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Toolshed Question, In reference to https://toolshed.g2.bx.psu.edu/view/youngkim/ezbamqc/caed0168f704
by Molik, David 30 Mar '16

30 Mar '16

We're uploading a tool to the Galaxy Toolshed and were wondering about sample files: Should .loc.sample files refer to sample data ( test-data ) or should they be generalized for integration into other instances of Galaxy? Also, how should dependencies be noted? Best, Dave

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file transference between different galaxy servers...
by Danilo Ceschin 30 Mar '16

30 Mar '16

hi, I have some big files uploaded at galaxy.ncgas-trinity.indiana.edu and I would like to use those file at https://usegalaxy.org/ Is there a way to transfer those files to avoid upload them again? My internet connection is very bad and it takes days just for one file. Thank in advance. sincerely yours, -- Danilo Ceschin PhD Fac. de Ciencias Agrarias IBAC - Instituto de Biotecnología Agropecuaria del Comahue Ruta 151 - Km 12,5 CP 8303 - Cinco Saltos - Río Negro Argentina

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Warning: Incorrect datetime value in Galaxy 16.01
by SAPET, Frederic 30 Mar '16

30 Mar '16

Hello When I try to upload a file, I can see this error in the log file : /softs/bioinfo/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py:450: Warning: Incorrect datetime value: '2016-03-29 07:25:29.220Z' for column 'update_time' at row 32 On the interface, the upload job seems to be stuck. The history will never be refreshed. Otherwise, if I manually click on the "refresh history" icon, it works. The error is not shown again and my file appears in the history. Does anybody see this ? I hope it will be easy to debug because this is annoying. Thank you. Fred --- Frederic Sapet Bioinformatics Research Engineer BIOGEMMA - Upstream Genomics Group Centre de Recherche de Chappes CS 90126 63720 CHAPPES FRANCE Tel : +33 (0)4 73 67 88 54 Fax : +33 (0)4 73 67 88 99 E-mail : frederic.sapet(a)biogemma.com<mailto:frederic.sapet@biogemma.com>

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Tool Visibility feature
by SAPET, Frederic 29 Mar '16

29 Mar '16

Hello I'm trying to set up this feature : https://wiki.galaxyproject.org/Admin/Config/Access%20Control it seems that some files have been moved from : lib/galaxy/tools/filters/ to lib/galaxy/tools/toolbox/filters/ by the way, when I uncomment " user_tool_filters = examples:restrict_upload_to_admins, examples:restrict_encode" in my galaxy.ini file, it does not work. When I click on "Manage your ToolBox filters" (/user/toolbox_filters?cntrller=user) in my User preferences panel, I'm facing this error : Internal Server Error Galaxy was unable to successfully complete your request URL: http://galaxy.biogemma.fr/user/toolbox_filters?cntrller=user sys.path: [ '/softs/bioinfo/galaxy-prod/eggs/Parsley-1.1-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/Fabric-1.7.0-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/ssh-1.7.14-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/paramiko-1.11.1-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/SVGFig-1.1.6-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/drmaa-0.7.6-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/Whoosh-2.4.1-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/Beaker-1.4-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/MySQL_python-1.2.3c1_5.1.41_static-py2.6-linux-x86_64-ucs4.egg', '/softs/bioinfo/galaxy-prod/eggs/sqlalchemy_migrate-0.9.6-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/Tempita-0.5.1-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/decorator-3.1.2-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/sqlparse-0.1.14-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/six-1.9.0-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/Babel-1.3-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/pytz-2013.9-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/mercurial-3.2.4-py2.6-linux-x86_64-ucs4.egg', '/softs/bioinfo/galaxy-prod/eggs/Mako-0.4.1-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/kombu-3.0.24-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/ordereddict-1.1-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/importlib-1.0.3-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/anyjson-0.3.3-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/PyYAML-3.10-py2.6-linux-x86_64-ucs4.egg', '/softs/bioinfo/galaxy-prod/eggs/WebHelpers-1.3-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg', '/softs/bioinfo/galaxy-prod/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg', '/softs/bioinfo/galaxy-prod/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg', '/softs/bioinfo/galaxy-prod/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg', '/softs/bioinfo/galaxy-prod/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg', '/softs/bioinfo/galaxy-prod/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg', '/softs/bioinfo/galaxy-prod/eggs/bx_python-0.7.2-py2.6-linux-x86_64-ucs4.egg', '/softs/bioinfo/galaxy-prod/eggs/SQLAlchemy-1.0.8-py2.6-linux-x86_64-ucs4.egg', '/softs/bioinfo/galaxy-prod/eggs/WebOb-0.8.5-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/Routes-2.1-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/repoze.lru-0.6-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/amqp-1.4.6-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/wchartype-0.1-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/docutils-0.7-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/PasteDeploy-1.5.0-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/Paste-1.7.5.1-py2.6.egg', '/softs/bioinfo/galaxy-prod/lib', '/usr/lib/python2.6/site-packages/pip-7.1.2-py2.6.egg', '/usr/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg', '/usr/lib/python2.6/site-packages/bz2file-0.98-py2.6.egg', '/usr/lib64/python26.zip', '/usr/lib64/python2.6', '/usr/lib64/python2.6/plat-linux2', '/usr/lib64/python2.6/lib-tk', '/usr/lib64/python2.6/lib-old', '/usr/lib64/python2.6/lib-dynload', '/usr/lib64/python2.6/site-packages/gtk-2.0', '/usr/lib64/python2.6/site-packages', '/usr/lib/python2.6/site-packages'] Module galaxy.web.framework.middleware.error:151 in __call__ >> app_iter = self.application(environ, sr_checker) Module paste.recursive:84 in __call__ >> return self.application(environ, start_response) Module galaxy.web.framework.middleware.remoteuser:143 in __call__ >> return self.app( environ, start_response ) Module paste.httpexceptions:633 in __call__ >> return self.application(environ, start_response) Module galaxy.web.framework.base:133 in __call__ >> return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:191 in handle_request >> body = method( trans, **kwargs ) Module galaxy.web.framework.decorators:68 in decorator >> return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.user:1331 in toolbox_filters >> tool_filters = get_filter_mapping( saved_user_tool_filters, trans.app.config.user_tool_filters ) Module galaxy.webapps.galaxy.controllers.user:1284 in get_filter_mapping >> module = __import__( module_name, globals(), fromlist=['temp_module'] ) ImportError: No module named examples Could you please provide me some help ? I have launched a git pull origin master before testing... Thank you. Fred

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If you need to use PBS Pro with Galaxy 16.01.
by SAPET, Frederic 29 Mar '16

29 Mar '16

Hello Using the previous version of Galaxy (before the 16.01) we were able to use PBS Pro as job management system. It was ok using PBS (/opt/pbs/12.2.4.142262) and DRMAA (pbs-drmaa-1.0.17). This only thing to do was to truncate the job name that Galaxy send to PBS. Indeed, in the file lib/galaxy/jobs/runners/__init__.py you need to add : self.job_name = self.job_name[:15] in the AsynchronousJobState class otherwise PBS will reject the job. Using the current version of Galaxy, this is not enough. You will need to change another file : lib/galaxy/jobs/runners/drmaa.py And change jt.jobName = ajs.job_name to jt.jobName = ajs.job_name[:15] in the DRMAAJobRunner class (around line 140) You will then avoid this error : galaxy.jobs.runners.drmaa ERROR 2016-03-24 15:23:23,880 (18) drmaa.Session.runJob() failed unconditionally Traceback (most recent call last): File "/softs/bioinfo/galaxy-prod/lib/galaxy/jobs/runners/drmaa.py", line 181, in queue_job external_job_id = self.ds.runJob(jt) File "/softs/bioinfo/galaxy-prod/.venv/lib/python2.7/site-packages/drmaa/session.py", line 314, in runJob c(drmaa_run_job, jid, sizeof(jid), jobTemplate) File "/softs/bioinfo/galaxy-prod/.venv/lib/python2.7/site-packages/drmaa/helpers.py", line 299, in c return f(*(args + (error_buffer, sizeof(error_buffer)))) File "/softs/bioinfo/galaxy-prod/.venv/lib/python2.7/site-packages/drmaa/errors.py", line 151, in error_check raise _ERRORS[code - 1](error_string) InvalidAttributeValueException: code 14: Illegal attribute or resource value: Illegal attribute or resource value galaxy.jobs.runners.drmaa ERROR 2016-03-24 15:23:23,883 (18) All attempts to submit job failed I hope this will help if you plan to use Galaxy over PBS Pro. We currently used PBS 12.2.4.142262, DRMAA 1.0.19 and the latest galaxy (after a git pull command) Fred --- Frederic Sapet Bioinformatics Research Engineer BIOGEMMA - Upstream Genomics Group Centre de Recherche de Chappes CS 90126 63720 CHAPPES FRANCE Tel : +33 (0)4 73 67 88 54 Fax : +33 (0)4 73 67 88 99 E-mail : frederic.sapet(a)biogemma.com<mailto:frederic.sapet@biogemma.com>

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Request help to configure local galaxy in Git
by Manonanthini Shanmuganathan 28 Mar '16

28 Mar '16

Hi Galaxy Developer, I have been trying to install Galaxy in my windows system using git.I have tried using cygwin also.I have been trying for this since March 2nd , I am getting this error, "ManoNathan@Mano MINGW64 ~/galaxy ((v16.01)) $ sh run.sh Fetching https://pypi.python.org/packages/source/v/virtualenv/virtualenv-13.1.2. tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 1679k 100 1679k 0 0 357k 0 0:00:04 0:00:04 --:--:-- 447k Verifying /tmp/galaxy-virtualenv-GUksti/virtualenv-13.1.2.tar.gz checksum is aabc8ef18cddbd8a2a9c7f92bc43e2fea54b1147330d65db920ef3ce9812e3dc Traceback (most recent call last): File "<string>", line 1, in <module> IOError: [Errno 2] No such file or directory: '/tmp/galaxy-virtualenv-GUksti/virtualenv-13.1.2.tar.gz' " So I am unable to run galaxy in my system.Please help me in this regard. I have installed XAMPP(for mysql and apache server) in my system(Windows 10). Thanks and Regards, Manonanthini Thangam PhD Scholar, Bioinformatics Lab, AU-KBC Research Centre, MIT Campus,Anna University, Chromepet,Chennai.

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Troubleshooting BAM file upload issues
by Amelia Ireland 25 Mar '16

25 Mar '16

I'm setting up a Galaxy instance on a new server and am having some issues with BAM file uploads. I'm using the BAM files supplied with JBrowse for testing purposes. I have Galaxy installed on my laptop and file uploads are working fine, so it's evidently an issue with the server and/or OS configuration. Attempting to upload a BAM file returns the message "The uploaded binary file contains inappropriate content" and the upload is empty. The server is running Scientific Linux and uses the Environment Modules system for dependency management. I can successfully upload bed and bigwig files, which suggests that samtools is being loaded and functioning correctly. If someone can suggest some troubleshooting steps, I would be most grateful. Thanks! Amelia Integrated Microbial Genomics (IMG) JGI / LBL

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package_bowtie_2_2_6 error
by changyu_fan 24 Mar '16

24 Mar '16

Hello All, We try to install bowtie2 package in galaxy but failed. Tool shed: toolshed.g2.bx.psu.edu Name: package_bowtie_2_2_6 Owner: iuc Here is the message: tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 89, in extract os.chmod( absolute_filepath, unix_permissions ) *"[Errno 2] No such file or directory: './database/tmp/tmp-toolshed-mtdpzqr7H/bowtie2-2.2.6/bowtie2-2.2.6/'"* Any help will be appreciated. Thanks Changyu

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Galaxy CloudMan with Galaxy 16.01
by Enis Afgan 24 Mar '16

24 Mar '16

Hello! *We have released a new version of Galaxy CloudMan on AWS.* CloudMan <https://wiki.galaxyproject.org/CloudMan/> offers an easy way to get a personal and completely functional instance of Galaxy in the cloud in just a few minutes, without any manual configuration or imposed quotas. Once running, you have complete control over Galaxy, including the ability to install new tools. Most notable changes include: * Galaxy 16.01 release * A fine-grained control over auto-scaling options * Several fixes to cluster sharing and cloning See the CHANGELOG <https://github.com/galaxyproject/cloudman/blob/master/CHANGELOG.md> for a more complete set of changes. Give it a whirl at launch.usegalaxy.org or take a look at the Getting Started <https://wiki.galaxyproject.org/CloudMan/GettingStarted> documentation.

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Re: [galaxy-dev] perl version 5.18.1 repository error
by Rathert, Philipp, Dr. 24 Mar '16

24 Mar '16

Dear Nicola, now it looks like package_gnu_coreutils_8_22 is generating an error gnu_coreutils <http://129.69.102.42/admin_toolshed/manage_repository_tool_dependencies?rep…> 8.22 package Error Shutting down process id 23231 because it generated no output for the defined timeout period of 3600.0 seconds. I didn't find anything an this error on the web and I am not sure how I can fix this... cheers, philipp -----Original message----- From: Nicola Soranzo <nsoranzo(a)tiscali.it> Sent: Wednesday 23rd March 2016 12:49 To: Rathert, Philipp, Dr. <philipp.rathert(a)ibc.uni-stuttgart.de>; galaxy-dev(a)lists.galaxyproject.org Subject: Re: [galaxy-dev] perl version 5.18.1 repository error Hi Philipp, can you try to reinstall the tool dependency? Go to the Admin interface, "Manage installed tools", click on the "package_perl_xml_parser_expat_2_41", then from the "Repository Actions" menu select "Manage tool dependencies", select the dependency in error and "Uninstall", then select it again and "Install" it. Cheers, Nicola On 23/03/16 08:06, Rathert, Philipp, Dr. wrote: Dear all, i am trying to install tool (meme-fimo) which needs package_perl_xml_parser_expat_2_41 that has a pearl 5.18.1 dependency. however, although the tool installs just fine it shows that package_perl_xml_parser_expat_2_41 has missing dependencies: Tool shed repository:package_perl_xml_parser_expat_2_41 Tool shed repository changeset revision:1ce3818a8eb9 Tool dependency status:Error Tool dependency installation error:Error installing tool dependency perl version 5.18.1: Unable to locate the repository directory for revision d905bb415eca of installed repository package_perl_5_18 owned by iuc. Tool dependency installation directory:././tool_deps/perl/5.18.1/iuc/package_perl_xml_parser_expat_2_41/1ce3818a8eb9 Is this an error of my local instance or is the revision missing on the toolshed? Thank you very much for your help. Cheers, philipp ___________________________________________________________ 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/

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