galaxy-dev December 2016

galaxy-dev@lists.galaxyproject.org

39 participants
37 discussions

Groovy tool for galaxy
by Anshul Tak 23 Aug '17

23 Aug '17

Hi, I have a question regarding galaxy. Can I execute groovy scipts using galaxy? I installed groovy in galaxy docker image and all the dependencies. However, when I try to execute a tool which require groovy engine it says "/export/galaxy-central/database/job_working_directory/000/2/tool_script.sh: line 9: groovy: command not found" So I understood the error that galaxy is not able to find groovy but ideally it should take the groovy engine as it is installed. Can you give me some pointers to solve this issue? -- With Regards, Anshul Tak

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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

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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

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Testing updated NCBI BLAST+ wrappers for version 2.5.0
by Peter Cock 19 Apr '17

19 Apr '17

Hello all, I have updated the NCBI BLAST+ wrappers on the Test Tool Shed, the wrapper is now at v0.2.00: https://testtoolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/ The main changes is this now depends on BLAST+ 2.5.0, and that is available via either BioConda or the Tool Shed: https://toolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_5_0/ https://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_5_0/ In order for the dependency to work smoothly on both BioConda and the Tool Shed system, we have changed the package name from "blast+" to just "blast". Given the NCBI stopped updated the original "legacy" BLAST some time ago, when combined with the version number this is no longer ambiguous. Jumping from using BLAST+ 2.2.31 to using BLAST+ 2.5.0 required updating lots of the test files for NCBI changes, including dropping the GI numbers in many outputs, expanding the percentage identity field from 2dp to 3dp, and also changing how -parse_deflines works with tabular output. The wrappers (deliberately) do not yet offer any new functionality added in the recent NCBI BLAST+ updates, in particular BLAST XML v2 is not yet available as an output with a datatype in Galaxy. At this point I would welcome feedback from those of you using the BLAST+ wrappers - including if you were able to install this with the dependencies from BioConda or the traditional Tool Shed packages. Once I'm confident that this is all OK, I will update the main Tool Shed (and think about adding new functionality in 2017). Thank you all, Peter

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installation error on venv dependencies.xml
by Linda Bakker 14 Mar '17

14 Mar '17

Hi All, I am having some problems with my tool dependencies to setup a python venv. Dependencies.xml looks like this: When i install my tool from the toolshed, it fails to install the venv dependency with this error message: I am not sure what the problem exactly seems to be. os.py should be a default python package right or do i need to specify it in the dependencies file? Can someone point me in the right direction of what the problem might be. Thanks! with regards , Linda Bakker -- Linda Bakker Bioinformatics Research Assistant Plant Research International, Wageningen UR Building 107 (Radix), room W1.Fa.054 Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands tel: +31-317-480756 email: linda.bakker(a)wur.nl

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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

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Question about Data Managers
by Carlos Lijeron 03 Feb '17

03 Feb '17

Everyone, I’m trying to setup various data managers to automatically download and index reference indices. However, I can’t figure out where to change the default location where these are saved. As you can see in the attached image, the default location for the indexes is the … /tool-data/dbkey/index_name However, I would like to save them in /projects/reference_datasets which is a shared location that has a lot of space available. Please advise. Thank you all ! Carlos. [cid:image001.png@01D25B9D.4F483110]

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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

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Fwd: Fwd: Usegalaxy.org Data Rsync Connection refused
by Christopher Previti 17 Jan '17

17 Jan '17

Dear all, I was wondering if anybody was able to get the rsync server datacache.g2.bx.psu.edu to work? Have there been non-documented changes? We still get following messages: rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/phiX . rsync: failed to connect to datacache.g2.bx.psu.edu (128.118.250.10): Connection refused (111) rsync error: error in socket IO (code 10) at clientserver.c(128) [Receiver=3.1.1] My colleague Georgios Nikolis and I are working on a local Galaxy installation at the DKFZ and would really like to use the pre-built indices. Cheers, Christopher Previti -------- Weitergeleitete Nachricht -------- Betreff: Fwd: [galaxy-dev] Usegalaxy.org Data Rsync Connection refused Datum: Tue, 13 Dec 2016 13:46:48 +0100 Von: Georgios Nikolis <g.nikolis(a)dkfz-heidelberg.de> An: Christopher Previti <christopher.previti(a)dkfz-heidelberg.de> *Georgios Nikolis* Genomics and Proteomics Core Facility High Throughput Sequencing (W190) IT Management Genomics Proteomics German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany phone: +49 6221 42-4659 g.nikolis(a)dkfz.de <http://www.dkfz.de/> www.dkfz.de <http://www.dkfz.de/> logo <http://www.dkfz.de> Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta VAT-ID No.: DE143293537 -------- Forwarded Message -------- Subject: [galaxy-dev] Usegalaxy.org Data Rsync Connection refused Date: Fri, 28 Oct 2016 15:23:14 +0200 From: Georgios Nikolis <g.nikolis(a)dkfz-heidelberg.de> To: galaxy-dev(a)lists.galaxyproject.org <galaxy-dev(a)lists.galaxyproject.org> Dear all, we are currently working on setting up a new local Galaxy installation and I would like to obtain the genome reference data available on the public Galaxy instance. I am following the instructions on the Wiki page (https://wiki.galaxyproject.org/Admin/UseGalaxyRsync), but I can't seem to be able to access datacache.g2.bx.psu.edu via rsync. rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/phiX . rsync: failed to connect to datacache.g2.bx.psu.edu (128.118.250.10): Connection refused (111) rsync error: error in socket IO (code 10) at clientserver.c(128) [Receiver=3.1.1] Does anyone know if the URL has changed in the meantime? Is there any alternative way to access this data? Thanks in advance! Best regards, Georgios -- *Georgios Nikolis* Genomics and Proteomics Core Facility High Throughput Sequencing (W190) IT Management Genomics Proteomics German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany phone: +49 6221 42-4659 g.nikolis(a)dkfz.de <http://www.dkfz.de/> www.dkfz.de <http://www.dkfz.de/> logo <http://www.dkfz.de> Management Board: Prof. Dr. Michael Boutros (interim), Prof. Dr. Josef Puchta VAT-ID No.: DE143293537

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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

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galaxy-dev December 2016