[galaxy-dev] job quotas
Hi, is it possible to restrict the number of concurrent jobs for a single user in a local instance of galaxy? I see that in the public site this feature is implemented, but I don't find documentation about how to implement this locally. I think it's not possible through pbs because all users submit jobs as the defauls galaxy user. Cheers, Ivan ___ 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/
Re: [galaxy-dev] Fwd: tool restrict access
Hi Jeremy, sorry for bother you again. I do some tests and the problem seems not in the semi-colons (the cheetah manual is not very clear in this sense, I put them but it did not solve the problem), but in the display tag which is simply incorrect in that position, a call to a python script is needed instead. May you suggest me how to sketch a simple python script that prints in the central section of the galaxy window a message like you are not authorized to execute this tool ? In this way maintainers of local instances of Galaxy can change the command section of the xml tools they want to hide like this: command #if $__user_email__ == not_auth.py #else data_source.py $output $__app__.config.output_size_limit #end if /command Cheers, I. Ivan, tool name=UCSC Main id=ucsc_table_direct1 tool_type=data_source descriptiontable browser/description command interpreter=python #if $__user_email__ == displayYou are not authorized to use this tool/display #else data_source.py $output $__app__.config.output_size_limit #end if /command ... and I got the error below, which seems connected to the cheetah syntax. Any idea of what I'm doing wrong? As is tradition in python, you need to put semi-colons after conditionals. E.g. -- #if $__user_email__ == : displayYou are not authorized to use this tool/display #else: data_source.py $output $__app__.config.output_size_limit #end if -- J. ___ 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/
Re: [galaxy-dev] Fwd: tool restrict access
Hi Jeremy, thank you for your answer. I followed your hint modifyng (for example) the ucsc_tablebrowser.xml as follows (not sure about the display tag to have a simple error message, but this is another problem): tool name=UCSC Main id=ucsc_table_direct1 tool_type=data_source descriptiontable browser/description command interpreter=python #if $__user_email__ == displayYou are not authorized to use this tool/display #else data_source.py $output $__app__.config.output_size_limit #end if /command ... and I got the error below, which seems connected to the cheetah syntax. Any idea of what I'm doing wrong? Cheers, I. Traceback (most recent call last): File /home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py, line 58, in run_job job_wrapper.prepare() File /home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py, line 411, in prepare self.command_line = self.tool.build_command_line( param_dict ) File /home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py, line 1691, in build_command_line command_line = fill_template( self.command, context=param_dict ) File /home/galaxy/galaxy-dist/lib/galaxy/util/template.py, line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File /home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.5-linux-x86_64-ucs4.egg/Cheetah/Template.py, line 1244, in __init__ self._compile(source, file, compilerSettings=compilerSettings) File /home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.5-linux-x86_64-ucs4.egg/Cheetah/Template.py, line 1538, in _compile keepRefToGeneratedCode=True) File /home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.5-linux-x86_64-ucs4.egg/Cheetah/Template.py, line 745, in compile compiler.compile() File /home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.5-linux-x86_64-ucs4.egg/Cheetah/Compiler.py, line 1670, in compile self._parser.parse() File /home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.5-linux-x86_64-ucs4.egg/Cheetah/Parser.py, line 1496, in parse self.assertEmptyOpenDirectivesStack() File /home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.5-linux-x86_64-ucs4.egg/Cheetah/Parser.py, line 2658, in assertEmptyOpenDirectivesStack raise ParseError(self, msg=errorMsg) ParseError: Some #directives are missing their corresponding #end ___ tag: if Line 2, column 8 Line|Cheetah Code |- 2 | ^ Ivan, #if $__user_email__ == displayYou are not authorized to use this tool/display #else command interpreter=python data_source.py $output $__app__.config.output_size_limit /command To make this approach work, the email check should go in the command tag. More information: If you're looking to require users to login before using any tools, you can use this flag in the universe config file: # Force everyone to log in (disable anonymous access). #require_login = False If you're looking to implement tool-based access control, the best approach is probably to use the same role-based approach that libraries use: https://bitbucket.org/galaxy/galaxy-central/issue/269/use-galaxy-security-to-restrict-tool Thanks, J. ___ 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/
[galaxy-dev] Fwd: tool restrict access
Hi, in order to restrict the access of a tool to logged users I'm trying to use Cheetah for editing the xml config file. I was wondering if a solution like the one below should work. Although no errors are reported while loading the tool it does not perform the check on the email address and anonymous users still see the tool. Any ideas of what it's wrong with this solution? Cheers, I. ?xml version=1.0? tool name=RSS site id=rss1 tool_type=data_source descriptionRSS site/description #if $__user_email__ == displayYou are not authorized to use this tool/display #else command interpreter=python data_source.py $output $__app__.config.output_size_limit /command options sanitize=False refresh=True/ #end if /tool Messaggio originale Oggetto: [galaxy-dev] tool restrict access Data: Mon, 02 Jan 2012 18:36:53 +0100 Mittente: Ivan Merelli ivan.mere...@itb.cnr.it A: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu Hi, how can I restrict the access of a Galaxy tool to a specific user in an login free instance of Galaxy? I see a suggestion in this post http://gmod.827538.n3.nabble.com/Galaxy-Tool-permission-Access-td3348890.html but it's really workround, I was seeking for a cleaner solution... Thanks, Ivan ___ 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/ ___ 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/
[galaxy-dev] tool restrict access
Hi, how can I restrict the access of a Galaxy tool to a specific user in an login free instance of Galaxy? I see a suggestion in this post http://gmod.827538.n3.nabble.com/Galaxy-Tool-permission-Access-td3348890.html but it's really workround, I was seeking for a cleaner solution... Thanks, Ivan ___ 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/
[galaxy-dev] rgenetics galaxy
Hi, I'm trying to use rgenetics in galaxy, but I have some problem in installting rpy-1.0.3 with R-2.13.1. I found this guide, which is about the same problem of mine: http://gmod.827538.n3.nabble.com/Rpy-1-0-3-and-R-2-13-1-td3359590.html but didn't work for me (although the part about the modulefile is quite obscure for me). The problem seems to be correlated to an header file (Rdevices.h) which is no more present in the latest R distribution. Any hints to solve this problem? May I use rpy2? Best, Ivan ___ 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/
Re: [galaxy-dev] microarray NGS
Dear Eric, thank you for your answer. Your workaround works for the pheno file. A related question is: the affybatch and the eset file formats require to upload two files (rispectively the pheno and the eset/affybatch). Is it normal to have finally only the pheno one in the History? I. Hi Ivan, I can provide an explanation about the first part at least. You are seeing that ##failed message due to a bug in Galaxy core code that I've previously raised on this list. The path you see there is where the .pheno file should (and does) end up after the tool is done. However, the code that generates the ##failed message is getting called before the .pheno file has been moved to that path from its temporary location. Hence, it can't be found there at that point in execution time. While requiring a workaround is not ideal, a very simple one does exist. In the history item for your uploaded dataset, click on the pencil (Edit attributes) and then click the button that says Auto-detect. Best, Eric From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] on behalf of Ivan Merelli [ivan.mere...@itb.cnr.it] Sent: Wednesday, November 09, 2011 7:12 AM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] microarray NGS Hi Galaxy Users, I'm interested in integrating microarray and NGS data. My problem concerns the uploading of an affybatch object in Galaxy (I have a local instance of galaxy, but exacly the same problem is present in http://main.g2.bx.psu.edu) After processing the upload, the only message in the green output data box of the history is something like: ##failed to find /galaxy/main_database/files/003/251/dataset_3251699_files/rexpression.pheno Can you help me in understanding what's wrong? In particular the data which I'm trying to upload are created with rexpression (incidentally, is it still supported or novel versions are attended?), because this package gives my some problems and I'm trying to upload manually some results (which seems ok on the disk) to see what is happening. Cheers, Ivan P.s. Maybe some other packages exists to deal with microarray data in Galaxy? e.g. retrieving data from GEO/ArrayExpress, normalizing them, show in a matrix differential expressed genes to join/confront them with novel NGS experiment... I know it's a lot of stuff.. ___ 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/ ___ 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/
[galaxy-dev] microarray NGS
Hi Galaxy Users, I'm interested in integrating microarray and NGS data. My problem concerns the uploading of an affybatch object in Galaxy (I have a local instance of galaxy, but exacly the same problem is present in http://main.g2.bx.psu.edu) After processing the upload, the only message in the green output data box of the history is something like: ##failed to find /galaxy/main_database/files/003/251/dataset_3251699_files/rexpression.pheno Can you help me in understanding what's wrong? In particular the data which I'm trying to upload are created with rexpression (incidentally, is it still supported or novel versions are attended?), because this package gives my some problems and I'm trying to upload manually some results (which seems ok on the disk) to see what is happening. Cheers, Ivan P.s. Maybe some other packages exists to deal with microarray data in Galaxy? e.g. retrieving data from GEO/ArrayExpress, normalizing them, show in a matrix differential expressed genes to join/confront them with novel NGS experiment... I know it's a lot of stuff.. ___ 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/
