[galaxy-dev] removing wrapper version info from tools?
Hi all, So I am trying to remove the version info (at the top of a tool page) entirely for all the tools. As I understand, those versions are the versions of the wrappers and not the tools themselves. Although I could change that, I would rather just not have the versions on the tool pages at all. We currently show all the versions of our tools on our landing page. Is there any way to remove the version part of the tool title entirely? I.e., if it originally says Map with BWA for Illumina (version 1.0.0), I just want it to say Map with BWA for Illumina. - Nik. -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w) ___ 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] removing wrapper version info from tools?
Hi Bjorn,
So I actually don't use the toolshed at all, we have a galaxy AMI that I
update and maintain. We have many of the canonical tools, but we also have
many custom tool interfaces on there, some of which I wrote. We also use
the latest version of the tool if possible. All of the XML files are local
to the instance and are not from the toolshed. I am referring to the
version that is used in the tool tag. That version number seems
arbitrary and the students that use our Galaxy are constantly confused as
to why the tool page has a different version than the tool itself. However,
it seems like there is no easy way to remove that part, so I think I will
just have to update the version numbers myself. What would be the best way
to have multiple versions of a tool *without* using the toolshed? Any help
is highly appreciated. Thanks!
- Nik.
On Tue, Jul 8, 2014 at 1:12 AM, Björn Grüning bjoern.gruen...@gmail.com
wrote:
Hi Nik,
Hi Bjorn,
Thanks for your response. It seems to me that the wrapper version is not
really that useful... the thing that is important is the version of the
underlying tool.
Sure, I agree. But on the other side the user should not care about the
version, and is on most cases not interested as long as it works :)
But as pointed out I would also like to shift to a more useful numbering,
that the arbitrary one we are using now.
I can certainly update the versions to be the versions of
the tool, if need be.
That will break many thing, if you combining your tools with the toolshed
and updates would be more complicated. Don't do that, at least not for
tools from the ToolShed. Try to convince the Tool Maintainers.
However, I wasn't aware that you could have multiple
versions of the same tool to choose from. How do I get that to work?
You can simply install multiple versions (revisions) from the same tool
from the Tool Shed. For example multimple Blast version.
I tried creating two different XML files with the same tool id, but that
didn't work. And how would I make sure the wrapper scripts pointed to the
correct version... it seems like I would have to tailor each script with
an
absolute path to the specific version?
No you need to have the Tool Shed managing that for you. Each version is a
separate tool with the same tool-id. Galaxy keeps track of every dependency
of a certain tool. So the same tool with different versions with different
dependencies will be working over time.
Please read more about all of that in the galaxy wiki, especially about
Tools and the Tool Shed:
https://wiki.galaxyproject.org/ToolShed
Cheers,
Bjoern
- Nik.
On Mon, Jul 7, 2014 at 11:56 PM, Björn Grüning bjoern.gruen...@gmail.com
wrote:
Hi Nik,
you can hack to tool rendering and omit the version string, but I would
not recommend that. The version will be a selectbox as soon as you have
multiple versions from the same tools installed. This is important for
reproducibility.
The best approach would be to fix the version string. Do you have any
suggestions?
For my wrappers I try to go with that version scheme:
{Tool-Version}.{wrapper-version}.
Cheers,
Bjoern
Am 08.07.2014 08:51, schrieb Nikhil Joshi:
Hi all,
So I am trying to remove the version info (at the top of a tool page)
entirely for all the tools. As I understand, those versions are the
versions of the wrappers and not the tools themselves. Although I could
change that, I would rather just not have the versions on the tool pages
at
all. We currently show all the versions of our tools on our landing
page.
Is there any way to remove the version part of the tool title entirely?
I.e., if it originally says Map with BWA for Illumina (version
1.0.0), I
just want it to say Map with BWA for Illumina.
- Nik.
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--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
530.752.2698 (w)
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[galaxy-dev] genotypeGVCFs in galaxy from GATK 3.0
Hi all, Is anyone working on (or has already created) wrappers for GATK 3.0? Specifically, I'm looking for a wrapper for genotypeGVCFs, but it seems like I would want all the GATK wrappers to be updated. Any help is highly appreciated! - Nik. -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w) ___ 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] automatically adding fasta files to built-in databases and selecting files questions
Hi all, We have a local install of Galaxy that we use for testing for our bioinformatics courses. I am creating some new tool interfaces for the install. I want to create a tool that will allow a user to automatically add a fasta database to the built-in databases (without needing to reboot the server). Is this possible? Along with that issue is that the number of databases for this tool can number in the thousands. Is there a way to easily search the built-in databases for the database you are looking for, and then use that database in a tool? Right now, it is an enormous drop down list which is really annoying and unwieldy. Finally, these tools can take multiple input files, but I really don't like the way galaxy handles that where you have to continually click on Add another file. Is there a method or work-around in galaxy where you can have a multi-file select? - Nik. -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w) ___ 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] auto removal of datasets when number of outputs cannot be determined until tool is run
Hi all, So I am using this documentationhttp://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number_of_Output_datasets_cannot_be_determined_until_tool_runto create a tool that has a variable number of output files based upon the input file. I have gotten it to work, however, the intermediate files which I create in the $__new_file_path__ directory (which are then copied into the database as history files) are not being deleted upon tool completion. Is there a way to get galaxy to automatically delete these files, or is there some programmatic way to do it? - Nik. -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w) ___ 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] database I/O error
Hi all, I have a client who is trying to run velvet on a small bacterial assembly in Galaxy. She is using our Core's custom Galaxy in the Amazon Cloud. It has had very few problems and we have been updating it and using it for years. However, after her assembly ran for a while, Galaxy crashed and now gives this error whenever you try to access it: Error Traceback: ⇝ OperationalError: (OperationalError) disk I/O error u'UPDATE galaxy_session SET update_time=?, is_valid=? WHERE galaxy_session.id = ?' ['2013-10-17 18:22:49.991937', 0, 110] URL: http://ec2-54-219-128-159.us-west-1.compute.amazonaws.com/user/logout Module weberror.evalexception.middleware:364 in respond view app_iter = self.application(environ, detect_start_response) Module paste.debug.prints:98 in __call__ view environ, self.app) Module paste.wsgilib:539 in intercept_output view app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ view return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ view return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ view return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:185 in handle_request view body = method( trans, **kwargs ) Module galaxy.webapps.galaxy.controllers.user:509 in logout view trans.handle_user_logout( logout_all=logout_all ) Module galaxy.web.framework:713 in handle_user_logout view self.sa_session.flush() Module sqlalchemy.orm.scoping:127 in do view return getattr(self.registry(), name)(*args, **kwargs) Module sqlalchemy.orm.session:1356 in flush view self._flush(objects) Module sqlalchemy.orm.session:1434 in _flush view flush_context.execute() Module sqlalchemy.orm.unitofwork:261 in execute view UOWExecutor().execute(self, tasks) Module sqlalchemy.orm.unitofwork:753 in execute view self.execute_save_steps(trans, task) Module sqlalchemy.orm.unitofwork:768 in execute_save_steps view self.save_objects(trans, task) Module sqlalchemy.orm.unitofwork:759 in save_objects view task.mapper._save_obj(task.polymorphic_tosave_objects, trans) Module sqlalchemy.orm.mapper:1413 in _save_obj view c = connection.execute(statement.values(value_params), params) Module sqlalchemy.engine.base:824 in execute view return Connection.executors[c](self, object, multiparams, params) Module sqlalchemy.engine.base:874 in _execute_clauseelement view return self.__execute_context(context) Module sqlalchemy.engine.base:896 in __execute_context view self._cursor_execute(context.cursor, context.statement, context.parameters[0], context=context) Module sqlalchemy.engine.base:950 in _cursor_execute view self._handle_dbapi_exception(e, statement, parameters, cursor, context) Module sqlalchemy.engine.base:931 in _handle_dbapi_exception view raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) OperationalError: (OperationalError) disk I/O error u'UPDATE galaxy_session SET update_time=?, is_valid=? WHERE galaxy_session.id = ?' ['2013-10-17 18:22:49.991937', 0, 110] I will be getting more information from her soon, but I just wanted to post this to see if anybody had any suggestions about what might be going on and perhaps how to fix it? Any help would be highly appreciated. Thanks! - Nik. -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w) ___ 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] workflow issues in local Galaxy....
I am not using CloudMan, but we do use a sqlite database. It seems to have that behavior when there is an output that connects to two inputs... but I think I need to do more investigating. I suppose we could try postgres and see if that works... - Nik. On Mon, Sep 16, 2013 at 2:04 PM, Björn Grüning bjo...@gruenings.eu wrote: Hi Nikhil, do you use the CloudMan?http://wiki.galaxyproject.org/CloudMan I have such a behaviour when I used the sqlite database and not postgresql. Cheers, Bjoern Hi all, So we use Galaxy to teach our bioinformatics courses and we have an install of Galaxy in the Amazon cloud that we have customized with various tools. However, we don't touch the Galaxy code base itself. Recently, we've been getting errors in creating and running workflows. We are getting locked database errors, sometimes the steps seem to run out of order, and sometimes the entire workflow just hangs. Also, the workflow editor seems to be having issues, like it allows connections between outputs and inputs of entirely different datatypes. Has anyone seen any issues like this? - Nik. -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w) ___ 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/ -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w) ___ 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] workflow issues in local Galaxy....
Hi all, So we use Galaxy to teach our bioinformatics courses and we have an install of Galaxy in the Amazon cloud that we have customized with various tools. However, we don't touch the Galaxy code base itself. Recently, we've been getting errors in creating and running workflows. We are getting locked database errors, sometimes the steps seem to run out of order, and sometimes the entire workflow just hangs. Also, the workflow editor seems to be having issues, like it allows connections between outputs and inputs of entirely different datatypes. Has anyone seen any issues like this? - Nik. -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w) ___ 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] directory copies as zero-length file from job_working_directory?
So I found the solution we used before... is there a reason this code
hasn't been changed? Is there a better way to do what I want to do?
Here is the solution we used:
Yes, you have to modify lib/galaxy/objectstore/__init__.py:
In class DiskObjectStore find the function 'update_from_file' (line ~340)
and replace:
try:
shutil.copy(file_name, self.get_filename(obj, **kwargs))
except IOError, ex:
log.critical('Error copying %s to %s: %s' % (file_name,
self._get_filename(obj, **kwargs), ex))
by:
try:
if os.path.isdir(file_name):
dir_name = self._get_filename(obj, **kwargs)
os.remove(dir_name)
shutil.copytree(file_name, dir_name)
else:
shutil.copy(file_name, self.get_filename(obj, **kwargs))
except IOError, ex:
log.critical('Error copying %s to %s: %s' % (file_name,
self._get_filename(obj, **kwargs), ex))
- Nik.
On Thu, Mar 28, 2013 at 7:06 PM, Nikhil Joshi najo...@ucdavis.edu wrote:
Hi all,
So I have a tool that I am writing a wrapper script for that produces a
directory of images as one of its outputs. This directory gets created
just fine in the job_working_directory, but then when the job finishes and
the contents of the job_working_directory are copied, the copy of the
images directory is a zero-length *file*. I seem to recall having this
problem before and finding a solution to it, but now I can't seem to find
it. Any ideas?
- Nik.
--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
530.752.2698 (w)
--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
530.752.2698 (w)
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[galaxy-dev] list of tool versions and galaxy ami?
Hi all, Is there a canonical list of current tool versions that are running in the public galaxy? Is there a way to get that list? Also, I was hoping that there might be a galaxy ami that I could use in the amazon cloud and by that I mean NOT a cloudman instance. I am looking for an instance that runs galaxy directly. Does that exist? - Nik. -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w) ___ 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] directory copies as zero-length file from job_working_directory?
Hi all, So I have a tool that I am writing a wrapper script for that produces a directory of images as one of its outputs. This directory gets created just fine in the job_working_directory, but then when the job finishes and the contents of the job_working_directory are copied, the copy of the images directory is a zero-length *file*. I seem to recall having this problem before and finding a solution to it, but now I can't seem to find it. Any ideas? - Nik. -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w) ___ 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 dropdown only 8px wide
Can someone point me to where this fix is... I can't find it anywhere and I am running into this problem as well. - Nik. On Mon, Mar 4, 2013 at 9:54 AM, Kelvin Chan kelvin.c...@seqmatic.comwrote: Nevermind, I noticed that the wiki page on Install galaxy was recently updated to show how to do this. -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Kelvin Chan Sent: Monday, March 04, 2013 9:50 AM To: 'Nate Coraor'; 'Björn Grüning' Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Datatype dropdown only 8px wide Hi Nate, I have checked and I am indeed in the Default branch. Is there an easy way to switch over to the stable branch via command line? -Kelvin -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Nate Coraor Sent: Monday, March 04, 2013 8:52 AM To: Björn Grüning Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Datatype dropdown only 8px wide All, Could you check whether you are running the default or stable branch of galaxy-dist? You can find out with the `hg branch` command. I believe this problem should only exist if you're running the default (development) branch, which is not recommended. Thanks, --nate On Mar 4, 2013, at 1:17 AM, Björn Grüning wrote: Hi Peter, i think it was fixed in 0ea9f51. You need to adopt static/style/base.less. Cheers, Bjoern I'm seeing something similar with a local galaxy-dist install that was also installed from bitbucket about 1.5-2 weeks ago, however, in my case, the width is set to 6px, e.g. div class=select2-container id=s2id_autogen2 style=width: 6px. In fact, I started seeing this after I upgraded a previous install - and based on this behavior, I did a complete re-install, but am still getting it. Does anyone know whether or not this has been fixed and pushed back to repository so we can pull the fix? On Fri, Mar 1, 2013 at 3:59 PM, Kelvin Chan kelvin.c...@seqmatic.com wrote: Hello, I am having a slight issue with the Datatype tab of the edit page. I am using a locally installed version of galaxy-dist obtained from bitbucket. I cannot see anything in the dropdown menu to change the datatype. According to the HTML, the box is only 8px wide. div class=select2-container id=s2id_autogen2 style=width: 8px Is there any way to fix this problem without having to re-install galaxy? Thanks, Kelvin ___ 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/ -- Peter Waltman, Ph.D. pwalt...@ucsc.edu 617.347.1876 ___ 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/ ___ 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/ ___ 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/ -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w) ___ 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] Datatype dropdown only 8px wide
P.S. I am not a galaxy developer :) On Wed, Mar 13, 2013 at 6:04 PM, Nikhil Joshi najo...@ucdavis.edu wrote: Can someone point me to where this fix is... I can't find it anywhere and I am running into this problem as well. - Nik. On Mon, Mar 4, 2013 at 9:54 AM, Kelvin Chan kelvin.c...@seqmatic.comwrote: Nevermind, I noticed that the wiki page on Install galaxy was recently updated to show how to do this. -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Kelvin Chan Sent: Monday, March 04, 2013 9:50 AM To: 'Nate Coraor'; 'Björn Grüning' Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Datatype dropdown only 8px wide Hi Nate, I have checked and I am indeed in the Default branch. Is there an easy way to switch over to the stable branch via command line? -Kelvin -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Nate Coraor Sent: Monday, March 04, 2013 8:52 AM To: Björn Grüning Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Datatype dropdown only 8px wide All, Could you check whether you are running the default or stable branch of galaxy-dist? You can find out with the `hg branch` command. I believe this problem should only exist if you're running the default (development) branch, which is not recommended. Thanks, --nate On Mar 4, 2013, at 1:17 AM, Björn Grüning wrote: Hi Peter, i think it was fixed in 0ea9f51. You need to adopt static/style/base.less. Cheers, Bjoern I'm seeing something similar with a local galaxy-dist install that was also installed from bitbucket about 1.5-2 weeks ago, however, in my case, the width is set to 6px, e.g. div class=select2-container id=s2id_autogen2 style=width: 6px. In fact, I started seeing this after I upgraded a previous install - and based on this behavior, I did a complete re-install, but am still getting it. Does anyone know whether or not this has been fixed and pushed back to repository so we can pull the fix? On Fri, Mar 1, 2013 at 3:59 PM, Kelvin Chan kelvin.c...@seqmatic.com wrote: Hello, I am having a slight issue with the Datatype tab of the edit page. I am using a locally installed version of galaxy-dist obtained from bitbucket. I cannot see anything in the dropdown menu to change the datatype. According to the HTML, the box is only 8px wide. div class=select2-container id=s2id_autogen2 style=width: 8px Is there any way to fix this problem without having to re-install galaxy? Thanks, Kelvin ___ 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/ -- Peter Waltman, Ph.D. pwalt...@ucsc.edu 617.347.1876 ___ 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/ ___ 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/ ___ 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/ -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w) -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w) ___ 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
Re: [galaxy-dev] Error in loading tools.
On Fri, Aug 3, 2012 at 11:07 PM, Nikhil Joshi najo...@ucdavis.edu wrote: Hey Mo, So I'm figuring out the same issues, and I think I have been able to figure it out but for sure you need to uncomment the tool_config_file and tool_path lines in your universe_wsgi.ini file, probably should create a new directory one above your install directory called shed_tools, and then restart galaxy. I also ran into the problem where I needed to create a TMPDIR shell variable that pointed to the correct tmp directory. I know you guys don't like the command line, so if this sounds like gibberish to you, I'm hoping the galaxy team can provide a simpler solution. - Nik. P.S. I'm working on creating a DESeq repository that can be automatically installed from the toolbox. I will let you know when I am successful. It was nice to meet you at the conference! :) On Wed, Aug 1, 2012 at 9:07 AM, Mohammad Heydarian mheydar...@gmail.com wrote: Thanks for this. I updated my local version of Galaxy Cloudman and tried loading a tool and got a new error: The tool_config_file setting in universe_wsgi.ini must include at least one shed tool configuration file name with a toolbox tag that includes a tool_path attribute value which is a directory relative to the Galaxy installation directory in order to automatically install tools from a Galaxy tool shed (e.g., the file name shed_tool_conf.xml whose toolbox tag is toolbox tool_path=../shed_tools). See the Automatic installation of Galaxy tool shed repository tools into a local Galaxy instance section of the Galaxy tool shed wiki for all of the details. Any help interpreting this would be greatly appreciated! Cheers, Mo Heydarian On Tue, Jul 31, 2012 at 4:11 PM, Dannon Baker dannonba...@me.com wrote: The problem here is that the public toolshed interface has been updated more recently than the galaxy install on that cloud instance. You should be good to go if you update galaxy (possible through the admin interface at your_ec2_instance/cloud/admin/) to the latest version. -Dannon On Jul 31, 2012, at 12:11 PM, Mohammad Heydarian mheydar...@gmail.com wrote: Hi Galaxy Community! Hope all is well. I've been trying to install some tools in my Galaxy Cloudman instance (using image: ami-da58aab3 ) from the main toolshed. When I try to install to local Galaxy I get the error: Not Found The resource could not be found. No action for /admin_toolshed/prepare_for_install I have tried to load tools on a couple of different Cloudman instances and tried to load a variety of tools and end up with the same error. Any help would be fantastic. Cheers, Mo Heydarian ___ 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/ -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w) -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w) ___ 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] Can't get automatic toolshed installation to work....
Hi Greg,
So I looked at the the URL from the log file and it was trying to
write to a tmp directory owned by root, so that was a problem. I
traced the problem to a python function (make_tmp_directory) where it
was using the environment variable TMPDIR, which was not defined.
So in our launch script we defined the variable and that seemed to
work. However, the repositories that I installed before fixing this
are in a limbo state. When I try to uninstall them I get that same
AttributeError below. Any ideas on how I can reset my installed
Galaxy toolshed repositories so that they are not in a limbo state?
I've included the entire traceback below:
Error Traceback:
View as: Interactive | Text | XML (full)
⇝ AttributeError: 'NoneType' object has no attribute 'startswith'
URL:
http://optidavis.genomecenter.ucdavis.edu:8080/admin_toolshed/browse_repositories?operation=deactivate+or+uninstallid=33b43b4e7093c91f
Module weberror.evalexception.middleware:364 in respond view
app_iter = self.application(environ, detect_start_response)
Module paste.debug.prints:98 in __call__ view
environ, self.app)
Module paste.wsgilib:539 in intercept_output view
app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__ view
return self.application(environ, start_response)
Module paste.httpexceptions:632 in __call__ view
return self.application(environ, start_response)
Module galaxy.web.framework.base:160 in __call__ view
body = method( trans, **kwargs )
Module galaxy.web.framework:184 in decorator view
return func( self, trans, *args, **kwargs )
Module galaxy.web.controllers.admin_toolshed:356 in
browse_repositories view
return self.deactivate_or_uninstall_repository( trans, **kwd )
Module galaxy.web.framework:184 in decorator view
return func( self, trans, *args, **kwargs )
Module galaxy.web.controllers.admin_toolshed:408 in
deactivate_or_uninstall_repository view
repository_install_dir = os.path.abspath ( relative_install_dir )
Module posixpath:343 in abspath view
if not isabs(path):
Module posixpath:53 in isabs view
return s.startswith('/')
AttributeError: 'NoneType' object has no attribute 'startswith'
Any help is highly appreciated! BTW, it was really nice to get to
talk to you at the conference. :)
- Nik.
On Fri, Aug 3, 2012 at 3:49 AM, Greg Von Kuster g...@bx.psu.edu wrote:
Hello Nikhil,
On Aug 2, 2012, at 9:32 PM, Nikhil Joshi wrote:
Hi all,
We just upgraded our local galaxy to the latest version and now I am
trying to get automatic tool installation to work properly. I changed
the universe_wsgi.ini file to enable the toolshed xml file,
Regarding this, do you mean that you have something like the following
setting?
tool_config_files = tool_conf.xml,shed_tool_conf.xml
I created
a shed_tools directory one above the galaxy install, and restarted
galaxy. But when I try to install a repository, I get this error as a
popup: Initializing repository installation failed.
From what tool shed are you trying to install Galaxy? When this pop-up is
displayed, the last line of your Galaxy paster log should be a url. If you
paste that url into a browser it will display a page that displays the entire
stack trace for the exception. We'll need to see this information in order
to determine the cause of the problem.
I tried this
with various repositories, but I get the same error. Then when I go
to Manage installed tool shed repositories, all of the repositories
I tried to install are stuck in the Cloning state. Finally, if I
try to uninstall any of them, I get this error, with a traceback:
AttributeError: 'NoneType' object has no attribute 'startswith'
Any ideas?
- Nik.
--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
530.752.2698 (w)
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--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
530.752.2698 (w)
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[galaxy-dev] Can't get automatic toolshed installation to work....
Hi all, We just upgraded our local galaxy to the latest version and now I am trying to get automatic tool installation to work properly. I changed the universe_wsgi.ini file to enable the toolshed xml file, I created a shed_tools directory one above the galaxy install, and restarted galaxy. But when I try to install a repository, I get this error as a popup: Initializing repository installation failed. I tried this with various repositories, but I get the same error. Then when I go to Manage installed tool shed repositories, all of the repositories I tried to install are stuck in the Cloning state. Finally, if I try to uninstall any of them, I get this error, with a traceback: AttributeError: 'NoneType' object has no attribute 'startswith' Any ideas? - Nik. -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w) ___ 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] strange error having to do with stderr redirection?
\x98package:base\xe2\x80\x99:\n\nattach, detach, environment, gc, load, save\n\naroma.light v1.22.0 (2011-10-31) successfully loaded. See ?aroma.light for help.\n', 1345] It seems that R produces some output on stdout that I can't get rid of yet, but it doesn't seem to affect the outcome... it doesn't explain why this error happens... Any ideas? Is R using some sort of weird encoding that the python can't get? - Nik. -- Nikhil Joshi Bioinformatics Programmer UC Davis Genome Center Davis, CA ___ 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] producing HTML output with images
Hi all, I am having trouble producing HTML output with images. In the past I have been able to produce HTML files with no images and it seemed to work fine. However, now I am writing a script that produces diagnostic images and I want to display all of the images on one page using HTML. I am using the files_path variable to create the plots in the working directory, and then I am using the extra_files_path variable to access the final plot from the html file. I look at the resulting HTML files and it points to the proper plot full path, and the plot DOES exist... but when I click to view the output, the plot doesn't render. It just shows an empty box with a broken image icon, however, the text does render. I copy the plot file, and I can view it fine by itself. I copy the plot and the html and I can view the page just fine offline, but galaxy doesn't want to render the image for some reason. What am I doing wrong? - Nik. -- Nikhil Joshi Bioinformatics Programmer UC Davis Genome Center Davis, CA ___ 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] producing HTML output with images
Well, I guess I figured it out... it turns out that galaxy does some internal magic to automatically add the path of the output directory to the filename when it is rendering the html. So what I needed to do was to create the file in the temporary job directory and then just use the file name without any path information in the html and galaxy does the rest. If anybody has any other advice or pitfalls to avoid, please feel free to let me know. - Nik. On Thu, Feb 16, 2012 at 8:15 PM, Nikhil Joshi najo...@ucdavis.edu wrote: Hi all, I am having trouble producing HTML output with images. In the past I have been able to produce HTML files with no images and it seemed to work fine. However, now I am writing a script that produces diagnostic images and I want to display all of the images on one page using HTML. I am using the files_path variable to create the plots in the working directory, and then I am using the extra_files_path variable to access the final plot from the html file. I look at the resulting HTML files and it points to the proper plot full path, and the plot DOES exist... but when I click to view the output, the plot doesn't render. It just shows an empty box with a broken image icon, however, the text does render. I copy the plot file, and I can view it fine by itself. I copy the plot and the html and I can view the page just fine offline, but galaxy doesn't want to render the image for some reason. What am I doing wrong? - Nik. -- Nikhil Joshi Bioinformatics Programmer UC Davis Genome Center Davis, CA -- Nikhil Joshi Bioinformatics Programmer UC Davis Genome Center Davis, CA ___ 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] downloading bowtie indexed files
Hi all, Just wondering if there is a way to download the bowtie indexed files after indexing. It seems that the indexed output is simply a meta-file that points to the directory where the indexed files are kept but what if I want to download all of the indexed files themselves? I wrote something to do this... basically I created an html page that is the output of bowtie-build which then points to the created files... but I'm wondering if there is an easier way...? - Nik. ___ 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] accessing files_path directory in subsequent analysis steps
Hi all, So I am writing XML files for an analysis pipeline. The first step in the pipeline is to index the reference, the resulting files of which I have put into the files_path directory that I get from using $output.files_path. But then I want to be able to get access to that path in a subsequent step when I choose the output of the indexing step as the input to the next step. So I have the user choose the indexed output (which is just an html page with links to the indexed reference files), and then I try to use $input.files_path and that doesn't work. Am I thinking about this in the right way? How would I find the files_path that was created for the output of the previous step so that I can use it as an input directory for the current step? - Nik ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Setting the output label based on input parameters?
It looks like the Cheetah syntax only is parsed within the command
tags so I figured out a way to do it... but it seems hackish. I
basically changed the string values of truevalue and falsevalue within the
parameter to be an English sentence that would become the label for the
output. I.e., in the input section:
param name=filter_reads type=boolean truevalue=Filtered Reads Fasta
falsevalue=Unfiltered Reads Fasta label=Filter reads?/
and in the output section:
data format=fasta name=output_fasta label=$filter_reads/
This seems wrong to do, but it does work. If anyone has a better method,
please let me know!
- Nik.
On Thu, Aug 25, 2011 at 2:36 PM, Nikhil Joshi najo...@ucdavis.edu wrote:
It's actually a boolean checkbox. so I basically want the label to
change based upon whether or not the checkbox is checked. Is there any way
to do that? Again, I've tried using the Cheetah syntax to do the #if #end
inside the output tags but that didn't work.
- Nik.
On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB swe...@staffmail.ed.ac.ukwrote:
I meant to say label=${input} or label=${input.value}.
If it's a select field then you can change the option values to the text
you want to add to your output label.
Shaun
Quoting Kanwei Li kan...@gmail.com on Wed, 24 Aug 2011 20:34:57 -0400:
Hi Nikhil,
The tool templates are Cheetah templates, so you can do things like:
outputs
%if param == True:
data format=txt name=blah label=Label1 /
%else
data format=txt name=blah label=Label2 /
%endif
/outputs
Thanks,
K
On Wed, Aug 24, 2011 at 8:24 PM, Nikhil Joshi najo...@ucdavis.edu
wrote:
Hi all,
Is there a way to set the label of the output based on the input
parameters? Perhaps by using the action tag? Basically, I want the
output label to be different if the user sets a particular parameter to
be
true.
- Nik.
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Scotland, with registration number SC005336.
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Re: [galaxy-dev] Setting the output label based on input parameters?
Hi Ross,
Yes, I did try that... but what I want is string parameter that changes
based on whether or not you've checked a checkbox (or a way to change the
label of the output based on whether or not the checkbox was checked). So
my idea below did work, but it seems like a hack. Which is why I was
wondering if there was a better way.
- Nik.
On Mon, Aug 29, 2011 at 2:55 AM, Ross ross.laza...@gmail.com wrote:
On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB swe...@staffmail.ed.ac.uk
wrote:
I meant to say label=${input} or label=${input.value}.
Nikhil, did you try as Shaun and others have suggested? Any available
string parameter can be used in a label as far as I can tell.
This is a common idiom - ask for a string ('title') to describe the
job/output for posterity, then in an output:
data format=foo name=output1 metadata_source=input1
label=${title}.myext/
There's even a built in ${on_string} if you just want the file name
plus some history ids?
On Mon, Aug 29, 2011 at 6:54 PM, Nikhil Joshi najo...@ucdavis.edu wrote:
It looks like the Cheetah syntax only is parsed within the command
tags so I figured out a way to do it... but it seems hackish. I
basically changed the string values of truevalue and falsevalue within
the
parameter to be an English sentence that would become the label for the
output. I.e., in the input section:
param name=filter_reads type=boolean truevalue=Filtered Reads
Fasta
falsevalue=Unfiltered Reads Fasta label=Filter reads?/
and in the output section:
data format=fasta name=output_fasta label=$filter_reads/
This seems wrong to do, but it does work. If anyone has a better method,
please let me know!
- Nik.
On Thu, Aug 25, 2011 at 2:36 PM, Nikhil Joshi najo...@ucdavis.edu
wrote:
It's actually a boolean checkbox. so I basically want the label to
change based upon whether or not the checkbox is checked. Is there any
way
to do that? Again, I've tried using the Cheetah syntax to do the #if
#end
inside the output tags but that didn't work.
- Nik.
On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB swe...@staffmail.ed.ac.uk
wrote:
I meant to say label=${input} or label=${input.value}.
If it's a select field then you can change the option values to the
text
you want to add to your output label.
Shaun
Quoting Kanwei Li kan...@gmail.com on Wed, 24 Aug 2011 20:34:57
-0400:
Hi Nikhil,
The tool templates are Cheetah templates, so you can do things like:
outputs
%if param == True:
data format=txt name=blah label=Label1 /
%else
data format=txt name=blah label=Label2 /
%endif
/outputs
Thanks,
K
On Wed, Aug 24, 2011 at 8:24 PM, Nikhil Joshi najo...@ucdavis.edu
wrote:
Hi all,
Is there a way to set the label of the output based on the input
parameters? Perhaps by using the action tag? Basically, I want
the
output label to be different if the user sets a particular parameter
to
be
true.
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Re: [galaxy-dev] outputting different numbers of files based on variables?
It seems that the conditional element can only be used WITHIN a data element in the outputs. But that won't do what I want. I know that you can use conditional in the inputs element in that way, but it will NOT work that way in the outputs element. However, I have found a way to do what I want using the filter element. I basically have all the outputs for both the single-end and paired-end reads, but I filter out the outputs based on whether the user chose single or paired end. If anyone has a better way to do it, I would love to know! - Nik. On Fri, Aug 26, 2011 at 4:26 PM, Duddy, John jdu...@illumina.com wrote: The BWA tool in NGS mapping does just what you want, just for inputs. The general idea is to use a conditional element and define your extra output in a when block. ** ** *John Duddy Sr. Staff Software Engineer Illumina, Inc. *9885 Towne Centre Drive San Diego, CA 92121 Tel: 858-736-3584 E-mail: jdu...@illumina.com ** ** *From:* galaxy-dev-boun...@lists.bx.psu.edu [mailto: galaxy-dev-boun...@lists.bx.psu.edu] *On Behalf Of *Nikhil Joshi *Sent:* Friday, August 26, 2011 3:57 PM *To:* galaxy-dev@lists.bx.psu.edu *Subject:* [galaxy-dev] outputting different numbers of files based on variables? ** ** Hi all, Is it possible to output a different number of files based on variables that the use has chosen? I have a program that will output different numbers of files based upon the input data. So, for example, if the user wants to use a single-end fastq file, the program outputs only one file, however, if the user chooses paired-end fastq files, it outputs three files. Is there any way to get that to work in just one tool? I could make separate tools for single vs. paired end, but I'd rather not. - Nik. ___ 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] Setting the output label based on input parameters?
Hi Kanwei, I tried that and it didn't seem to work. It seems like Galaxy parses the output name BEFORE execution... although that doesn't make sense. In any case, I couldn't get it to work. Also, in the example below the % should really be # right? Anything anyone can think of that I might be doing wrong? - Nik. On Wed, Aug 24, 2011 at 5:34 PM, Kanwei Li kan...@gmail.com wrote: Hi Nikhil, The tool templates are Cheetah templates, so you can do things like: outputs %if param == True: data format=txt name=blah label=Label1 / %else data format=txt name=blah label=Label2 / %endif /outputs Thanks, K On Wed, Aug 24, 2011 at 8:24 PM, Nikhil Joshi najo...@ucdavis.edu wrote: Hi all, Is there a way to set the label of the output based on the input parameters? Perhaps by using the action tag? Basically, I want the output label to be different if the user sets a particular parameter to be true. - Nik. ___ 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] creating new input/output formats
Hi all, Is there a relatively easy way to create your own input/output formats? Some of the formats from programs that I am trying to install on our local Galaxy do not exist as an option. Any ideas? - Nik. ___ 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] Setting the output label based on input parameters?
It's actually a boolean checkbox. so I basically want the label to
change based upon whether or not the checkbox is checked. Is there any way
to do that? Again, I've tried using the Cheetah syntax to do the #if #end
inside the output tags but that didn't work.
- Nik.
On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB swe...@staffmail.ed.ac.ukwrote:
I meant to say label=${input} or label=${input.value}.
If it's a select field then you can change the option values to the text
you want to add to your output label.
Shaun
Quoting Kanwei Li kan...@gmail.com on Wed, 24 Aug 2011 20:34:57 -0400:
Hi Nikhil,
The tool templates are Cheetah templates, so you can do things like:
outputs
%if param == True:
data format=txt name=blah label=Label1 /
%else
data format=txt name=blah label=Label2 /
%endif
/outputs
Thanks,
K
On Wed, Aug 24, 2011 at 8:24 PM, Nikhil Joshi najo...@ucdavis.edu
wrote:
Hi all,
Is there a way to set the label of the output based on the input
parameters? Perhaps by using the action tag? Basically, I want the
output label to be different if the user sets a particular parameter to
be
true.
- Nik.
__**_
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[galaxy-dev] Setting the output label based on input parameters?
Hi all, Is there a way to set the label of the output based on the input parameters? Perhaps by using the action tag? Basically, I want the output label to be different if the user sets a particular parameter to be true. - Nik. ___ 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/
