[galaxy-dev] Problem with editing permissions on Galaxy libraries
Hi, Since an undetermined period of time in our instance, the edit permission panel under admin management of libraries shows an unexpected aspect: The modify library item part of the form is normal, with 2 fields for Roles associated and Roles not associated. However, none of the other parts of the form (access library, add library item, manage library permissions) have the Roles not associated fields. I am not saying that these fields are empty, they are just absent. With the consequence that we cannot really manage anymore the library access rights. Any hints ? Is it a bug or a feature (such as a consequence of managing bad something else somewhere else) ? Thanks Chris Christophe Antoniewski Drosophila Genetics and Epigenetics Laboratoire de Biologie du Développement 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 http://bio-dev.snv.jussieu.fr/ Tel +33 1 44 27 34 39 Fax +33 1 44 27 34 45 Mobile +33 6 68 60 51 50 http://drosophile.org ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] sysadmin help
Hi Donny, Thanks for the heads up about the broken link, I've fixed it. Other than that, are you running in to problems connecting Galaxy to your existing cluster? --nate On Tue, Jan 28, 2014 at 9:29 PM, Shrum, Donald C dcsh...@admin.fsu.eduwrote: Hi all, I could use a little basic help. I'm setting up a proof of concept galaxy server that will run in conjunction with our HPC here at FSU. Ultimately this will serve as a template where we will allow some users to run galaxy on a VM and use it as a mechanism for submitting/managing jobs on our cluster. I've installed Galaxy on a VM that mounts our HPC file system and managed to import an ecoli .fa file. My plan was to run bowtie2 on our HPC. https://rcc.fsu.edu/software/bowtie2 Disclaimer... I'm a sysadmin and other than compiling software my knowledge in bioinformatics is sorely lacking ;) I'm looking at the docs here https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#PBS I get a 404 for details on Torque - http://www.clusterresources.com/pages/products/torque-resource-manager.php Any help would be greatly appreciated. Additionally, if my intended use for Galaxy seems out of the scope of what would be useful, please let me know. Thanks, Donny Shrum FSU Research Computing Center ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Error when searching for tools in local instance.
Hi Sam, No it did not fix the issue. When I checked we were in fact in the stable branch. I am sorry for my delayed response, --Ricardo Perez - Original Message - From: sam guerler aysam.guer...@gmail.com To: Ricardo Perez ricky_...@neo.tamu.edu Cc: Galaxy-dev Galaxy-dev galaxy-dev@lists.bx.psu.edu Sent: Friday, January 24, 2014 5:21:56 PM Subject: Re: [galaxy-dev] Error when searching for tools in local instance. Hey Ricardo, Did that fix your issue? Does the problem occur in one of the branches? If yes, please let me know which one. Thanks, Sam On Wed, Jan 22, 2014 at 10:51 AM, Perez, Ricardo ricky_...@neo.tamu.edu wrote: Hello Sam, I believe we are using the default branch. I will try to change branches now. Thank you, --Ricardo Perez - Original Message - From: sam guerler aysam.guer...@gmail.com To: Ricardo Perez ricky_...@neo.tamu.edu Cc: Galaxy-dev Galaxy-dev galaxy-dev@lists.bx.psu.edu Sent: Tuesday, January 21, 2014 3:19:07 PM Subject: Re: [galaxy-dev] Error when searching for tools in local instance. Hi Ricardo, Are you using the newest version from the stable branch or from default? Thanks, Sam On Tue, Jan 21, 2014 at 3:53 PM, Perez, Ricardo ricky_...@neo.tamu.edu wrote: Dear All, When I go to my Galaxy Distibution I go the following place: Admin - Manage installed tool shed repositories When I search for a tool in here with the provided search bar, I get the following (I believe this is a bug): URL: https://galaxy.tamu.edu/admin_toolshed/browse_repositories?async=falsesort=namepage=1show_item_checkboxes=falsef-deleted=Falsef-free-text-search=search File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 229 in decorator return func( self, trans, *args, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 153 in browse_repositories return self.installed_repository_grid( trans, **kwd ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 138 in __call__ query = column.filter( trans, trans.user, query, column_filter ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 616 in filter clause_list.append( column.get_filter( trans, user, column_filter ) ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 400 in get_filter return self.get_single_filter( user, column_filter ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 413 in get_single_filter if self.key.find( '.' ) -1: AttributeError: 'NoneType' object has no attribute 'find' How would I go to fix this. Thank you, --Ricardo Perez ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Nightly testing status on the (Test) Tool Shed
Hi all, Are both the main and test Tool Sheds currently meant to be running nightly tests again? I've not really got back into Galaxy tool testing since Christmas. Most of my tools' test results look sensible, but there seem to be some issues still, e.g. http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler Not tested since 2014-01-04 http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr 2014-01-29 missing blast_datatypes dependency (why?) 2014-01-28 showing failed tests for sambamba_filter (wrong tool) Regards, Peter ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Nightly testing status on the (Test) Tool Shed
Hi Peter, On Jan 29, 2014, at 12:55 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, Are both the main and test Tool Sheds currently meant to be running nightly tests again? Yes I've not really got back into Galaxy tool testing since Christmas. Most of my tools' test results look sensible, but there seem to be some issues still, e.g. http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler Not tested since 2014-01-04 I've reset the do_not_test column on the record above ( it was set to not allow testing ), so it should now be tested. http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr 2014-01-29 missing blast_datatypes dependency (why?) 2014-01-28 showing failed tests for sambamba_filter (wrong tool) I'll have to take a look at the above issue. I'm completely swamped though, so it will be a while. Regards, Peter ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] datatype for executables
Thanks for your answer. Yes, the idea is to have runnable executables such as executable binaries and shell scripts to run via a parallelizing tool Swift. As for security, current plan is to run Swift enabled Galaxy tools in controlled cloud instances, which we are already doing. With this datatype, we are planning to design a suite of generic tools such that any arbitrary executable can be parallelized within Galaxy and can be run on Clouds and remote clusters. Is it possible to write a type file bin_or_exe which can detect the executable bit of data before they are part of Galaxy's indexed data. Thanks, Ketan On Tue, Jan 28, 2014 at 2:42 AM, Peter Cock p.j.a.c...@googlemail.comwrote: On Tuesday, January 28, 2014, Ketan Maheshwari ketancmaheshw...@gmail.com wrote: Is there a data type in Galaxy that identifies executables uniquely, eg. from the executable bit in the file perms or some other way? Thanks, Galaxy's data types are for data files - runnable tools/executables are handled via XML tool wrappers which define their options etc. Are you really asking about creating a datatype for a binary executable file? Or letting users run arbitrary tools? Even the idea of electing users run an arbitrary R script is dangerous enough from a security point of view. Peter ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] RNA-seq
Hi, My name is Karla Fernández a student of a University in Nuevo Leon in Monterrey, Mexico (UANL). The reason for this mail is because i'm going to work with differential gene expression of the yeast Pichia pastoris and i'd seen that the complete genome and annotations of this yeast are absent in programs like bowtie, tophat and cufflinks, I wondered if it might be possible to upload the genome and annotations of these yeast for my DGE. Thank you so much QBP. Karla Fernández Cano ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
