[galaxy-dev] bug with Galaxy form validation and dynamic_options population of drop-down menus where option values are integers
Hello, If you have a form with an input like this: param name=input1 type=select dynamic_options=get_options() / And the options dynamically generated have integers as values, e.g. options tuples like this: [ One, 1, 1 ], [ Two, 2, 0 ], [ Three, 3, 0 ] When you try to submit the galaxy form you always get the validation error An invalid option was selected, please verify. regards, Leandro ___ 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] uploading multiple files into one dataset
Dear list, Our lab's proteomics data is frequently outputted into 50 files containing different fractions of proteins. The files are locally stored and not present on the Galaxy server. We've planned to somehow (inside galaxy) merge these files and split them into tasks so they can be run on the cluster. We would either merge/split the files by concatenation, or untar/tar files at every job, depending on filetype and tool. No problems so far. However, I have been looking around for a way to upload 50 files simultaneously to galaxy and convert to one dataset, and this does not seem to be supported. Before starting to create a hack to make this work, which doesn't seem especially trivial to me, I'd like to know if I should instead use libraries. From what I've seen, libraries are not treated as datasets in Galaxy but rather contain datasets. If there was a tar all sets in library and import to history I'd be using that, but I've only encountered tar/zip sets and download locally which would be a bit of a workaround. I haven't found much on this subject in the mailing list, has this functionality been requested before? cheers, jorrit boekel ___ 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] Problem previewing a tool in the Toolshed
Hi Carlos, You can certainly add support for a sqlite database datatype to your local galaxy instance. As you say, it may be no more complex / fragile than h5 or other binary datatypes - I've not gone far enough down the analysis path to provide good reasons why it may or may not be reasonable, so perhaps I spoke too soon. If you have questions about how to add support for new datatypes, see our wiki at http://wiki.g2.bx.psu.edu/Admin/Datatypes. Thanks! Greg Von Kuster On Feb 29, 2012, at 11:59 AM, Carlos Borroto wrote: Hi Greg, Thanks for looking and resolving this issue. After deleting all the files in the repo and re-adding them, everything is working as expected. Please see my comments inline about the other two issues. On Tue, Feb 28, 2012 at 1:57 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Carlos, I've uploaded a fix for the problem you saw when attempting to reset all metadata on your cummerbund tool. Thanks for reporting this issue. Looking at your change sets, it seems that you are attempting to use the public tool shed hosted by Penn State as a source code repository for your tool development efforts. If so, this is not the intent the public tool shed - it's intent is rather to share fully functional tools with others in the Galaxy community (fully functional implies that the tools was developed in an environment that included a Galaxy instance, and the tool proved to be functional within the Galaxy instance before it was uploaded to the tool shed). The tool shed inspects every change set and performs certain functions based on the content of the change set. For example, if a change set includes a tool, an attempt to load the tool will be made to generate information about the tool. Data types included in a change set are processed as well. Because of this, it is best to upload changes to the tool shed that contain development efforts that are in a finished state. See my additional inline comments and questions in your message. Thanks! Greg Von Kuster On Feb 15, 2012, at 2:24 PM, Carlos Borroto wrote: Hi Greg, Thanks for your answer. Would be great to get the tool to preview correctly but is not a big deal. I'm having a few more problems. I'm getting this error from time to time when I do hg push or even when I delete all files from the toolshed and upload new ones: Version information for the tools included in the cummerbund repository is missing. Reset all of this repository's metadata in the tool shed, then set the installed tool versions from the installed repository's Repository Actions menu. The fix that I've pushed to the tool shed should hopefully resolve this issue. Doing a Reset metadata in the toolshed doesn't solve this issue. I can't find how to do then set the installed tool versions from the installed repository's Repository Actions menu. I'm also having problem including a datatype with the tool. One of the outputs of the tool is a sqlite database. I have this datatypes_conf.xml: ?xml version=1.0? datatypes registration datatype extension=sqlite type=galaxy.datatypes.binary:Binary mimetype=application/octet-stream subclass=True display_in_upload=true/ /registration /datatypes Still sqlite doesn't appear as an option when I try to upload a file to Galaxy. The new datatype does appear if I choose the edit a dataset attributes. I'm not quite sure what your intentions are here, but attempting to make a Galaxy datatypes be a sqlite database sounds like it will be complex and fragile, One of the steps for cummeRbund library is the creation of a sqlite database. Generating this database is by far the step taking most of the processing time. cummeRbund author made it possible to pass as an input a previously generated sqlite database, this greatly cuts the processing time for subsequent analysis of the same cuffdiff ouput. I don't see why having a sqlite binary data type would be different than let say BigBed, BAM or h5 binary data types. Could you please comment on why you think it would be complex and fragile?. Lastly, when I try to upload a sqlite database I get this error: An error occurred running this job: The uploaded binary file contains inappropriate content Uploading a sqlite database to the tool shed will certainly result in this behavior as our code inspectors will not handle this types o content. Sorry I didn't explained myself clearly, I'm not uploading the sqlite database to the tool shed. I'm uploading it to a history so I can use it with my newly developed tool. Kind regards, Carlos ___ 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] HMMER wrappers
On Wed, Feb 29, 2012 at 5:56 PM, Edward Kirton eskir...@lbl.gov wrote: hi, peter - i will fix the description and upload hmmsearch and infernal today. Great. Assuming hmmscan and hmmsearch have (almost) the same command line API, there is something to be said for presenting them as one tool in Galaxy, with a drop down selection between them (with help text about which is recommend adapted from the HMMER blog post). One could even have an automatic selection by a wrapper script based on the number of query sequences and the number of HMMs. My thinking here is the detail of hmmscan vs hmmsearch is purely an implementation detail that the end user shouldn't have to worry about. Or just duplicate most of the XML code and have two wrappers. But as far as I know there isn't (yet) a nice way of reusing XML snippets between tool wrappers... which would be handy. Thanks, 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/
[galaxy-dev] en/disable field based on the state of checkbox/radiobutton
Hello, From looking at the documentation for tool config syntax and I wasn't able to spot a way to have a field enabled or disabled based on the state of a radio button or checkbox. Is this possible? If I missed the documentation please point me in the right direction. I have two use cases for this: the first is that I want the user to be able to either select from a group of preselected values (in my case genome lengths) or enter their own value in a numeric field; the second is that I'd like the user to be able to select from a data file that has been stored on our server or a data file from their history. Thank you, Keith ___ 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] HMMER wrappers
great suggestion; i'll make those changes On Wed, Feb 29, 2012 at 10:05 AM, Peter Cock p.j.a.c...@googlemail.comwrote: On Wed, Feb 29, 2012 at 5:56 PM, Edward Kirton eskir...@lbl.gov wrote: hi, peter - i will fix the description and upload hmmsearch and infernal today. Great. Assuming hmmscan and hmmsearch have (almost) the same command line API, there is something to be said for presenting them as one tool in Galaxy, with a drop down selection between them (with help text about which is recommend adapted from the HMMER blog post). One could even have an automatic selection by a wrapper script based on the number of query sequences and the number of HMMs. My thinking here is the detail of hmmscan vs hmmsearch is purely an implementation detail that the end user shouldn't have to worry about. Or just duplicate most of the XML code and have two wrappers. But as far as I know there isn't (yet) a nice way of reusing XML snippets between tool wrappers... which would be handy. Thanks, 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/
Re: [galaxy-dev] Problem previewing a tool in the Toolshed
Is your datatype lading into your Galaxy instance correctly (either when you start your Galaxy instance or when you install your tool from the tool shed)? If so, it should be displaying in the upload form. What does your paster log say? On Feb 29, 2012, at 1:06 PM, Carlos Borroto wrote: Hi Greg, I did follow that link and I think the datatypes_conf.xml in the tool repository is correctly written: ?xml version=1.0? datatypes registration datatype extension=sqlite type=galaxy.datatypes.binary:Binary mimetype=application/octet-stream subclass=True display_in_upload=true/ /registration /datatypes I thought by adding display_in_upload=true that would make the datatype to appear as an option when uploading a file, but this is not happening. Do I need to declare type as for example galaxy.datatypes.binary:Sqlite3 for this to work? If I have to, I'm guessing I would have to do what is explained here: http://wiki.g2.bx.psu.edu/Tool%20Shed#Including_proprietary_data_types_that_use_class_modules_contained_in_your_repository Thanks, Carlos On Wed, Feb 29, 2012 at 12:14 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Carlos, You can certainly add support for a sqlite database datatype to your local galaxy instance. As you say, it may be no more complex / fragile than h5 or other binary datatypes - I've not gone far enough down the analysis path to provide good reasons why it may or may not be reasonable, so perhaps I spoke too soon. If you have questions about how to add support for new datatypes, see our wiki at http://wiki.g2.bx.psu.edu/Admin/Datatypes. Thanks! Greg Von Kuster On Feb 29, 2012, at 11:59 AM, Carlos Borroto wrote: Hi Greg, Thanks for looking and resolving this issue. After deleting all the files in the repo and re-adding them, everything is working as expected. Please see my comments inline about the other two issues. On Tue, Feb 28, 2012 at 1:57 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Carlos, I've uploaded a fix for the problem you saw when attempting to reset all metadata on your cummerbund tool. Thanks for reporting this issue. Looking at your change sets, it seems that you are attempting to use the public tool shed hosted by Penn State as a source code repository for your tool development efforts. If so, this is not the intent the public tool shed - it's intent is rather to share fully functional tools with others in the Galaxy community (fully functional implies that the tools was developed in an environment that included a Galaxy instance, and the tool proved to be functional within the Galaxy instance before it was uploaded to the tool shed). The tool shed inspects every change set and performs certain functions based on the content of the change set. For example, if a change set includes a tool, an attempt to load the tool will be made to generate information about the tool. Data types included in a change set are processed as well. Because of this, it is best to upload changes to the tool shed that contain development efforts that are in a finished state. See my additional inline comments and questions in your message. Thanks! Greg Von Kuster On Feb 15, 2012, at 2:24 PM, Carlos Borroto wrote: Hi Greg, Thanks for your answer. Would be great to get the tool to preview correctly but is not a big deal. I'm having a few more problems. I'm getting this error from time to time when I do hg push or even when I delete all files from the toolshed and upload new ones: Version information for the tools included in the cummerbund repository is missing. Reset all of this repository's metadata in the tool shed, then set the installed tool versions from the installed repository's Repository Actions menu. The fix that I've pushed to the tool shed should hopefully resolve this issue. Doing a Reset metadata in the toolshed doesn't solve this issue. I can't find how to do then set the installed tool versions from the installed repository's Repository Actions menu. I'm also having problem including a datatype with the tool. One of the outputs of the tool is a sqlite database. I have this datatypes_conf.xml: ?xml version=1.0? datatypes registration datatype extension=sqlite type=galaxy.datatypes.binary:Binary mimetype=application/octet-stream subclass=True display_in_upload=true/ /registration /datatypes Still sqlite doesn't appear as an option when I try to upload a file to Galaxy. The new datatype does appear if I choose the edit a dataset attributes. I'm not quite sure what your intentions are here, but attempting to make a Galaxy datatypes be a sqlite database sounds like it will be complex and fragile, One of the steps for cummeRbund library is the creation of a sqlite database. Generating this database is by far the step taking most of the processing time. cummeRbund author made it possible to pass as
[galaxy-dev] Possible Galaxy memory leak?
Hi all-- Our group is running a local instance of Galaxy on a Linux box. We have been noticing a memory issue, where if we leave the server running for a few days, soon all available memory (~8gb) will be used up to the point where the tools fail because they are unable to allocate new memory. While we haven't done any rigorous testing, this issue seems to be independent of the specific tools we run, and actually seems to still appear if we do not run any tools at all. The process python is what is taking up all the memory, and the issue is not instantaneous but happens over time. Restarting the server frees the memory immediately. Is this a known issue? If so, is there a known fix for it? Any insight on this would be much appreciated, as it is complicating our efforts to automate long work-flows. Thank you so much for your time Josh Gross, Western Washington University. ___ 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] Possible Galaxy memory leak?
We had intermittent issues like this for an embarrassingly long time at MSI, but since we applied this patch https://bitbucket.org/galaxy/galaxy-central/pull-request/36/fix-for-dynamic_optionspy Galaxy has been running smoothly for weeks. Seems unlikely this is the problem in your case (unless you have pulled in tools with make use of dynamic options), but it something to consider. -John On Wed, Feb 29, 2012 at 2:08 PM, Joshua Gross gros...@students.wwu.edu wrote: Hi all-- Our group is running a local instance of Galaxy on a Linux box. We have been noticing a memory issue, where if we leave the server running for a few days, soon all available memory (~8gb) will be used up to the point where the tools fail because they are unable to allocate new memory. While we haven't done any rigorous testing, this issue seems to be independent of the specific tools we run, and actually seems to still appear if we do not run any tools at all. The process python is what is taking up all the memory, and the issue is not instantaneous but happens over time. Restarting the server frees the memory immediately. Is this a known issue? If so, is there a known fix for it? Any insight on this would be much appreciated, as it is complicating our efforts to automate long work-flows. Thank you so much for your time Josh Gross, Western Washington University. ___ 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] Potential issue with eggs ?
Good evening all, I am seeing the following issue when attempting to start galaxy. Traceback (most recent call last): File ./scripts/paster.py, line 34, in module command.run() File /home/home/galaxy/software/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py, line 84, in run invoke(command, command_name, options, args[1:]) File /home/home/galaxy/software/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py, line 123, in invoke exit_code = runner.run(args) File /home/home/galaxy/software/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py, line 218, in run result = self.command() File /home/home/galaxy/software/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py, line 276, in command relative_to=base, global_conf=vars) File /home/home/galaxy/software/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py, line 313, in loadapp **kw) File /home/home/galaxy/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File /home/home/galaxy/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 224, in loadobj global_conf=global_conf) File /home/home/galaxy/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 248, in loadcontext global_conf=global_conf) File /home/home/galaxy/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 278, in _loadconfig return loader.get_context(object_type, name, global_conf) File /home/home/galaxy/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 413, in get_context section) File /home/home/galaxy/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 458, in _context_from_explicit value = import_string(found_expr) File /home/home/galaxy/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 18, in import_string return pkg_resources.EntryPoint.parse(x=+s).load(False) File /home/home/galaxy/software/galaxy-central/lib/pkg_resources.py, line 1954, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File /home/home/galaxy/software/galaxy-central/lib/galaxy/web/buildapp.py, line 19, in module from galaxy import config, jobs, util, tools File /home/home/galaxy/software/galaxy-central/lib/galaxy/jobs/__init__.py, line 4, in module from galaxy import util, model EOFError: EOF read where object expected Removing PID file paster.pid Would this suggest that the eggs are bad? What would be the best way to remedy the situation Thanks Michael. ___ 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/
