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

Mapping users to slurm
by Pardo Diaz, Alfonso 14 Mar '16

14 Mar '16

Hello, I have connected my galaxy to a Slurm cluster via DRMAA. Galaxy can send jobs to the cluster without problems. But then I configure galaxy to use “real users” I got this error: "User myuser(a)mydomain.es is not mapped to any real user, and not permitted to start jobs” Could you help me? Tanks!! This is my job_con.xml: <?xml version="1.0"?> <job_conf> <plugins workers="6"> <plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" workers="2"> <param id="drmaa_library_path">/opt/slurm-drmaa/lib/libdrmaa.so</param> </plugin> </plugins> <handlers default="handlers"> <handler id="main" tags="handlers"/> </handlers> <destinations default="drmaa"> <destination id="drmaa" runner="drmaa"> <param id="galaxy_external_runjob_script">/opt/galaxy/scripts/drmaa_external_runner.py</param> <param id="galaxy_external_killjob_script">/opt/galaxy/scripts/drmaa_external_killer.py</param> <param id="galaxy_external_chown_script">/opt/galaxy/scripts/external_chown_script.py</param> </destination> </destinations> </job_conf> this is my auth_conf.xml: <?xml version="1.0"?> <auth> <authenticator> <type>ldap</type> <options> <auto-register>True</auto-register> <allow-password-change>False</allow-password-change> <server>ldap://ldap.ceta-ciemat.es</server> <login-use-username>True</login-use-username> <continue-on-failure>False</continue-on-failure> <search-filter>(|(mail={email})(uid={username}))</search-filter> <search-fields>uid,mail,dn</search-fields> <search-base>ou=xxxxxx,dc=xxxxx,dc=xxxxx</search-base> <bind-user>{dn}</bind-user> <bind-password>{password}</bind-password> <auto-register-username>{uid}</auto-register-username> <auto-register-email>{mail}</auto-register-email> <login-use-username>True</login-use-username> </options> </authenticator> <authenticator> <type>localdb</type> <options>  <allow-password-change>true</allow-password-change> </options> </authenticator> </auth> And this is my galaxy.ini: [server:main] port = 8080 host = 0.0.0.0 use_threadpool = True threadpool_kill_thread_limit = 10800 [filter:gzip] [filter:proxy-prefix] prefix = /galaxy [app:main] paste.app_factory = galaxy.web.buildapp:app_factory database_connection = postgres://xxxxxxxx:xxxxxx@xxxxx/galaxy_project database_engine_option_server_side_cursors = True database_engine_option_strategy = threadlocal new_file_path = database/tmp tool_config_file = config/tool_conf.xml,config/shed_tool_conf.xml tool_dependency_dir = dependency_dir cluster_files_directory = database/pbs smtp_server = localhost use_nglims = False nglims_config_file = tool-data/nglims.yaml debug = true use_interactive = True require_login = True allow_user_creation = False allow_user_deletion = True allow_user_impersonation = True allow_user_dataset_purge = True new_user_dataset_access_role_default_private = True auth_config_file = config/auth_conf.xml enable_quotas = True expose_dataset_path = False job_config_file = config/job_conf.xml enable_job_recovery = True outputs_to_working_directory = True drmaa_external_runjob_script = scripts/drmaa_external_runner.py drmaa_external_killjob_script = scripts/drmaa_external_killer.py external_chown_script = scripts/external_chown_script.py ---------------------------- Confidencialidad: Este mensaje y sus ficheros adjuntos se dirige exclusivamente a su destinatario y puede contener informaci�n privilegiada o confidencial. Si no es vd. el destinatario indicado, queda notificado de que la utilizaci�n, divulgaci�n y/o copia sin autorizaci�n est� prohibida en virtud de la legislaci�n vigente. Si ha recibido este mensaje por error, le rogamos que nos lo comunique inmediatamente respondiendo al mensaje y proceda a su destrucci�n. Disclaimer: This message and its attached files is intended exclusively for its recipients and may contain confidential information. If you received this e-mail in error you are hereby notified that any dissemination, copy or disclosure of this communication is strictly prohibited and may be unlawful. In this case, please notify us by a reply and delete this email and its contents immediately. ----------------------------

1 0

Scaling tools: data available?
by Peter van Heusden 14 Mar '16

14 Mar '16

Hi there We're researching the resource (CPU time and memory) requirements for RNA STAR at the moment. Specifically, we'd like to build up a database of input size to resource usage so that we can use this to feed a dynamic destination mapper (currently our STAR configuration uses a thumbsuck for RAM and CPU requirements that is not optimal but works in many cases). Has anyone collected these metrics before? And more generally, is anyone collecting metrics for a range of bioinformatics tools? A database like this could be very useful! Thanks! Peter

2 3

RV: Error attempting to display contents of library (New data library)
by Juan Vladimir de la Rosa Medina 11 Mar '16

11 Mar '16

Hi Dannon, Thank you for your help, surprisingly now I can upload datasets to the data library without any change. I wanted to take a snapshot of the screen in a previous step to adding the datasets to the data library, before to make the changes in the files you explained in the link, when I realize that all works fine. I can't understand what happened. Anyway here I attached the screen snapshot prior to the datasets were added to the Data library, and other snapshot showing that inexplicably everything is working fine now. [cid:image002.png@01D17BD3.6BCDA450] [cid:image006.png@01D17BD3.6BCDA450] Juan Vladimir Enviado desde Correo<https://go.microsoft.com/fwlink/?LinkId=550986> para Windows 10 De: Dannon Baker<mailto:dannon.baker@gmail.com> Enviado: viernes, 11 de marzo de 2016 1:23 Para: Juan Vladimir de la Rosa Medina<mailto:jvdelarosa@hotmail.com> CC: galaxy-dev(a)lists.galaxyproject.org<mailto:galaxy-dev@lists.galaxyproject.org> Asunto: Re: [galaxy-dev] Error attempting to display contents of library (New data library) Hi Juan, I'm working on a few errors I've uncovered trying to track down your issue here, but my hunch is you're hitting a different one. The branch is here if you want to try it: https://github.com/dannon/galaxy/commits/library_errors Do you have any non-ascii characters in a particular field that you've noticed? Perhaps in a dataset name, or filepath? Barring that, can you send me a screenshot of exactly what you're seeing prior to running into the error? -Dannon On Sat, Mar 5, 2016 at 1:43 PM, Juan Vladimir de la Rosa Medina < jvdelarosa(a)hotmail.com> wrote: > Hello to everybody, > > > > I’m trying to Access to my data files into a local instance of galaxy, > installed in a virtual machine with Debian Jessie 8.2.0 (with Python 2.7.9 > installed), using the data libraries as administrator (I’m handling big > data files). To do this task I have changed the option library_import_path > into the config/galaxy.ini file to the path > (“/home/jvdelarosa/Bioinformatica/BioDatos/”) where my files are located, > as is explained in the Galaxy wiki section (“Uploading Files to a Data > Library”). > > > > As administrator I can create a new data library, but when I’m trying to > add datasets following the instructions explained in the section mentioned > above, an error message is showed on the web browser. > > > > *“Error attempting to display contents of library (New data library): > 'ascii' codec can't decode byte 0xc3 in position 1: ordinal not in > range(128).”* > > > > I have to mention that I haven’t had any problem with other local galaxy > instances I have installed in the past with the same O.S. > > > > I have been searching on the web about the same problem in galaxy with no > success. > > > > Can anyone explain what’s happening with my local instance of galaxy and > if there is any solution? > > > > A lot of thanks in advance. > > > > ___________________________________________________________ > 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: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ >

1 0

Missing dependency issue
by Scott Szakonyi 11 Mar '16

11 Mar '16

Hello all, I'm having an issue with a missing dependency for readline 6.2. When I try to install or repair, I get the following error message: configure: error: in `/vectorbase/web/Galaxy/galaxy/data/galaxy/tmp/tmp-toolshed-mtd3fhemK/readline-6.2': configure: error: cannot compute suffix of object files: cannot compile See `config.log' for more details. I've tried to locate the config.log file without success, so this is all I have to go on. Has anyone else encountered this sort of issue, and if so, how did you solve it? Thanks! -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu

3 4

backslash in string for galaxy tool
by Jasper Koehorst 11 Mar '16

11 Mar '16

I am creating a tool which allows you to query RDF files. However when performing a \n in the query it is replaced by Xn. Other special characters such as > are replaced by an __gt__ . How can I either allow galaxy to accept \n entries or that the backslash is replaced by something like __bs__ ? As Xn is not replaceable.

2 2

Error attempting to display contents of library (New data library)
by Juan Vladimir de la Rosa Medina 10 Mar '16

10 Mar '16

Hello to everybody, I’m trying to Access to my data files into a local instance of galaxy, installed in a virtual machine with Debian Jessie 8.2.0 (with Python 2.7.9 installed), using the data libraries as administrator (I’m handling big data files). To do this task I have changed the option library_import_path into the config/galaxy.ini file to the path (“/home/jvdelarosa/Bioinformatica/BioDatos/”) where my files are located, as is explained in the Galaxy wiki section (“Uploading Files to a Data Library”). As administrator I can create a new data library, but when I’m trying to add datasets following the instructions explained in the section mentioned above, an error message is showed on the web browser. “Error attempting to display contents of library (New data library): 'ascii' codec can't decode byte 0xc3 in position 1: ordinal not in range(128).” I have to mention that I haven’t had any problem with other local galaxy instances I have installed in the past with the same O.S. I have been searching on the web about the same problem in galaxy with no success. Can anyone explain what’s happening with my local instance of galaxy and if there is any solution? A lot of thanks in advance.

2 1

quota api error
by Fabien Mareuil 09 Mar '16

09 Mar '16

Hi, We got an error when we used API to see a quota detail, we get the following traceback: 157.99.60.167 - - [08/Mar/2016:10:13:58 +0200] "GET /api/quotas HTTP/1.1" 200 - "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:44.0) Gecko/20100101 Firefox/44.0" galaxy.web.framework.decorators ERROR 2016-03-08 10:14:10,273 Uncaught exception in exposed API method: Traceback (most recent call last): File ".../lib/galaxy/web/framework/decorators.py", line 142, in decorator rval = dumps( rval, indent=4, sort_keys=True ) File ".../lib/galaxy/util/json.py", line 65, in safe_dumps dumped = json.dumps( *args, allow_nan=False, **kwargs ) File "/usr/lib64/python2.6/json/__init__.py", line 237, in dumps **kw).encode(obj) File "/usr/lib64/python2.6/json/encoder.py", line 367, in encode chunks = list(self.iterencode(o)) File "/usr/lib64/python2.6/json/encoder.py", line 309, in _iterencode for chunk in self._iterencode_dict(o, markers): File "/usr/lib64/python2.6/json/encoder.py", line 275, in _iterencode_dict for chunk in self._iterencode(value, markers): File "/usr/lib64/python2.6/json/encoder.py", line 306, in _iterencode for chunk in self._iterencode_list(o, markers): File "/usr/lib64/python2.6/json/encoder.py", line 204, in _iterencode_list for chunk in self._iterencode(value, markers): File "/usr/lib64/python2.6/json/encoder.py", line 309, in _iterencode for chunk in self._iterencode_dict(o, markers): File "/usr/lib64/python2.6/json/encoder.py", line 275, in _iterencode_dict for chunk in self._iterencode(value, markers): File "/usr/lib64/python2.6/json/encoder.py", line 309, in _iterencode for chunk in self._iterencode_dict(o, markers): File "/usr/lib64/python2.6/json/encoder.py", line 275, in _iterencode_dict for chunk in self._iterencode(value, markers): File "/usr/lib64/python2.6/json/encoder.py", line 317, in _iterencode for chunk in self._iterencode_default(o, markers): File "/usr/lib64/python2.6/json/encoder.py", line 323, in _iterencode_default newobj = self.default(o) File "/usr/lib64/python2.6/json/encoder.py", line 344, in default raise TypeError(repr(o) + " is not JSON serializable") TypeError: Decimal('856488698767') is not JSON serializable json can't serialize Decimal object. I tested it with simplejson and it works. An other solution is to convert the Decimal object to a float before the dumps. Thanks a lot for your help Best regards, -- Fabien Mareuil | Centre d'Informatique pour la Biologie fabien.mareuil(a)pasteur.fr <mailto:fabien.mareuil@pasteur.fr> | Institut Pasteur 25,28 rue du Docteur Roux 75015 Paris, France

2 3

iRODS
by Mikael Loaec 09 Mar '16

09 Mar '16

Hi, @URGI, we have sucessfully tested connexion of galaxy instance with an iRODS. We have a pdf doc 67ko) explaining how we implement it if you want, but don't know if i can send attachement on this mailinglist ? We (URGI) are also very interresting in data pull/push tools for Galaxy-iRODS integration. Let us know when you will begin working on it. Regards, Mikael LOAEC Systems and Networks Administrator URGI INRA

3 2

Error installing from main toolshed
by Anmol Hemrom 09 Mar '16

09 Mar '16

Hi, I am getting error " HTTPError: HTTP Error 500: Internal Server Error" while installing tools from the main toolshed. I tried from different galaxy instances and got the same error. I have tried to export revision of a tool, that too threw the same error. Is it a temporary issue with main toolshed? The testtoolshed is not working as well. Thanks Anmol

2 1

iRODS
by Mohamed Kassam 08 Mar '16

08 Mar '16

Dear all, I would like to use our interlan iRODs to pull data. I searched and i find that there is an object store for that. How it works ? DO I need to configure something else ? Thanks in advance, Mohamed

3 2