates an environment with python2, then if there is a tool dependency that has a conda package built for only python3 I'm getting an error because of a conflict between that package and python2 (not surprisingly), but AFAIU conda environments are bound to one particular version of python (or is that incorrect?). Thanks for any help with this and best wishes, Wolfgang

4 9

Compiling dependencies in galaxy yields error
by evan clark 01 Nov '16

01 Nov '16

I was installing a tool from the galaxy toolshed and one of the dependencies was missing due to a bad link. I modified the install files to use the same version of the the software except from a local directory, however galaxy renders a large error when compiling. If I compile the source in the same location outside of galaxy it compiles and installs correctly. The specific package I am attempting to install is ghostscript for homer package.

2 4

Local Galaxy Workflow Sharing
by Rachel Bell 31 Oct '16

31 Oct '16

Hi, I am looking to share a workflow I've created in Local Galaxy with an individual user via email address - where they will access the workflow on main galaxy. When I select 'Share/Download' the following error message appears: [cid:59dde9c4-0f20-4cb6-9c14-1875f09657c4] I'd really appreciate some guidance on this, I'm guessing it is maybe a permissions thing in one of the config files? Thanks in advance, Rachel Bell Bioinformatics Technician Premaitha Health Rutherford House Manchester Science Park Manchester, M15 6SZ, UK T: +44 (0) 161 667 1068 M: +44 (0) 7875 191 219 www.premaitha.com<http://www.premaitha.com/> This e-mail including any attachments is intended for the addressee only. It is private and confidential. If you have received this message in error, we apologise, but please notify us and remove it from your system. You must take no action based on this email, nor must you copy or disclose it or any part of its contents to any person or organisation. Please note that email communications may be monitored. Premaitha Limited, trading as Premaitha Health, is registered in England with registered number 8436676. Its registered office is at Rutherford House, Manchester Science Park, Manchester, M15 6SZ, UK.

2 1

November 2016 Galactic News
by Dave Clements 31 Oct '16

31 Oct '16

1 0

Error for Picard CollectInsertSizeMetrics
by Raphenya, Amogelang 31 Oct '16

31 Oct '16

1 0