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GCCBOSC 2018 Training Topic Nominations are Open!
by Dave Clements 14 Dec '17

14 Dec '17

Hello all, This email in 5 words: *Nominate a training topic now <http://bit.ly/gccbosc2018-tr-nom>!* Or, the longer version: The joint 2018 Galaxy Community and Bioinformatics Open Source Conferences <https://gccbosc2018.sched.com/> start with training and *the training topics are determined by you*. Please take a few minutes to consider what you would like to learn (or teach) at GCCBOSC2018. Any topic(s) of interest to these communities can be *nominated <http://bit.ly/gccbosc2018-tr-nom>.* GCCBOSC2018 <https://gccbosc2018.sched.com/> will be held 25-30 June in Portland, Oregon, United States, and will feature two days of training - the second of which is multi-track and will feature content for both the BOSC and Galaxy communities. Nominations can cover a wide range of topics. For example: - How to use open source software using just a web browser (e.g., Intro to Using Galaxy) - How to use software packages (The Newbie's Guide to BioRuby) - Advanced applications of software (Genome Assembly with Galaxy, or Proteomics with BioPython) - Software installation and configuration (Tool Wrapping for Galaxy, or Using CloudLaunch) - Open source community (Building a Curation Community using Apollo, or Training using the Galaxy Training Network) *These are only examples.* If you are looking for ideas, see topics nominated for GCC2017 <https://docs.google.com/document/d/1jyCndVqfXx-HsyFJ4hjaK075vDbPM1kE58qO2lJ…> , GCC2016 <http://bit.ly/gcc2016noms>, GCC2015 <http://bit.ly/gcc2015vote>, and the Galaxy Events page <https://galaxyproject.org/events/>, which lists what training the community is offering outside of GCCs. *Training is not limited to Galaxy-related topics. Don't be afraid to think inside the BOSC!* Basically, if you think our communities will be interested in a topic, then please nominate it <http://bit.ly/gccbosc2018-tr-nom>! Nominated topics will be published <https://galaxyproject.org/events/gccbosc2018/training/> as they come in. *Topic Nominations close January 7*. Topics will be compiled into a uniform list by the GCCBOSC2018 organizers, and then voted on by the community starting one week later. Looking forward to seeing you in Portland! Dave Clements, on behalf of the GCCBOSC 2018 Organizers -- https://galaxyproject.org/ https://usegalaxy.org/

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History Share : options
by Christophe Caron 14 Dec '17

14 Dec '17

Hi When a user wants to share a history ti a user, it seems the are several use cases after validation. In some cases, no question and the history is shared, but in some other use cases Galaxy request more informations with one, two or three questions (list below). 1/ Make datasets public so anyone can access them ? 2/ Make datasets private to me and the user(s) with whom I am sharing ? 3/ Share Anyway ? We try to identify the source of these different proposals. It seems to be link with role and dataset owner ...but not sure. Any advice or clue ? Is there any documentation of potential links between these options end user roles ? Thanks Christophe Thanks

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Network errors when downloading files
by William, Van Der Pol 14 Dec '17

14 Dec '17

Hello, We've noticed when our users try to download files from our galaxy instance, they are getting a network error and receiving an empty 0 Byte file. I've checked the directory where the datasets are stored and can see that the files in question exist and contain the expected data, but something is interfering with downloading them through the GUI. Do you guys have any suggestions on what could be causing this error? Thanks -Liam Help keep the CCTS funded. Please include the following text on relevant publications: "This publication was made possible by the UAB Center for Clinical and Translational Science Grant Number UL1TR001417 from the National Center for Advancing Translational Sciences (NCATS) of the National Institutes of Health (NIH)."

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Dynamic Tool UI based on script
by Evan Clark 07 Dec '17

07 Dec '17

Is it possible to execute a script within a tool xml confit to retrieve some data and append to the ui depending on the requested data. I.e if I wanted to get a list of files and provide them as select options before hitting the execute button. --- Sent from VMware Boxer

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December 2017 News of the Galaxy
by Dave Clements 07 Dec '17

07 Dec '17

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Galaxy moves files form job directory but attempts to look for them at original path
by Evan Clark 30 Nov '17

30 Nov '17

Below is an error obtained from our galaxy install. We have custom directories sets for the files directory and the jobs directory. Galaxy appears to move the files but then attempts to look for them at the original path. I have tried unsetting these options but it still persists. galaxy.jobs DEBUG 2017-11-24 17:53:19,057 finish(): Moved /var/web_services/galaxy/database/jobs_directory/000/320/galaxy_dataset_431.dat to /mnt/ceph/home/galaxy/galaxy/files_directory/000/dataset_401.dat galaxy.model.metadata DEBUG 2017-11-24 17:53:19,128 setting metadata externally failed for HistoryDatasetAssociation 431: [Errno 2] No such file or directory galaxy.jobs.runners ERROR 2017-11-24 17:53:19,319 (320/179084) Job wrapper finish method failed Traceback (most recent call last): File "/var/web_services/galaxy/lib/galaxy/jobs/runners/__init__.py", line 630, in finish_job job_state.job_wrapper.finish( stdout, stderr, exit_code ) File "/var/web_services/galaxy/lib/galaxy/jobs/__init__.py", line 1266, in finish dataset.datatype.set_meta( dataset, overwrite=False ) File "/var/web_services/galaxy/lib/galaxy/datatypes/binary.py", line 391, in set_meta exit_code = subprocess.call( args=command, stderr=open( stderr_name, 'wb' ) ) File "/usr/lib64/python2.7/subprocess.py", line 524, in call return Popen(*popenargs, **kwargs).wait() File "/usr/lib64/python2.7/subprocess.py", line 711, in __init__ errread, errwrite) File "/usr/lib64/python2.7/subprocess.py", line 1327, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory galaxy.jobs ERROR 2017-11-24 17:53:19,337 fail(): Missing output file in working directory: [Errno 2] No such file or directory: '/var/web_services/galaxy/database/jobs_directory/000/320/galaxy_dataset_431.dat'

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TR: Close cluster
by Arnaud Cheuk 30 Nov '17

30 Nov '17

Hi, I would like to close my cluster, but when click on delete permanently, I see the cluster is still active. Could you help me to close the cluster? cduanra-galaxy-cloud-17-11-28t22-14 Appliance: Galaxy CloudMan Version: 17.05 Cloud: amazon-us-east-n-virginia RUNNING http://52.202.138.61/cloud Best, Arnaud

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external display and data editing
by Nils Paulhe 22 Nov '17

22 Nov '17

Dear list, I'm working on data visualization / display in galaxy. I'm wondering if it's possible to save a resource edited from the viewer plugin or an external display in the current history. In my opinion the easier / proper way is to use an external display to show / edit the resources and upload the edited files in the current history using galaxy API. Does anyone have tried something similar? Cheers Nils

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GMOD hackathon before PAG San Diego in January
by Scott Cain 21 Nov '17

21 Nov '17

Hi all, This January before PAG on the Wednesday and Thursday before PAG (January 10-11) in San Diego we are planning a GMOD hackathon. We expect that participants will be interested in solving problems/creating solutions related to Tripal, JBrowse, Apollo, and Galaxy but if you're interested in another GMOD project, by all means, let us know! We expect this hackathon to overlap with the Tripal hackathon that is on January 11 (I'm pretty sure; right Stephen?) If you are interested in attending this hackathon, please let me know so I can be sure we have an appropriately sized space. And if you're coming for the pre-PAG hackathon, consider staying for PAG, since there is always a lot of GMOD-related content at the meeting! Thanks, Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research

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broken after upgrade to 17.09 : uploading files via the API
by Hans-Rudolf Hotz 20 Nov '17

20 Nov '17

Dear All If I execute the following command: python import_with_dbkey.py *** file.bam hg19sub the bam files will be added to the user's history the code (import_with_dbkey.py) is as follows: import sys sys.path.append('***/bioblend-0.10.0-py2.7.egg') sys.path.append('***/requests_toolbelt-0.7.0-py2.7.egg') from bioblend.galaxy import GalaxyInstance from bioblend.galaxy.tools import ToolClient url = "http://galaxy-dev.fmi.ch" key = "***" history_id = sys.argv[1] file_path = sys.argv[2] dbkey= sys.argv[3] gi = GalaxyInstance(url=url, key=key) toolClient = ToolClient(gi) uploadedFile = toolClient.upload_file(file_path, history_id, dbkey=dbkey) Now, if I use the virtual environment from Galaxy, I get: (.venv)-bash-4.2$ python import_with_dbkey.py *** file.bam hg19sub Traceback (most recent call last): File "/***/galaxy/tools/fmi__api_helpers/import_with_dbkey.py", line 40, in <module> uploadedFile = toolClient.upload_file(file_path, history_id, dbkey=dbkey) File "/***/galaxy/.venv/lib/python2.7/site-packages/bioblend/galaxy/tools/__init__.py", line 148, in upload_file return self._tool_post(payload, files_attached=True) File "/***/galaxy/.venv/lib/python2.7/site-packages/bioblend/galaxy/tools/__init__.py", line 218, in _tool_post return Client._post(self, payload, files_attached=files_attached) File "/***/galaxy/.venv/lib/python2.7/site-packages/bioblend/galaxy/client.py", line 171, in _post files_attached=files_attached) File "/***/galaxy/.venv/lib/python2.7/site-packages/bioblend/galaxyclient.py", line 131, in make_post_request r.status_code, body=r.text) bioblend.galaxy.client.ConnectionError: Unexpected response from galaxy: 400: <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN"> <html><head> <title>400 Bad Request</title> </head><body> <h1>Bad Request</h1> <p>Your browser sent a request that this server could not understand.<br /> </p> </body></html> (.venv)-bash-4.2$ ...and the file does not get uploaded. I will continue investigating the difference between the python modules used, but maybe someone has a clue and could help me Thank you very much Hans-Rudolf

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