Hi Lance, Thank you for the pull request. I think this is an excellent way to handle patches until the toolshed itself provides a better mechanism, particularly for the devteam owned repositories; other repository owners may prefer different methods of providing patches, but they can be contacted directly by using the contact form on the toolshed. Future enhancements to the toolshed will integrate better methods of providing this functionality, but that likely some ways off. Any suggestions and community contributions on this would be appreciated. FreeBayes has been updated in the Toolshed to 0.9.6_9608597d12e127c847ae03aa03440ab63992fedf, with mostly minor differences from your pull request. Please let us know if you experience any issues installing or using the updated version (0.0.3). Thanks, Dan On Aug 30, 2012, at 11:35 AM, Lance Parsons wrote: > I have been using the FreeBayes tool in our local Galaxy instance for > some time. As FreeBayes is a rapidly evolving tool, it has been very > helpful to have Daniel Blankenberg work on keeping an updated wrapper. > > Recently, I've run into a rather troublesome bug in FreeBayes > (https://github.com/ekg/freebayes/issues/22) that is causing it to > crash on nearly every real dataset. Luckily, the bug has been fixed > in the latest version of FreeBayes > (0.9.6_9608597d12e127c847ae03aa03440ab63992fedf). > > Unfortunately, the latest version has a few parameter changes that > require an update to the wrapper code. I've taken the liberty to make > some changes to the wrapper and they seem to work. However, now that > I have the tool installed from the Tool Shed, I'm not sure of the > best way to 1) incorporate this update into my local galaxy instance > and 2) contribute this change back to the Tool Shed. > > The best solution is to get the Tool Shed updated and then pull that > update into my production Galaxy instance, however, I'm wondering if > there is a way I could push "hot-fixes" to my production instance > without causing me headaches down the line when the Tool Shed is > inevitably updated. > > As far as coordinating updates of Tool Shed tools, I suppose the > process might be different for different tool authors. I was > wondering, however, if anyone had thoughts on how this might work > best. I've created a clone of the galaxy tool shed repository in > Bitbucket (https://bitbucket.org/lance_parsons/freebayes/) and given > Daniel and Greg access to it in hopes that would make things > easier.Let me know if there is a better way to coordinate, etc. > > Thanks again. > > > -- > Lance Parsons - Scientific Programmer > 134 Carl C. Icahn Laboratory > Lewis-Sigler Institute for Integrative Genomics > Princeton 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/

Hi Lance, This has to do with the way that the updating currently works. Since the migrated version is 0.0.2, the automatic update will only update that particular Tool version (newest version of 0.0.2). To get 0.0.3, you need to install it as a new tool. This way you are able to have both versions installed and available e.g. for having a reproducible rerun functionality. In the latest Galaxy-central / upcoming Galaxy-dist release, only the newest version is shown in the lefthand tool panel. Future enhancements will include allowing the selection of different tool versions from within the tool interface (e.g. allowing the rerun of an older version to use a newer version) and to show and allow updating (installing) new tool versions from the same interface (e.g. 2 to 3). Thanks for using Galaxy, Dan On Aug 31, 2012, at 11:47 AM, Lance Parsons wrote: > Thanks for the quick turnaround Dan. Much appreciated. When I tried > to test updating Freebayes from the toolshed, I get a message that no > updates are available. Perhaps it takes some time before they are > recognized? Or am I missing something? > > Lance > > Daniel Blankenberg wrote: >> Hi Lance, >> >> Thank you for the pull request. I think this is an excellent way to >> handle patches until the toolshed itself provides a better >> mechanism, particularly for the devteam owned repositories; other >> repository owners may prefer different methods of providing patches, >> but they can be contacted directly by using the contact form on the >> toolshed. Future enhancements to the toolshed will integrate better >> methods of providing this functionality, but that likely some ways >> off. Any suggestions and community contributions on this would be >> appreciated. >> >> >> FreeBayes has been updated in the Toolshed to >> 0.9.6_9608597d12e127c847ae03aa03440ab63992fedf, with mostly minor >> differences from your pull request. Please let us know if you >> experience any issues installing or using the updated version (0.0.3). >> >> >> Thanks, >> >> Dan >> >> >> On Aug 30, 2012, at 11:35 AM, Lance Parsons wrote: >> >>> I have been using the FreeBayes tool in our local Galaxy instance >>> for some time. As FreeBayes is a rapidly evolving tool, it has >>> been very helpful to have Daniel Blankenberg work on keeping an >>> updated wrapper. >>> >>> Recently, I've run into a rather troublesome bug in FreeBayes >>> (https://github.com/ekg/freebayes/issues/22) that is causing it to >>> crash on nearly every real dataset. Luckily, the bug has been >>> fixed in the latest version of FreeBayes >>> (0.9.6_9608597d12e127c847ae03aa03440ab63992fedf). >>> >>> Unfortunately, the latest version has a few parameter changes that >>> require an update to the wrapper code. I've taken the liberty to >>> make some changes to the wrapper and they seem to work. However, >>> now that I have the tool installed from the Tool Shed, I'm not sure >>> of the best way to 1) incorporate this update into my local galaxy >>> instance and 2) contribute this change back to the Tool Shed. >>> >>> The best solution is to get the Tool Shed updated and then pull >>> that update into my production Galaxy instance, however, I'm >>> wondering if there is a way I could push "hot-fixes" to my >>> production instance without causing me headaches down the line when >>> the Tool Shed is inevitably updated. >>> >>> As far as coordinating updates of Tool Shed tools, I suppose the >>> process might be different for different tool authors. I was >>> wondering, however, if anyone had thoughts on how this might work >>> best. I've created a clone of the galaxy tool shed repository in >>> Bitbucket (https://bitbucket.org/lance_parsons/freebayes/) and >>> given Daniel and Greg access to it in hopes that would make things >>> easier.Let me know if there is a better way to coordinate, etc. >>> >>> Thanks again. >>> >>> >>> -- >>> Lance Parsons - Scientific Programmer >>> 134 Carl C. Icahn Laboratory >>> Lewis-Sigler Institute for Integrative Genomics >>> Princeton 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/ >> > > -- > Lance Parsons - Scientific Programmer > 134 Carl C. Icahn Laboratory > Lewis-Sigler Institute for Integrative Genomics > Princeton University >

Hi Lance, You'll need to execute the following sql manually in your Galaxy database. update tool_shed_repository set status = 'New' where status = 'Cloning'; Next, you'll have to update your production Galaxy instance code base to at least changeset 2531e085f262 (the human-readable changeset revision is 7503). This revision is required to install the freebayes tool from the main Galaxy tool shed. You can also choose to wait until the next Galaxy release to upgrade if you do not need the freebayes tool in your local instance immediately. Sorry for the inconvenience on this. Greg Von Kuster On Aug 31, 2012, at 3:59 PM, Lance Parsons wrote: > Thanks for the explanation. That makes sense. I went ahead and > installed the new version along with dependencies in my development > environments and all went well. Then in production, the installation > seems to have failed and I'm now stuck with freebayes in the > "cloning" status. I tried to deactivate and uninstall it so I could > try again to monitor what went wrong and I just get an error: > > Error - <type 'exceptions.AttributeError'>: 'NoneType' object has no > attribute 'startswith' > URL: > http://galaxy.princeton.edu/admin_toolshed/browse_repositories?operation=... > File > '/data/local/galaxy/galaxy-prod/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', > line 143 in __call__ > app_iter = self.application(environ, start_response) > File > '/data/local/galaxy/galaxy-prod/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', > line 80 in __call__ > return self.application(environ, start_response) > File > '/data/local/galaxy/galaxy-prod/lib/galaxy/web/framework/middleware/remoteuser.py', > line 91 in __call__ > return self.app( environ, start_response ) > File > '/data/local/galaxy/galaxy-prod/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', > line 632 in __call__ > return self.application(environ, start_response) > File > '/data/local/galaxy/galaxy-prod/lib/galaxy/web/framework/base.py', > line 160 in __call__ > body = method( trans, **kwargs ) > File > '/data/local/galaxy/galaxy-prod/lib/galaxy/web/framework/__init__.py', line > 184 in decorator > return func( self, trans, *args, **kwargs ) > File > '/data/local/galaxy/galaxy-prod/lib/galaxy/web/controllers/admin_toolshed.py', > line 356 in browse_repositories > return self.deactivate_or_uninstall_repository( trans, **kwd ) > File > '/data/local/galaxy/galaxy-prod/lib/galaxy/web/framework/__init__.py', line > 184 in decorator > return func( self, trans, *args, **kwargs ) > File > '/data/local/galaxy/galaxy-prod/lib/galaxy/web/controllers/admin_toolshed.py', > line 408 in deactivate_or_uninstall_repository > repository_install_dir = os.path.abspath ( relative_install_dir ) > File '/usr/local/python/lib/python2.6/posixpath.py', line 342 in abspath > if not isabs(path): > File '/usr/local/python/lib/python2.6/posixpath.py', line 52 in isabs > return s.startswith('/') > AttributeError: 'NoneType' object has no attribute 'startswith' > > Any thoughts on how I can get rid of the partially installed > freebayes tool? Or how to troubleshoot the failing installation? > > Lance > > Daniel Blankenberg wrote: >> Hi Lance, >> >> This has to do with the way that the updating currently works. Since >> the migrated version is 0.0.2, the automatic update will only update >> that particular Tool version (newest version of 0.0.2). To get >> 0.0.3, you need to install it as a new tool. This way you are able >> to have both versions installed and available e.g. for having a >> reproducible rerun functionality. In the latest Galaxy-central / >> upcoming Galaxy-dist release, only the newest version is shown in >> the lefthand tool panel. >> >> Future enhancements will include allowing the selection of different >> tool versions from within the tool interface (e.g. allowing the >> rerun of an older version to use a newer version) and to show and >> allow updating (installing) new tool versions from the same >> interface (e.g. 2 to 3). >> >> >> Thanks for using Galaxy, >> >> Dan >> >> >> On Aug 31, 2012, at 11:47 AM, Lance Parsons wrote: >> >>> Thanks for the quick turnaround Dan. Much appreciated. When I >>> tried to test updating Freebayes from the toolshed, I get a message >>> that no updates are available. Perhaps it takes some time before >>> they are recognized? Or am I missing something? >>> >>> Lance >>> >>> Daniel Blankenberg wrote: >>>> Hi Lance, >>>> >>>> Thank you for the pull request. I think this is an excellent way >>>> to handle patches until the toolshed itself provides a better >>>> mechanism, particularly for the devteam owned repositories; other >>>> repository owners may prefer different methods of providing >>>> patches, but they can be contacted directly by using the contact >>>> form on the toolshed. Future enhancements to the toolshed will >>>> integrate better methods of providing this functionality, but that >>>> likely some ways off. Any suggestions and community contributions >>>> on this would be appreciated. >>>> >>>> >>>> FreeBayes has been updated in the Toolshed to >>>> 0.9.6_9608597d12e127c847ae03aa03440ab63992fedf, with mostly minor >>>> differences from your pull request. Please let us know if you >>>> experience any issues installing or using the updated version (0.0.3). >>>> >>>> >>>> Thanks, >>>> >>>> Dan >>>> >>>> >>>> On Aug 30, 2012, at 11:35 AM, Lance Parsons wrote: >>>> >>>>> I have been using the FreeBayes tool in our local Galaxy instance >>>>> for some time. As FreeBayes is a rapidly evolving tool, it has >>>>> been very helpful to have Daniel Blankenberg work on keeping an >>>>> updated wrapper. >>>>> >>>>> Recently, I've run into a rather troublesome bug in FreeBayes >>>>> (https://github.com/ekg/freebayes/issues/22) that is causing it >>>>> to crash on nearly every real dataset. Luckily, the bug has been >>>>> fixed in the latest version of FreeBayes >>>>> (0.9.6_9608597d12e127c847ae03aa03440ab63992fedf). >>>>> >>>>> Unfortunately, the latest version has a few parameter changes >>>>> that require an update to the wrapper code. I've taken the >>>>> liberty to make some changes to the wrapper and they seem to >>>>> work. However, now that I have the tool installed from the Tool >>>>> Shed, I'm not sure of the best way to 1) incorporate this update >>>>> into my local galaxy instance and 2) contribute this change back >>>>> to the Tool Shed. >>>>> >>>>> The best solution is to get the Tool Shed updated and then pull >>>>> that update into my production Galaxy instance, however, I'm >>>>> wondering if there is a way I could push "hot-fixes" to my >>>>> production instance without causing me headaches down the line >>>>> when the Tool Shed is inevitably updated. >>>>> >>>>> As far as coordinating updates of Tool Shed tools, I suppose the >>>>> process might be different for different tool authors. I was >>>>> wondering, however, if anyone had thoughts on how this might work >>>>> best. I've created a clone of the galaxy tool shed repository in >>>>> Bitbucket (https://bitbucket.org/lance_parsons/freebayes/) and >>>>> given Daniel and Greg access to it in hopes that would make >>>>> things easier.Let me know if there is a better way to coordinate, >>>>> etc. >>>>> >>>>> Thanks again. >>>>> >>>>> >>>>> -- >>>>> Lance Parsons - Scientific Programmer >>>>> 134 Carl C. Icahn Laboratory >>>>> Lewis-Sigler Institute for Integrative Genomics >>>>> Princeton 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/ >>>> >>> >>> -- >>> Lance Parsons - Scientific Programmer >>> 134 Carl C. Icahn Laboratory >>> Lewis-Sigler Institute for Integrative Genomics >>> Princeton University >>> >> > > -- > Lance Parsons - Scientific Programmer > 134 Carl C. Icahn Laboratory > Lewis-Sigler Institute for Integrative Genomics > Princeton 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/