Re: [galaxy-dev] A tool with no inputs
One of my colleagues is having trouble developing a peculiar tool: it has no inputs. This makes sense in our local context - it fetches some constantly updating remote data for the current user - but implementing it has escaped our skill. Galaxy complains about a tool with no params (i.e. an empty inputs). It complains about a tool with no inputs tag. Hidden input fields don't seem to work (i.e. looks like I'm getting the cached value of the form). From: Duddy, John jdu...@illumina.com Doesn't this violate one of the basic tenets of Galaxy - reproducibility? Without the ability to provide full traceability to the inputs, one can make no guarantees about the outputs. I think that condition is being met - the resulting dataset depends on no inputs but the time of fetching, and so traceability is satisfied, just like many remote and updating data sources. In any event, our pragmatic need in this case is for such a tool without any need for reproducibility. Which leads me to note the strange behaviour seen when the only input is a hidden field. When the inputs are: inputs param name=input_seq_file type=data format=fasta label=Input sequences help=The sequences to have MLST profiles constructed for. / param name=offset type=hidden value=0 / /inputs this works as expected: a dataset selection dropdown and a hidden field (seen in the source). But if you delete the non-hidden parameter: inputs param name=offset type=hidden value=0 / /inputs Galaxy doesn't generate an error, reports loading the tool, and puts an entry in the tool panel. However the link for the tool in question is malformed, missing a tool identifier and when clicked only reloads the middle welcome panel. I haven't worked out where and why this is happening, but at the least it's an uninformative error. Paul Agapow (paul-michael.aga...@hpa.org.uk) Bioinformatics, Centre for Infections, Health Protection Agency - ** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk ** ___ 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] User list and disk space?
Thank you so much!!! It works really fine! I suspected something akin to that but I couldn't find the right attributes. But I still have a question: It comprises the datasets stored in libraries right? Is there a way to ignore them? Thanks again, L-A Greg Von Kuster wrote: Hello Louise, I've pasted a diff below for the file ~/lib/galaxy/web/controller/admin.py that will provide what you want, I believe. I didn't have time to fully test, but it gives you the idea. You can make things prettier by wrapping the returned value in galaxy.datatypes.data.nice_size diff -r 56be3f4871cd lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Fri May 13 21:24:03 2011 -0400 +++ b/lib/galaxy/web/controllers/admin.py Mon May 16 14:15:23 2011 -0400 @@ -41,6 +41,13 @@ if user.galaxy_sessions: return self.format( user.galaxy_sessions[ 0 ].update_time ) return 'never' +class DiskUseageColumn( grids.GridColumn ): +def get_value( self, trans, grid, user ): +disk_used = 0 +for history in user.active_histories: +for hda in history.active_datasets: +disk_used += hda.get_size() +return disk_used # Grid definition webapp = galaxy @@ -65,6 +72,7 @@ ExternalColumn( External, attach_popup=False ), LastLoginColumn( Last Login, format=time_ago ), StatusColumn( Status, attach_popup=False ), +DiskUseageColumn( Disk Used, attach_popup=False ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( Deleted, key=deleted, visible=False, filterable=advanced ) ] On May 16, 2011, at 10:18 AM, Louise-Amelie Schmitt wrote: Hello I would like to add a column in the admin panel's user list with the sum of the file size of every dataset in each user's histories that don't belong to any ibrary. Is there a way to do that? I had a look at lib/galaxy/web/controller/admin.py and templates/grid_base.mako but I fail to see where the query variable (containing the items, therefore the users) come from in the mako template, so I didn't figure out what each column class in admin.py actually manipulates in the get_value() methods. Regards, L-A ___ 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/ Greg Von Kuster Galaxy Development Team g...@bx.psu.edu mailto:g...@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/
Re: [galaxy-dev] User list and disk space?
Louise, The original code would not eliminate a dataset file that was pointed to by a LibraryDatasetDatasetAssociation, and then imported from the data library into the user's history, creating a HistoryDatasetAssociation that points to the same file. I've added a bit of code below that should eliminate datasets falling into this category - not tested at all though... On May 17, 2011, at 8:42 AM, Louise-Amelie Schmitt wrote: But I still have a question: It comprises the datasets stored in libraries right? Is there a way to ignore them? Greg Von Kuster wrote: Hello Louise, I've pasted a diff below for the file ~/lib/galaxy/web/controller/admin.py that will provide what you want, I believe. I didn't have time to fully test, but it gives you the idea. You can make things prettier by wrapping the returned value in galaxy.datatypes.data.nice_size diff -r 56be3f4871cd lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Fri May 13 21:24:03 2011 -0400 +++ b/lib/galaxy/web/controllers/admin.py Mon May 16 14:15:23 2011 -0400 @@ -41,6 +41,13 @@ if user.galaxy_sessions: return self.format( user.galaxy_sessions[ 0 ].update_time ) return 'never' +class DiskUseageColumn( grids.GridColumn ): +def get_value( self, trans, grid, user ): +disk_used = 0 +for history in user.active_histories: +for hda in history.active_datasets: dataset = hda.dataset if not dataset.active_library_associations: +disk_used += hda.get_size() +return disk_used # Grid definition webapp = galaxy @@ -65,6 +72,7 @@ ExternalColumn( External, attach_popup=False ), LastLoginColumn( Last Login, format=time_ago ), StatusColumn( Status, attach_popup=False ), +DiskUseageColumn( Disk Used, attach_popup=False ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( Deleted, key=deleted, visible=False, filterable=advanced ) ] On May 16, 2011, at 10:18 AM, Louise-Amelie Schmitt wrote: Hello I would like to add a column in the admin panel's user list with the sum of the file size of every dataset in each user's histories that don't belong to any ibrary. Is there a way to do that? I had a look at lib/galaxy/web/controller/admin.py and templates/grid_base.mako but I fail to see where the query variable (containing the items, therefore the users) come from in the mako template, so I didn't figure out what each column class in admin.py actually manipulates in the get_value() methods. Regards, L-A ___ 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/ Greg Von Kuster Galaxy Development Team g...@bx.psu.edu mailto:g...@bx.psu.edu Greg Von Kuster Galaxy Development Team g...@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/
Re: [galaxy-dev] User list and disk space?
Possibly, but it would require an enable flag in the config since instances with hundreds of users could pose problems with rendering delays. If someone will proved the precise specs for what yo9u want, I'll add it to my list, but it will be awhile before I get to ti. For example, should dataset files that have both LibraryDatasetDatasetAssociations and HistoryDatasetAssociations be eliminated from the total? On May 17, 2011, at 9:10 AM, Peter Cock wrote: On May 16, 2011, at 10:18 AM, Louise-Amelie Schmitt wrote: Hello I would like to add a column in the admin panel's user list with the sum of the file size of every dataset in each user's histories that don't belong to any ibrary. Is there a way to do that? On Mon, May 16, 2011 at 7:18 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Louise, I've pasted a diff below for the file ~/lib/galaxy/web/controller/admin.py that will provide what you want, I believe. I didn't have time to fully test, but it gives you the idea. You can make things prettier by wrapping the returned value in galaxy.datatypes.data.nice_size That sounds really useful - it is something that you plan on adding to Galaxy officially? Thanks, Peter Greg Von Kuster Galaxy Development Team g...@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/
Re: [galaxy-dev] User list and disk space?
Peter Cock wrote: That sounds really useful - it is something that you plan on adding to Galaxy officially? Yes, I'm working on adding a lot of user- and admin- side access to various numbers about disk usage (used by histories, used by deleted data, etc. and disk quotas. I hope to have this done shortly after the GCC. Thanks, --nate 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/ ___ 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] User list and disk space?
Looks like it's working, a couple of values were reduced :) Thank you so much!!! L-A Greg Von Kuster wrote: Louise, The original code would not eliminate a dataset file that was pointed to by a LibraryDatasetDatasetAssociation, and then imported from the data library into the user's history, creating a HistoryDatasetAssociation that points to the same file. I've added a bit of code below that should eliminate datasets falling into this category - not tested at all though... On May 17, 2011, at 8:42 AM, Louise-Amelie Schmitt wrote: But I still have a question: It comprises the datasets stored in libraries right? Is there a way to ignore them? Greg Von Kuster wrote: Hello Louise, I've pasted a diff below for the file ~/lib/galaxy/web/controller/admin.py that will provide what you want, I believe. I didn't have time to fully test, but it gives you the idea. You can make things prettier by wrapping the returned value in galaxy.datatypes.data.nice_size diff -r 56be3f4871cd lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Fri May 13 21:24:03 2011 -0400 +++ b/lib/galaxy/web/controllers/admin.py Mon May 16 14:15:23 2011 -0400 @@ -41,6 +41,13 @@ if user.galaxy_sessions: return self.format( user.galaxy_sessions[ 0 ].update_time ) return 'never' +class DiskUseageColumn( grids.GridColumn ): +def get_value( self, trans, grid, user ): +disk_used = 0 +for history in user.active_histories: +for hda in history.active_datasets: dataset = hda.dataset if not dataset.active_library_associations: +disk_used += hda.get_size() +return disk_used # Grid definition webapp = galaxy @@ -65,6 +72,7 @@ ExternalColumn( External, attach_popup=False ), LastLoginColumn( Last Login, format=time_ago ), StatusColumn( Status, attach_popup=False ), +DiskUseageColumn( Disk Used, attach_popup=False ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( Deleted, key=deleted, visible=False, filterable=advanced ) ] On May 16, 2011, at 10:18 AM, Louise-Amelie Schmitt wrote: Hello I would like to add a column in the admin panel's user list with the sum of the file size of every dataset in each user's histories that don't belong to any ibrary. Is there a way to do that? I had a look at lib/galaxy/web/controller/admin.py and templates/grid_base.mako but I fail to see where the query variable (containing the items, therefore the users) come from in the mako template, so I didn't figure out what each column class in admin.py actually manipulates in the get_value() methods. Regards, L-A ___ 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/ Greg Von Kuster Galaxy Development Team g...@bx.psu.edu mailto:g...@bx.psu.edu Greg Von Kuster Galaxy Development Team g...@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] Database/Build
I'd like to get a better understanding of the point of the database/build attribute, and pose the question of when is the appropriate time to have it set? In our case at the Jackson Laboratory, the most common build is NCBI37/MM9. However, the feeling of many folks here, is that this should not be set on our fastq files. The only place we really run into trouble is with cufflinks. If you haven't set the db when you get to cufflinks you'll get an error. Our suggestion is that there should be one of two options: 1) Tophat has the ability to set the database of the output files based on the genome that was selected for alignment. 2) There should be a module that can be plugged into a workflow that would set the database of the file prior to passing the file to cufflinks (or any other two that requires the database attribute to be set). We are curious if anyone else is running into this issue, and how it is being solved. We're thinking about hacking the Tophat wrapper, but I wanted to check with others before I did this. Thanks, Dave ___ 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] galaxy doesn't start with drmaa job runner
I am trying to configure galaxy with sge/drmaa scheduler. The galaxy process is
starting up fine without any drmaa configuration. However the galaxy daemon
doesn't start properly when I add drmaa configuration lines as shown below. I
have set SGE_ROOT and DRMAA_LIBRARY_PATH variables properly. Am I missing
something important here?
# drmaa configuration:
{{{
start_job_runners = drmaa
default_cluster_job_runner = drmaa:///
}}
# paster.log file - with drmaa config the process dies with Loaded job runner:
galaxy.jobs.runners.local:LocalJobRunner as last line in the log file. With
local job runner the galaxy starts fine as shown below:
{{{
galaxy.jobs DEBUG 2011-05-17 09:59:58,959 Loaded job runner:
galaxy.jobs.runners.local:LocalJobRunner
galaxy.jobs INFO 2011-05-17 09:59:58,959 job manager started
galaxy.jobs INFO 2011-05-17 09:59:59,325 job stopper started
galaxy.sample_tracking.external_service_types DEBUG 2011-05-17 09:59:59,330
Loaded external_service_type: Simple unknown sequencer 1.0.0
galaxy.sample_tracking.external_service_types DEBUG 2011-05-17 09:59:59,333
Loaded external_service_type: Applied Biosystems SOLiD 1.0.0
galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,349 Enabling 'mobile'
controller, class: Mobile
galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,417 Enabling
'library_common' controller, class: LibraryCommon
galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,435 Enabling 'admin'
controller, class: AdminGalaxy
galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,451 Enabling 'requests'
controller, class: Requests
galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,455 Enabling
'external_services' controller, class: ExternalServiceController
galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,474 Enabling 'page'
controller, class: PageController
galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,480 Enabling
'visualization' controller, class: VisualizationController
galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,549 Enabling 'tracks'
controller, class: TracksController
galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,550 Enabling
'requests_common' controller, class: RequestsCommon
galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,556 Enabling 'request_type'
controller, class: RequestType
galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,561 Enabling
'external_service' controller, class: ExternalService
galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,562 Enabling 'library'
controller, class: Library
galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,746 Enabling 'workflow'
controller, class: WorkflowController
galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,752 Enabling
'library_admin' controller, class: LibraryAdmin
galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,756 Enabling 'async'
controller, class: ASync
galaxy.web.framework.base DEBUG 2011-05-17 10:00:00,026 Enabling 'history'
controller, class: HistoryController
galaxy.web.framework.base DEBUG 2011-05-17 10:00:00,031 Enabling 'error'
controller, class: Error
galaxy.web.framework.base DEBUG 2011-05-17 10:00:00,090 Enabling
'requests_admin' controller, class: RequestsAdmin
galaxy.web.framework.base DEBUG 2011-05-17 10:00:00,095 Enabling 'ucsc_proxy'
controller, class: UCSCProxy
galaxy.web.framework.base DEBUG 2011-05-17 10:00:00,104 Enabling 'forms'
controller, class: Forms
galaxy.web.framework.base DEBUG 2011-05-17 10:00:00,137 Enabling 'dataset'
controller, class: DatasetInterface
galaxy.web.framework.base DEBUG 2011-05-17 10:00:00,143 Enabling 'tool_runner'
controller, class: ToolRunner
galaxy.web.framework.base DEBUG 2011-05-17 10:00:00,148 Enabling 'tag'
controller, class: TagsController
galaxy.web.framework.base DEBUG 2011-05-17 10:00:00,158 Enabling 'user'
controller, class: User
galaxy.web.framework.base DEBUG 2011-05-17 10:00:00,165 Enabling 'root'
controller, class: RootController
galaxy.web.buildapp DEBUG 2011-05-17 10:00:00,189 Enabling 'httpexceptions'
middleware
galaxy.web.buildapp DEBUG 2011-05-17 10:00:00,195 Enabling 'recursive'
middleware
galaxy.web.buildapp DEBUG 2011-05-17 10:00:00,220 Enabling 'print debug'
middleware
/share/apps/galaxy/shantanu-temp-workspace/galaxy-cluster-test/galaxy-dist-50e249442c5a/eggs/WebError-0.8a-py2.6.egg/weberror/exceptions/serial_number_generator.py:11:
DeprecationWarning: the md5 module is deprecated; use hashlib instead
import md5
galaxy.web.buildapp DEBUG 2011-05-17 10:00:00,726 Enabling 'eval exceptions'
middleware
galaxy.web.buildapp DEBUG 2011-05-17 10:00:00,740 Enabling 'trans logger'
middleware
galaxy.web.buildapp DEBUG 2011-05-17 10:00:00,740 Enabling 'config' middleware
galaxy.web.buildapp DEBUG 2011-05-17 10:00:00,744 Enabling 'x-forwarded-host'
middleware
Starting server in PID 10170.
serving on 0.0.0.0:8081 view at http://127.0.0.1:8081
}}}
--
Thanks,
Shantanu.
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Re: [galaxy-dev] Database/Build
I'll just chime in quickly with an agreement that FASTQ files should not have dbkeys set. They don't yet belong to a build/reference genome version. Some tools/workflows may currently require a FASTQ file to have the dbkey set, but this should be considered a work-around for a defect in a tool xml. I'll let someone else on the team address Tophat and the suggestions specifically. Thanks for using Galaxy, Dan On May 17, 2011, at 10:57 AM, Dave Walton wrote: I'd like to get a better understanding of the point of the database/build attribute, and pose the question of when is the appropriate time to have it set? In our case at the Jackson Laboratory, the most common build is NCBI37/MM9. However, the feeling of many folks here, is that this should not be set on our fastq files. The only place we really run into trouble is with cufflinks. If you haven't set the db when you get to cufflinks you'll get an error. Our suggestion is that there should be one of two options: 1) Tophat has the ability to set the database of the output files based on the genome that was selected for alignment. 2) There should be a module that can be plugged into a workflow that would set the database of the file prior to passing the file to cufflinks (or any other two that requires the database attribute to be set). We are curious if anyone else is running into this issue, and how it is being solved. We're thinking about hacking the Tophat wrapper, but I wanted to check with others before I did this. Thanks, Dave ___ 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/
Re: [galaxy-dev] Database/Build
Dave, The fact that the Tophat wrapper was not setting the genome based on the alignment genome was actually a bug, but I just fixed it in changeset 5570:0c1251f25c6b. Let us know if you have further questions. Regards, Kelly On May 17, 2011, at 10:57 AM, Dave Walton wrote: I'd like to get a better understanding of the point of the database/ build attribute, and pose the question of when is the appropriate time to have it set? In our case at the Jackson Laboratory, the most common build is NCBI37/MM9. However, the feeling of many folks here, is that this should not be set on our fastq files. The only place we really run into trouble is with cufflinks. If you haven't set the db when you get to cufflinks you'll get an error. Our suggestion is that there should be one of two options: 1) Tophat has the ability to set the database of the output files based on the genome that was selected for alignment. 2) There should be a module that can be plugged into a workflow that would set the database of the file prior to passing the file to cufflinks (or any other two that requires the database attribute to be set). We are curious if anyone else is running into this issue, and how it is being solved. We're thinking about hacking the Tophat wrapper, but I wanted to check with others before I did this. Thanks, Dave ___ 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] Select first/last N rows from grouped tabular files (e.g. top BLAST hits)
Hi all, I'm wondering if the following task can be done in Galaxy with the standard tools. The specific example is selecting the top (e.g. 3) match sequences for each blast query, but I see this problem as much more general than a Select top BLAST hits tool. I want to select the first few (e.g. 1) rows of each group in a tabular file, where the group criteria is having certain columns equal (e.g. the first 2). e.g. Tabular BLAST output has columns of query ID, match ID, etc. queryA match1 ... queryA match2 ... queryA match2 ... queryA match3 ... queryA match4 ... queryA match4 ... queryA match4 ... queryB match5 ... queryB match5 ... queryC match6 ... queryC match7 ... In this example, some of my queries have more than one HSP per match (more than one line with the same first two columns). If I group on the first two columns, the groups are: queryA match1 ... queryA match2 ... queryA match2 ... queryA match3 ... queryA match4 ... queryA match4 ... queryA match4 ... queryB match5 ... queryB match5 ... queryC match6 ... queryC match7 ... If I then take the first row in each group, that gives me just the first HSP for each query+match combination. queryA match1 ... queryA match2 ... queryA match3 ... queryA match4 ... queryB match5 ... queryC match6 ... queryC match7 ... If for example I wanted only the top 3 matches for each query, I could repeat the proposed tool one more time but with different settings - this time grouping on the first column only: queryA match1 ... queryA match2 ... queryA match3 ... queryB match5 ... queryC match6 ... queryC match7 ... I hope I've conveyed the idea here. The existing tools Select first lines from a dataset and Select last lines from a dataset are related, but do this at the file level. Does this make sense? Does it seem like a useful tool to write if there isn't anything like this already present? Or might it be simpler to just write a Select top BLAST hits tool? 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] library_upload_from_import_dir
Hi,
I'm a Galaxy and Python newbie and I'm working on project that desires
to upload files from a directory to the Galaxy server. We'd like to
physically copy the files rather than maintain references to them.
I'm starting by following the examples in scripts/api/README. All the
display and library_create_library examples work. However, the
library_upload_from_import_dir fails. In my universe...ini,
library_import_dir is defined to be /home/dgeorge/galaxy/import and
there is a bed directory under that with a short file, bed1.bed in the
correct format. I'm not sure what to provide for the last parameter,
the dbkey - maybe that's my problem?
I ran:
./library_upload_from_import_dir.py 59d2fd4e020e178f8c48e61150e513c2
http://localhost:8080/api/libraries/f597429621d6eb2b/contents
c6ca0ddb55be603a10e891fff2e902c3 bed bed hg19
And I get the error:
Exception happened during processing of request from ('127.0.0.1',
38857)
Traceback (most recent call last):
File
/home/dgeorge/galaxy/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/http
server.py, line 1053, in process_request_in_thread
self.finish_request(request, client_address)
File /usr/lib/python2.6/SocketServer.py, line 322, in finish_request
self.RequestHandlerClass(request, client_address, self)
File /usr/lib/python2.6/SocketServer.py, line 618, in __init__
self.finish()
File /usr/lib/python2.6/SocketServer.py, line 661, in finish
self.wfile.flush()
File /usr/lib/python2.6/socket.py, line 297, in flush
self._sock.sendall(buffer(data, write_offset, buffer_size))
error: [Errno 32] Broken pipe
Any ideas or suggestions?
Thanks!
David George
Staff Software Engineer
Illumina, Inc.
25861 Industrial Blvd.
Hayward, CA 94545
Tel: 510-670-9326
Fax: 510-670-9302
Email: dgeo...@illumina.com mailto:dgeo...@illumina.com
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Re: [galaxy-dev] Reciprocal Best Hits (RBH) from BLAST tabular output
Hi Peter, I think the tool shed would be appropriate for this... -K On Tue, May 17, 2011 at 6:23 AM, Peter Cock p.j.a.c...@googlemail.comwrote: On Wed, May 4, 2011 at 9:59 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, I mentioned just over a month ago that I had written a Galaxy tool to do find Reciprocal Best Hits (RBH) from BLAST tabular output or similar (e.g. Bill Pearson's FASTA tabular output). http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-March/004799.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-April/004825.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-April/004829.html The only problem I had was setting default columns, which I consider to be a minor bug in Galaxy: https://bitbucket.org/galaxy/galaxy-central/issue/507 Regardless of this small usability issue, would the Galaxy team like to add this tool to the main distribution (to sit along with my BLAST+ wrappers), or should I submit it to the tool shed? If you want to merge it, the following change set should suffice: https://bitbucket.org/peterjc/galaxy-central/changeset/198bf927ca30 I made a subsequent change set to test giving column defaults as value=c2 rather than value=c2 which makes no difference, but if this is how default column values are meant to be given, take this change too: https://bitbucket.org/peterjc/galaxy-central/changeset/198bf927ca30 A third commit fixes a typo in the help: https://bitbucket.org/peterjc/galaxy-central/changeset/2be6c0bc76ea Would the Galaxy team like to merge this tool into the trunk (and if so, do you have any suggestions for improvements or changes), or should I put it up on the Galaxy Tool Shed instead? 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/
