Re: [galaxy-dev] How to Uninstall NCBI_Blast_Plus from ToolShed
Hi Rodolfo, > On Tue, Aug 6, 2013 at 11:41 AM, Peter Cock wrote: > > On Tue, Aug 6, 2013 at 5:30 PM, Rodolfo Aramayo wrote: > >> Dave, > >> > >> It did contain errors as reported by tailing the last part of the > >> INSTALLATION.log > >> > >> Thanks > >> > >> --Rodolfo > > > > Looks like your BOOST is too new for BLAST 2.2.26+ (which > > just recently became a problem on the Galaxy Tool Shed testing > > system as well). > > > > In the short term I'm hoping to update the Tool Shed repository > > to use the NCBI provided pre-compiled binaries. I'm in discussion > > with Galaxy's Dave Bouvier about how best to do that, perhaps > > with some relatively new functionality added to Galaxy. Next, > > updating the BLAST+ version (and the unit tests to match). > > > > I would suggest right now you manually install BLAST+ using > > the NCBI provided binaries. > > > > Peter > > Boost is a funny thing > Changes a lot > A package compiled with one Boost version might fail to compile with a > newer one. I have seen it a lot > You either have to download Boost and link to the specific version you > want before compiling your package or provide pre-compiled binaries > The question I have is: How many Galaxy packages have Boos as a > dependency for compilation? and if the answer is: a lot, then would it > be smart for Galaxy to have a place where it can keep versions of > these commonly-used libraries so that they can be linked by packages > that need to be compiled 'in-situ' or would it be just more efficient > to provide pre-compiled binaries? > Something tells me that pre-compiled binaries might not take full > advantage of the hardware they are and that compiling is better... > So, should ToolShed installation require automatic download of a set > of pre-defined commonly-used libraries? As Peter already mentioned, the plan is to link specific versions of a tool to one specific version of boost. boost will also be installed and compiled. We plan to have a orphan tool dependency for every boost version like that one: http://testtoolshed.g2.bx.psu.edu/view/iuc/package_boost_1_53 To see how it should work, please have a look at my RDKit repository: http://testtoolshed.g2.bx.psu.edu/view/bgruening/rdkit Regarding your concerns about performance limitations with pre-compiled binaries, you are probably right. But do not forget the installation and compilation happens on one cluster node and the other nodes may also be different. So even with compiled versions you are not guaranteed to take full advantages of your hardware. Cheers, Bjoern > > --Rodolfo > ___ > 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/ ___ 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] How to Uninstall NCBI_Blast_Plus from ToolShed
On Wed, Aug 7, 2013 at 3:41 AM, Rodolfo Aramayo wrote: > On Tue, Aug 6, 2013 at 11:41 AM, Peter Cock wrote: >> >> Looks like your BOOST is too new for BLAST 2.2.26+ (which >> just recently became a problem on the Galaxy Tool Shed testing >> system as well). >> >> In the short term I'm hoping to update the Tool Shed repository >> to use the NCBI provided pre-compiled binaries. I'm in discussion >> with Galaxy's Dave Bouvier about how best to do that, perhaps >> with some relatively new functionality added to Galaxy. Next, >> updating the BLAST+ version (and the unit tests to match). >> >> I would suggest right now you manually install BLAST+ using >> the NCBI provided binaries. >> >> Peter > > Boost is a funny thing > Changes a lot > A package compiled with one Boost version might fail to compile with a > newer one. I have seen it a lot > You either have to download Boost and link to the specific version you > want before compiling your package or provide pre-compiled binaries > The question I have is: How many Galaxy packages have Boos as a > dependency for compilation? and if the answer is: a lot, then would it > be smart for Galaxy to have a place where it can keep versions of > these commonly-used libraries so that they can be linked by packages > that need to be compiled 'in-situ' or would it be just more efficient > to provide pre-compiled binaries? > Something tells me that pre-compiled binaries might not take full > advantage of the hardware they are and that compiling is better... > So, should ToolShed installation require automatic download of a set > of pre-defined commonly-used libraries? That's probably possible via a Tool Shed dependency, Bjoern has been working on this on the Test Tool Shed: http://testtoolshed.g2.bx.psu.edu/view/bgruening/package_boost_1_53 Now under a shared IUC account: http://testtoolshed.g2.bx.psu.edu/view/iuc/package_boost_1_53 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] How to Uninstall NCBI_Blast_Plus from ToolShed
On Tue, Aug 6, 2013 at 11:41 AM, Peter Cock wrote: > On Tue, Aug 6, 2013 at 5:30 PM, Rodolfo Aramayo wrote: >> Dave, >> >> It did contain errors as reported by tailing the last part of the >> INSTALLATION.log >> >> Thanks >> >> --Rodolfo > > Looks like your BOOST is too new for BLAST 2.2.26+ (which > just recently became a problem on the Galaxy Tool Shed testing > system as well). > > In the short term I'm hoping to update the Tool Shed repository > to use the NCBI provided pre-compiled binaries. I'm in discussion > with Galaxy's Dave Bouvier about how best to do that, perhaps > with some relatively new functionality added to Galaxy. Next, > updating the BLAST+ version (and the unit tests to match). > > I would suggest right now you manually install BLAST+ using > the NCBI provided binaries. > > Peter Boost is a funny thing Changes a lot A package compiled with one Boost version might fail to compile with a newer one. I have seen it a lot You either have to download Boost and link to the specific version you want before compiling your package or provide pre-compiled binaries The question I have is: How many Galaxy packages have Boos as a dependency for compilation? and if the answer is: a lot, then would it be smart for Galaxy to have a place where it can keep versions of these commonly-used libraries so that they can be linked by packages that need to be compiled 'in-situ' or would it be just more efficient to provide pre-compiled binaries? Something tells me that pre-compiled binaries might not take full advantage of the hardware they are and that compiling is better... So, should ToolShed installation require automatic download of a set of pre-defined commonly-used libraries? --Rodolfo ___ 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] How to Uninstall NCBI_Blast_Plus from ToolShed
On Tue, Aug 6, 2013 at 5:30 PM, Rodolfo Aramayo wrote: > Dave, > > It did contain errors as reported by tailing the last part of the > INSTALLATION.log > > Thanks > > --Rodolfo Looks like your BOOST is too new for BLAST 2.2.26+ (which just recently became a problem on the Galaxy Tool Shed testing system as well). In the short term I'm hoping to update the Tool Shed repository to use the NCBI provided pre-compiled binaries. I'm in discussion with Galaxy's Dave Bouvier about how best to do that, perhaps with some relatively new functionality added to Galaxy. Next, updating the BLAST+ version (and the unit tests to match). I would suggest right now you manually install BLAST+ using the NCBI provided binaries. 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] How to Uninstall NCBI_Blast_Plus from ToolShed
Hi Rodolfo, There was a bug with regard to displaying the Installation status of a tool dcependency installed into Galaxy along with a repository from the Tool Shed. I have corrected this bug in the mentioned change set, so if you upgrade your Galaxy code to the mentioned revision, the installation status will now be displayed. Greg Von Kuster On Aug 6, 2013, at 10:29 AM, Rodolfo Aramayo wrote: > You are very welcome > So...what happened?? > Thanks > > --R > > On Tue, Aug 6, 2013 at 9:26 AM, Greg Von Kuster wrote: >> Hello Rodolfo, >> >> The following issue is resolved in 10319:61de03c05cf6 - thank for reporting >> this. >> >> Greg Von Kuster >> >> On Aug 5, 2013, at 3:50 PM, Rodolfo Aramayo wrote: >> >>> >>> I did and it worked well it installed Blast 2.2.26+ >>> >>> However there are two problems: >>> >>> 1. On the admin page "Installed tool shed repository 'ncbi_blast_plus'" >>> The name, Version and Type display correct values. However the >>> 'Installation status' shows no text >> >> >> >> >> > ___ > 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/ ___ 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] How to Uninstall NCBI_Blast_Plus from ToolShed
You are very welcome So...what happened?? Thanks --R On Tue, Aug 6, 2013 at 9:26 AM, Greg Von Kuster wrote: > Hello Rodolfo, > > The following issue is resolved in 10319:61de03c05cf6 - thank for reporting > this. > > Greg Von Kuster > > On Aug 5, 2013, at 3:50 PM, Rodolfo Aramayo wrote: > >> >> I did and it worked well it installed Blast 2.2.26+ >> >> However there are two problems: >> >> 1. On the admin page "Installed tool shed repository 'ncbi_blast_plus'" >> The name, Version and Type display correct values. However the >> 'Installation status' shows no text > > > > > ___ 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] How to Uninstall NCBI_Blast_Plus from ToolShed
Hello Rodolfo, The following issue is resolved in 10319:61de03c05cf6 - thank for reporting this. Greg Von Kuster On Aug 5, 2013, at 3:50 PM, Rodolfo Aramayo wrote: > > I did and it worked well it installed Blast 2.2.26+ > > However there are two problems: > > 1. On the admin page "Installed tool shed repository 'ncbi_blast_plus'" > The name, Version and Type display correct values. However the > 'Installation status' shows no text ___ 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] How to Uninstall NCBI_Blast_Plus from ToolShed
Rodolfo, --Dave B. On 8/5/13 15:50:46.000, Rodolfo Aramayo wrote: Dave, See below On Mon, Aug 5, 2013 at 1:55 PM, Dave Bouvier wrote: Rodolfo, Please keep the thread on the mailing list by using the "Reply all" option. Apologies You should now be able to go to the manage repository page, select the tool dependency, then select 'Manage tool dependencies' from the repository actions dropdown and reinstall the blast+ tool dependency. --Dave B. I did and it worked well it installed Blast 2.2.26+ However there are two problems: 1. On the admin page "Installed tool shed repository 'ncbi_blast_plus'" The name, Version and Type display correct values. However the 'Installation status' shows no text 2. When I run the same blast job I was able to run before (using Blast+ 2.2.28+...that I installed) I get the following: error An error occurred with this dataset: blastn: 2.2.26+ Package: blast 2.2.26, build Aug 5 2013 14:01:30 Fatal error: Exit code 255 () Error: NCBI C++ Exception: "/usr/local/galaxy/galaxy-dist/database/tmp/tmpyhSi2d/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp", line 689: Critical: Obviously it is the installed Blast that is at fault in here Did the blast+ tool dependency compile without errors? You should be able to see any errors by clicking on the installed tool dependency, then expanding the blast+ folder and clicking on INSTALLATION.log Thanks --R On 8/5/13 14:03:14.000, Rodolfo Aramayo wrote: Dear Dave, Answers below... On Thu, Aug 1, 2013 at 9:44 AM, Dave Bouvier wrote: Rodolfo, In order to simplify tracking down this issue, could you provide the changeset revision of Galaxy that is running on tamu.edu? To retrieve the revision, execute the following command in your galaxy root directory: hg id fd4113962c32+ (stable) To clarify, our understanding is that you installed the ncbi_blast_plus repository from the main tool shed, and it installed correctly. You then uninstalled the repository, and it also uninstalled properly. You then attempted to reinstall the repository, and encountered the error message cited in your email. Can you confirm the above? This is correct We further understand that the repository is stuck in the 'installing' state. YES and in the "Manage installed tool shed repositories" says now (after having to restart Galaxy for another reason): "Installed, Missing tool dependencies" What options are available from the popup menu next to the ncbi_blast_plus repository on the manage installed repositories page? If I click on the little arrow, it says: Get updates Deactivate or uninstall 'Deactivate or uninstall' is available, can you try uninstalling again, and see if that functions correctly? It worked! Before I was not able to do it as I was getting an ugly galaxy error page But now it did uninstall and removed and was able to clone correctly. However, the directory: ./bioinfosoft/galaxy_dependencies/blast+/2.2.26+/devteam/ncbi_blast_plus/9dabbfd73c8a/bin/ is empty! Should I repopulate it with the one I have in my backup?? Thanks --Rodolfo --Dave B. On 8/1/13 07:38:22.000, Rodolfo Aramayo wrote: People, I successfully installed NCBI_Blast_Plus from the toolshed The tool, however, failed to work giving the following error: Fatal error: Exit code 255 () Error: NCBI C++ Exception: "/usr/local/galaxy/galaxy-dist/database/tmp/tmpwL5OFq/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp", line 689: Critical: ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL pointer. I then tried uninstalling/reinstalling the tool However I now get an eternal 'installing' grey message and when I click 'manage the repo' I get: # URL: http://galaxy.tamu.edu/admin_toolshed/manage_repository?id=ff08d6222f8e14990ad98c3bdd778cf31920e6108c41c80f File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 221 in decorator return func( self, trans, *args, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 561 in manage_repository repository = suc.get_installed_tool_shed_repository( trans, repository_id ) File '/usr/
Re: [galaxy-dev] How to Uninstall NCBI_Blast_Plus from ToolShed
Dave, See below On Mon, Aug 5, 2013 at 1:55 PM, Dave Bouvier wrote: > Rodolfo, > > Please keep the thread on the mailing list by using the "Reply all" option. Apologies > > You should now be able to go to the manage repository page, select the tool > dependency, then select 'Manage tool dependencies' from the repository > actions dropdown and reinstall the blast+ tool dependency. > >--Dave B. I did and it worked well it installed Blast 2.2.26+ However there are two problems: 1. On the admin page "Installed tool shed repository 'ncbi_blast_plus'" The name, Version and Type display correct values. However the 'Installation status' shows no text 2. When I run the same blast job I was able to run before (using Blast+ 2.2.28+...that I installed) I get the following: error An error occurred with this dataset: blastn: 2.2.26+ Package: blast 2.2.26, build Aug 5 2013 14:01:30 Fatal error: Exit code 255 () Error: NCBI C++ Exception: "/usr/local/galaxy/galaxy-dist/database/tmp/tmpyhSi2d/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp", line 689: Critical: Obviously it is the installed Blast that is at fault in here Thanks --R > > > On 8/5/13 14:03:14.000, Rodolfo Aramayo wrote: >> >> Dear Dave, >> >> Answers below... >> >> On Thu, Aug 1, 2013 at 9:44 AM, Dave Bouvier wrote: >>> >>> Rodolfo, >>> >>> In order to simplify tracking down this issue, could you provide the >>> changeset revision of Galaxy that is running on tamu.edu? To retrieve the >>> revision, execute the following command in your galaxy root directory: >>> >>> hg id >> >> >> fd4113962c32+ (stable) >> >>> >>> To clarify, our understanding is that you installed the ncbi_blast_plus >>> repository from the main tool shed, and it installed correctly. You then >>> uninstalled the repository, and it also uninstalled properly. You then >>> attempted to reinstall the repository, and encountered the error message >>> cited in your email. >>> >>> Can you confirm the above? >> >> >> This is correct >> >>> >>> We further understand that the repository is stuck in the 'installing' >>> state. >> >> >> YES and in the "Manage installed tool shed repositories" says now >> (after having to restart Galaxy for another reason): >> >> "Installed, Missing tool dependencies" >> >> >> What options are available from the popup menu next to the >>> >>> ncbi_blast_plus repository on the manage installed repositories page? >> >> >> If I click on the little arrow, it says: >> >> Get updates >> Deactivate or uninstall >> >>> 'Deactivate or uninstall' is available, can you try uninstalling again, >>> and >>> see if that functions correctly? >> >> >> It worked! >> >> Before I was not able to do it as I was getting an ugly galaxy error page >> But now it did uninstall and removed and was able to clone correctly. >> However, the directory: >> >> >> ./bioinfosoft/galaxy_dependencies/blast+/2.2.26+/devteam/ncbi_blast_plus/9dabbfd73c8a/bin/ >> >> is empty! >> >> >> Should I repopulate it with the one I have in my backup?? >> >> Thanks >> >> --Rodolfo >> >> >>> >>> --Dave B. >>> >>> >>> On 8/1/13 07:38:22.000, Rodolfo Aramayo wrote: People, I successfully installed NCBI_Blast_Plus from the toolshed The tool, however, failed to work giving the following error: Fatal error: Exit code 255 () Error: NCBI C++ Exception: "/usr/local/galaxy/galaxy-dist/database/tmp/tmpwL5OFq/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp", line 689: Critical: ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL pointer. I then tried uninstalling/reinstalling the tool However I now get an eternal 'installing' grey message and when I click 'manage the repo' I get: # URL: http://galaxy.tamu.edu/admin_toolshed/manage_repository?id=ff08d6222f8e14990ad98c3bdd778cf31920e6108c41c80f File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 221 in decorator return func( self, trans, *args, **kwargs ) File '/usr/local/galaxy/galax
Re: [galaxy-dev] How to Uninstall NCBI_Blast_Plus from ToolShed
Rodolfo, Please keep the thread on the mailing list by using the "Reply all" option. You should now be able to go to the manage repository page, select the tool dependency, then select 'Manage tool dependencies' from the repository actions dropdown and reinstall the blast+ tool dependency. --Dave B. On 8/5/13 14:03:14.000, Rodolfo Aramayo wrote: Dear Dave, Answers below... On Thu, Aug 1, 2013 at 9:44 AM, Dave Bouvier wrote: Rodolfo, In order to simplify tracking down this issue, could you provide the changeset revision of Galaxy that is running on tamu.edu? To retrieve the revision, execute the following command in your galaxy root directory: hg id fd4113962c32+ (stable) To clarify, our understanding is that you installed the ncbi_blast_plus repository from the main tool shed, and it installed correctly. You then uninstalled the repository, and it also uninstalled properly. You then attempted to reinstall the repository, and encountered the error message cited in your email. Can you confirm the above? This is correct We further understand that the repository is stuck in the 'installing' state. YES and in the "Manage installed tool shed repositories" says now (after having to restart Galaxy for another reason): "Installed, Missing tool dependencies" What options are available from the popup menu next to the ncbi_blast_plus repository on the manage installed repositories page? If I click on the little arrow, it says: Get updates Deactivate or uninstall 'Deactivate or uninstall' is available, can you try uninstalling again, and see if that functions correctly? It worked! Before I was not able to do it as I was getting an ugly galaxy error page But now it did uninstall and removed and was able to clone correctly. However, the directory: ./bioinfosoft/galaxy_dependencies/blast+/2.2.26+/devteam/ncbi_blast_plus/9dabbfd73c8a/bin/ is empty! Should I repopulate it with the one I have in my backup?? Thanks --Rodolfo --Dave B. On 8/1/13 07:38:22.000, Rodolfo Aramayo wrote: People, I successfully installed NCBI_Blast_Plus from the toolshed The tool, however, failed to work giving the following error: Fatal error: Exit code 255 () Error: NCBI C++ Exception: "/usr/local/galaxy/galaxy-dist/database/tmp/tmpwL5OFq/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp", line 689: Critical: ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL pointer. I then tried uninstalling/reinstalling the tool However I now get an eternal 'installing' grey message and when I click 'manage the repo' I get: # URL: http://galaxy.tamu.edu/admin_toolshed/manage_repository?id=ff08d6222f8e14990ad98c3bdd778cf31920e6108c41c80f File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 221 in decorator return func( self, trans, *args, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 561 in manage_repository repository = suc.get_installed_tool_shed_repository( trans, repository_id ) File '/usr/local/galaxy/galaxy-dist/lib/tool_shed/util/shed_util_common.py', line 515 in get_installed_tool_shed_repository return trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( id ) ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/security/__init__.py', line 60 in decode_id return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( "!" ) ) ValueError: invalid literal for int() with base 10: 'cb73864b36ce6a1b' # How can I totally uninstall and re-install this tool? Thanks ___ 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/ ___ 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://l
Re: [galaxy-dev] How to Uninstall NCBI_Blast_Plus from ToolShed
Greg, Please see my previous responses to Dave I believe there are issues with the Tool Shed itself Thanks --R On Mon, Aug 5, 2013 at 1:42 PM, Greg Von Kuster wrote: > The statement "there are still issues with the Tool Shed itself" is not > confirmed, correct? I believe we're still waiting on the response to Dave's > initial response below. Or did I miss it??? > > On Thu, Aug 1, 2013 at 9:44 AM, Dave Bouvier wrote: > > Rodolfo, > > In order to simplify tracking down this issue, could you provide the > changeset revision of Galaxy that is running on tamu.edu? To retrieve the > revision, execute the following command in your galaxy root directory: > > hg id > > To clarify, our understanding is that you installed the ncbi_blast_plus > repository from the main tool shed, and it installed correctly. You then > uninstalled the repository, and it also uninstalled properly. You then > attempted to reinstall the repository, and encountered the error message > cited in your email. > > Can you confirm the above? > > We further understand that the repository is stuck in the 'installing' > state. What options are available from the popup menu next to the > ncbi_blast_plus repository on the manage installed repositories page? If > 'Deactivate or uninstall' is available, can you try uninstalling again, and > see if that functions correctly? > > --Dave B. > > > > On Aug 5, 2013, at 2:35 PM, Peter Cock wrote: > > On Mon, Aug 5, 2013 at 6:50 PM, Rodolfo Aramayo wrote: > > Dear Peter, > > APOLOGIES for the delayed response > > Please see below for details.. > > > OK, so there are still issues with the Tool Shed itself, > but the BLAST issue seems to have gone away when > using a newer version (compiled). I'm working on using > the NCBI provided binaries if possible, but updating > the Galaxy BLAST+ bundle to a newer version of > the underlying BLAST tools is planned. > > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > > ___ 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] How to Uninstall NCBI_Blast_Plus from ToolShed
The statement "there are still issues with the Tool Shed itself" is not confirmed, correct? I believe we're still waiting on the response to Dave's initial response below. Or did I miss it??? On Thu, Aug 1, 2013 at 9:44 AM, Dave Bouvier wrote: > Rodolfo, > > In order to simplify tracking down this issue, could you provide the > changeset revision of Galaxy that is running on tamu.edu? To retrieve the > revision, execute the following command in your galaxy root directory: > > hg id > > To clarify, our understanding is that you installed the ncbi_blast_plus > repository from the main tool shed, and it installed correctly. You then > uninstalled the repository, and it also uninstalled properly. You then > attempted to reinstall the repository, and encountered the error message > cited in your email. > > Can you confirm the above? > > We further understand that the repository is stuck in the 'installing' > state. What options are available from the popup menu next to the > ncbi_blast_plus repository on the manage installed repositories page? If > 'Deactivate or uninstall' is available, can you try uninstalling again, and > see if that functions correctly? > > --Dave B. On Aug 5, 2013, at 2:35 PM, Peter Cock wrote: > On Mon, Aug 5, 2013 at 6:50 PM, Rodolfo Aramayo wrote: >> Dear Peter, >> >> APOLOGIES for the delayed response >> >> Please see below for details.. >> > > OK, so there are still issues with the Tool Shed itself, > but the BLAST issue seems to have gone away when > using a newer version (compiled). I'm working on using > the NCBI provided binaries if possible, but updating > the Galaxy BLAST+ bundle to a newer version of > the underlying BLAST tools is planned. > > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ 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] How to Uninstall NCBI_Blast_Plus from ToolShed
On Mon, Aug 5, 2013 at 6:50 PM, Rodolfo Aramayo wrote: > Dear Peter, > > APOLOGIES for the delayed response > > Please see below for details.. > OK, so there are still issues with the Tool Shed itself, but the BLAST issue seems to have gone away when using a newer version (compiled). I'm working on using the NCBI provided binaries if possible, but updating the Galaxy BLAST+ bundle to a newer version of the underlying BLAST tools is planned. 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] How to Uninstall NCBI_Blast_Plus from ToolShed
Dave, Also, when I click on: "Get repository update" I get the following error: ## URL: http://galaxy.tamu.edu/admin_toolshed/check_for_updates?id=ff08d6222f8e14990ad98c3bdd778cf31920e6108c41c80f File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 221 in decorator return func( self, trans, *args, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 202 in check_for_updates repository = suc.get_installed_tool_shed_repository( trans, repository_id ) File '/usr/local/galaxy/galaxy-dist/lib/tool_shed/util/shed_util_common.py', line 515 in get_installed_tool_shed_repository return trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( id ) ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/security/__init__.py', line 60 in decode_id return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( "!" ) ) ValueError: invalid literal for int() with base 10: 'cb73864b36ce6a1b' ## Thanks --R On Thu, Aug 1, 2013 at 9:44 AM, Dave Bouvier wrote: > Rodolfo, > > In order to simplify tracking down this issue, could you provide the > changeset revision of Galaxy that is running on tamu.edu? To retrieve the > revision, execute the following command in your galaxy root directory: > > hg id > > To clarify, our understanding is that you installed the ncbi_blast_plus > repository from the main tool shed, and it installed correctly. You then > uninstalled the repository, and it also uninstalled properly. You then > attempted to reinstall the repository, and encountered the error message > cited in your email. > > Can you confirm the above? > > We further understand that the repository is stuck in the 'installing' > state. What options are available from the popup menu next to the > ncbi_blast_plus repository on the manage installed repositories page? If > 'Deactivate or uninstall' is available, can you try uninstalling again, and > see if that functions correctly? > >--Dave B. > > > On 8/1/13 07:38:22.000, Rodolfo Aramayo wrote: >> >> People, >> >> I successfully installed NCBI_Blast_Plus from the toolshed >> The tool, however, failed to work giving the following error: >> >> Fatal error: Exit code 255 () >> Error: NCBI C++ Exception: >> >> "/usr/local/galaxy/galaxy-dist/database/tmp/tmpwL5OFq/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp", >> line 689: Critical: ncbi::CObject::ThrowNullPointerException() - >> Attempt to access NULL pointer. >> >> I then tried uninstalling/reinstalling the tool >> >> However I now get an eternal 'installing' grey message and when I >> click 'manage the repo' I get: >> >> # >> >> URL: >> http://galaxy.tamu.edu/admin_toolshed/manage_repository?id=ff08d6222f8e14990ad98c3bdd778cf31920e6108c41c80f >> File >> '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', >> line 149 in __call__ >>app_iter = self.application(environ, sr_checker) >> File >> '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', >> line 84 in __call__ >>return self.application(environ, start_response) >> File >> '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', >> line 633 in __call__ >>return self.application(environ, start_response) >> File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', >> line 132 in __call__ >>return self.handle_request( environ, start_response ) >> File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', >> line 190 in handle_request >>body = method( trans, **kwargs ) >> File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', >> line 221 in decorator >>return func( self, trans, *args, **kwargs ) >> File >> '/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', >> line 561 in manage_repository >>repository = suc.get_installed_tool_shed_repository( trans, >> repository_id ) >> File >> '/usr/local/galaxy/galaxy-dist/lib/tool_shed/util/shed_util_common.py', >> line 515 in get_installed_tool_shed_repositor
Re: [galaxy-dev] How to Uninstall NCBI_Blast_Plus from ToolShed
Dear Peter, APOLOGIES for the delayed response Please see below for details.. On Thu, Aug 1, 2013 at 8:51 AM, Peter Cock wrote: > On Thu, Aug 1, 2013 at 2:47 PM, Rodolfo Aramayo wrote: >> On Thu, Aug 1, 2013 at 8:40 AM, Peter Cock wrote: > > I've seen that kind of error from NCBI BLAST+ before - do you > know which of the BLAST tools was this, and what the query > was? The repo was: repos/devteam/ncbi_blast_plus/9dabbfd73c8a/ncbi_blast_plus The query was: Output from velvetoptimiser /repos/simon-gladman/velvet_optimiser/43c89d82a7d3/velvet_optimiser >>> >>> OK, so this was a nucleotide FASTA file from an assembly, right? >> >> Yes >> >>> What were you searching with BLAST? e.g. BLASTN against NT, >>> BLASTX against NR, etc. >> >> Search was blastn, task megablast of the assembly as query against an >> in-house made (and installed into galaxy) of a blastn database for >> Chromosomes 1 to 7 of Neurospora crassa >> Database was produced with: >> makeblastdb -in Ncrassa_wt_Chr01.Chr07_v12 -dbtype nucl -title >> Ncrassa_wt_Chr01.Chr07_v12 -parse_seqids -hash_index >> and "installed" into the "blastdb.loc" file as required > > Can you run this blastn search 'by hand' at the terminal? Yes, yes and no > Does that crash too? No and I do not know Please let me explain. I have set up the user galaxy account such that it has access to a directory called 'bioinfosoft' where all bioinformatics-related software is installed, including Blast+ Galaxy has 'access' to this directory and there I have compiled Blast+ 2.2.28+ Now, when I installed Blast+ via the toolshed, the toolshed Blast+ package did download and install what I believe it was the 2.2.26+ version of Blast+? If I recall correctly, I got an error message that went away while the Blast+ package was being compiled by the toolshed The errors I got running Blast did all occur when using that particular version of Blast+ (2.2.26) I then removed or uninstalled the packaged and tried to re-install again, but, as I said, it hanged there forever, installing... To my surprise when I re-run the jobs, they all worked well. This is, Blast worked like a charm BUT it did because it is NOT using the Blast packaged that was installed by the toolshed but the Blast package I compiled myself (2.2.28+) (SEE LOG AT END OF THIS MESSAGE...) Comparing the directory of galaxy with those of my backups I can see that the packaged Blast 2.2.26+ that was installed by the toolshed in the directory: ./bioinfosoft/galaxy_dependencies/blast+/2.2.26+/devteam/ncbi_blast_plus/9dabbfd73c8a/bin/ is no longer there.. The directory: ./bioinfosoft/galaxy_dependencies/blast+/2.2.26+/devteam/ncbi_blast_plus/9dabbfd73c8a/ is present but it is empty Therefore to answer your questions: > Can you run this blastn search 'by hand' at the terminal? Yes, I can but I would be using a different version of Blast+ > Does that crash too? No, because I would be using a different version of Blast+ > > The error sounds very similar to this report which turned out > to be due to a corrupted BLAST database - so also try > recreating your DB: > http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=644962 Regarding this last comment..basically a corrupt database is not the problem in this case as demonstrated by the fact that I can run Blast on those databases Having said that, yes I have observed that depending on how one runs the makeblastdb command and depending on the type of fasta files used, you can end up with corrupt output. Some identifiers and symbols present in the fasta ID can interfere with makeblastdb (especially some produced by the JGI) In summary, yes Blast+ is working but because is not using the compiled Blast+ binaries installed by the toolshed package The problem I have is that I would like to be able to properly uninstall and re-install the Blast+ toolsheed so that things work as they were originally supossed to On the other hand, if you guys upgrade the package, this might be a non-issue as the toolshed would just simply generate new directories... Last, I noticed the command used in the compilation is different from the one I normally use The command I use is: tar -xzvf ncbi-blast-2.2.28+-src.tar.gz cd ncbi-blast-2.2.28+-src/c++ ./configure --prefix=/usr/local/galaxy/bioinfosoft/blast-2.2.28+ --with-64 --with-bincopy --with-mt --without-debug --with-static | tee c.log make | tee m.log make check make install Many Thanks --Rodolfo > > Peter LOG: galaxy.jobs.handler INFO 2013-08-05 12:11:30,841 (2405) Job dispatched galaxy.tools DEBUG 2013-08-05 12:11:31,018 Building dependency shell command for dependency 'blastn' galaxy.tools WARNING 2013-08-05 12:11:31,018 Failed to resolve dependency on 'blastn', ignoring galaxy.tools DEBUG 2013-08-05 12:11:31,018 Building dependency shell command for dependency 'blast+' galaxy.tools WARNING 2013-08-05 12:11:31,018 Failed to resolve dependency on 'blast+', ignoring galaxy.job
Re: [galaxy-dev] How to Uninstall NCBI_Blast_Plus from ToolShed
Rodolfo, In order to simplify tracking down this issue, could you provide the changeset revision of Galaxy that is running on tamu.edu? To retrieve the revision, execute the following command in your galaxy root directory: hg id To clarify, our understanding is that you installed the ncbi_blast_plus repository from the main tool shed, and it installed correctly. You then uninstalled the repository, and it also uninstalled properly. You then attempted to reinstall the repository, and encountered the error message cited in your email. Can you confirm the above? We further understand that the repository is stuck in the 'installing' state. What options are available from the popup menu next to the ncbi_blast_plus repository on the manage installed repositories page? If 'Deactivate or uninstall' is available, can you try uninstalling again, and see if that functions correctly? --Dave B. On 8/1/13 07:38:22.000, Rodolfo Aramayo wrote: People, I successfully installed NCBI_Blast_Plus from the toolshed The tool, however, failed to work giving the following error: Fatal error: Exit code 255 () Error: NCBI C++ Exception: "/usr/local/galaxy/galaxy-dist/database/tmp/tmpwL5OFq/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp", line 689: Critical: ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL pointer. I then tried uninstalling/reinstalling the tool However I now get an eternal 'installing' grey message and when I click 'manage the repo' I get: # URL: http://galaxy.tamu.edu/admin_toolshed/manage_repository?id=ff08d6222f8e14990ad98c3bdd778cf31920e6108c41c80f File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 221 in decorator return func( self, trans, *args, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 561 in manage_repository repository = suc.get_installed_tool_shed_repository( trans, repository_id ) File '/usr/local/galaxy/galaxy-dist/lib/tool_shed/util/shed_util_common.py', line 515 in get_installed_tool_shed_repository return trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( id ) ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/security/__init__.py', line 60 in decode_id return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( "!" ) ) ValueError: invalid literal for int() with base 10: 'cb73864b36ce6a1b' # How can I totally uninstall and re-install this tool? Thanks ___ 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/ ___ 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] How to Uninstall NCBI_Blast_Plus from ToolShed
On Thu, Aug 1, 2013 at 2:47 PM, Rodolfo Aramayo wrote: > On Thu, Aug 1, 2013 at 8:40 AM, Peter Cock wrote: I've seen that kind of error from NCBI BLAST+ before - do you know which of the BLAST tools was this, and what the query was? >>> >>> The repo was: >>> repos/devteam/ncbi_blast_plus/9dabbfd73c8a/ncbi_blast_plus >>> >>> The query was: >>> Output from velvetoptimiser >>> /repos/simon-gladman/velvet_optimiser/43c89d82a7d3/velvet_optimiser >> >> OK, so this was a nucleotide FASTA file from an assembly, right? > > Yes > >> What were you searching with BLAST? e.g. BLASTN against NT, >> BLASTX against NR, etc. > > Search was blastn, task megablast of the assembly as query against an > in-house made (and installed into galaxy) of a blastn database for > Chromosomes 1 to 7 of Neurospora crassa > Database was produced with: > makeblastdb -in Ncrassa_wt_Chr01.Chr07_v12 -dbtype nucl -title > Ncrassa_wt_Chr01.Chr07_v12 -parse_seqids -hash_index > and "installed" into the "blastdb.loc" file as required Can you run this blastn search 'by hand' at the terminal? Does that crash too? The error sounds very similar to this report which turned out to be due to a corrupted BLAST database - so also try recreating your DB: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=644962 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] How to Uninstall NCBI_Blast_Plus from ToolShed
On Thu, Aug 1, 2013 at 8:40 AM, Peter Cock wrote: > On Thu, Aug 1, 2013 at 1:41 PM, Rodolfo Aramayo wrote: >> On Thu, Aug 1, 2013 at 6:49 AM, Peter Cock wrote: >>> On Thu, Aug 1, 2013 at 12:38 PM, Rodolfo Aramayo wrote: People, I successfully installed NCBI_Blast_Plus from the toolshed The tool, however, failed to work giving the following error: Fatal error: Exit code 255 () Error: NCBI C++ Exception: "/usr/local/galaxy/galaxy-dist/database/tmp/tmpwL5OFq/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp", line 689: Critical: ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL pointer. >>> >>> I've seen that kind of error from NCBI BLAST+ before - do you >>> know which of the BLAST tools was this, and what the query >>> was? >> >> The repo was: >> repos/devteam/ncbi_blast_plus/9dabbfd73c8a/ncbi_blast_plus >> >> The query was: >> Output from velvetoptimiser >> /repos/simon-gladman/velvet_optimiser/43c89d82a7d3/velvet_optimiser > > OK, so this was a nucleotide FASTA file from an assembly, right? Yes > What were you searching with BLAST? e.g. BLASTN against NT, > BLASTX against NR, etc. Search was blastn, task megablast of the assembly as query against an in-house made (and installed into galaxy) of a blastn database for Chromosomes 1 to 7 of Neurospora crassa Database was produced with: makeblastdb -in Ncrassa_wt_Chr01.Chr07_v12 -dbtype nucl -title Ncrassa_wt_Chr01.Chr07_v12 -parse_seqids -hash_index and "installed" into the "blastdb.loc" file as required Thanks > How can I totally uninstall and re-install this tool? Thanks >>> >>> You seem to have found a bug in the Tool Shed, so thank you >>> for reporting this. >> >> You are welcome >> >> But any ideas on how to properly uninstall and re-install the tool?? >> > > Hopefully Greg from the Galaxy team will be able to help with this. > > 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] How to Uninstall NCBI_Blast_Plus from ToolShed
On Thu, Aug 1, 2013 at 1:41 PM, Rodolfo Aramayo wrote: > On Thu, Aug 1, 2013 at 6:49 AM, Peter Cock wrote: >> On Thu, Aug 1, 2013 at 12:38 PM, Rodolfo Aramayo wrote: >>> People, >>> >>> I successfully installed NCBI_Blast_Plus from the toolshed >>> The tool, however, failed to work giving the following error: >>> >>> Fatal error: Exit code 255 () >>> Error: NCBI C++ Exception: >>> >>> "/usr/local/galaxy/galaxy-dist/database/tmp/tmpwL5OFq/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp", >>> line 689: Critical: ncbi::CObject::ThrowNullPointerException() - >>> Attempt to access NULL pointer. >> >> I've seen that kind of error from NCBI BLAST+ before - do you >> know which of the BLAST tools was this, and what the query >> was? > > The repo was: > repos/devteam/ncbi_blast_plus/9dabbfd73c8a/ncbi_blast_plus > > The query was: > Output from velvetoptimiser > /repos/simon-gladman/velvet_optimiser/43c89d82a7d3/velvet_optimiser OK, so this was a nucleotide FASTA file from an assembly, right? What were you searching with BLAST? e.g. BLASTN against NT, BLASTX against NR, etc. >>> >>> How can I totally uninstall and re-install this tool? >>> >>> Thanks >> >> You seem to have found a bug in the Tool Shed, so thank you >> for reporting this. > > You are welcome > > But any ideas on how to properly uninstall and re-install the tool?? > Hopefully Greg from the Galaxy team will be able to help with this. 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] How to Uninstall NCBI_Blast_Plus from ToolShed
On Thu, Aug 1, 2013 at 6:49 AM, Peter Cock wrote: > On Thu, Aug 1, 2013 at 12:38 PM, Rodolfo Aramayo wrote: >> People, >> >> I successfully installed NCBI_Blast_Plus from the toolshed >> The tool, however, failed to work giving the following error: >> >> Fatal error: Exit code 255 () >> Error: NCBI C++ Exception: >> >> "/usr/local/galaxy/galaxy-dist/database/tmp/tmpwL5OFq/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp", >> line 689: Critical: ncbi::CObject::ThrowNullPointerException() - >> Attempt to access NULL pointer. > > I've seen that kind of error from NCBI BLAST+ before - do you > know which of the BLAST tools was this, and what the query > was? The repo was: repos/devteam/ncbi_blast_plus/9dabbfd73c8a/ncbi_blast_plus The query was: Output from velvetoptimiser /repos/simon-gladman/velvet_optimiser/43c89d82a7d3/velvet_optimiser > >> I then tried uninstalling/reinstalling the tool >> > > I doubt that will make any difference at all - this null pointer > exception is not a problem from Galaxy. > >> However I now get an eternal 'installing' grey message and when I >> click 'manage the repo' I get: >> >> # >> >> URL: >> http://galaxy.tamu.edu/admin_toolshed/manage_repository?id=ff08d6222f8e14990ad98c3bdd778cf31920e6108c41c80f >> File >> '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', >> line 149 in __call__ >> app_iter = self.application(environ, sr_checker) >> File >> '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', >> line 84 in __call__ >> return self.application(environ, start_response) >> File >> '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', >> line 633 in __call__ >> return self.application(environ, start_response) >> File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', >> line 132 in __call__ >> return self.handle_request( environ, start_response ) >> File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', >> line 190 in handle_request >> body = method( trans, **kwargs ) >> File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', >> line 221 in decorator >> return func( self, trans, *args, **kwargs ) >> File >> '/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', >> line 561 in manage_repository >> repository = suc.get_installed_tool_shed_repository( trans, repository_id ) >> File '/usr/local/galaxy/galaxy-dist/lib/tool_shed/util/shed_util_common.py', >> line 515 in get_installed_tool_shed_repository >> return trans.sa_session.query( trans.model.ToolShedRepository ).get( >> trans.security.decode_id( id ) ) >> File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/security/__init__.py', >> line 60 in decode_id >> return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( "!" ) >> ) >> ValueError: invalid literal for int() with base 10: 'cb73864b36ce6a1b' >> >> # >> >> How can I totally uninstall and re-install this tool? >> >> Thanks > > You seem to have found a bug in the Tool Shed, so thank you > for reporting this. You are welcome But any ideas on how to properly uninstall and re-install the tool?? Thanks --R > > 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] How to Uninstall NCBI_Blast_Plus from ToolShed
On Thu, Aug 1, 2013 at 12:38 PM, Rodolfo Aramayo wrote: > People, > > I successfully installed NCBI_Blast_Plus from the toolshed > The tool, however, failed to work giving the following error: > > Fatal error: Exit code 255 () > Error: NCBI C++ Exception: > > "/usr/local/galaxy/galaxy-dist/database/tmp/tmpwL5OFq/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp", > line 689: Critical: ncbi::CObject::ThrowNullPointerException() - > Attempt to access NULL pointer. I've seen that kind of error from NCBI BLAST+ before - do you know which of the BLAST tools was this, and what the query was? > I then tried uninstalling/reinstalling the tool > I doubt that will make any difference at all - this null pointer exception is not a problem from Galaxy. > However I now get an eternal 'installing' grey message and when I > click 'manage the repo' I get: > > # > > URL: > http://galaxy.tamu.edu/admin_toolshed/manage_repository?id=ff08d6222f8e14990ad98c3bdd778cf31920e6108c41c80f > File > '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', > line 149 in __call__ > app_iter = self.application(environ, sr_checker) > File > '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', > line 84 in __call__ > return self.application(environ, start_response) > File > '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', > line 633 in __call__ > return self.application(environ, start_response) > File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', > line 132 in __call__ > return self.handle_request( environ, start_response ) > File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', > line 190 in handle_request > body = method( trans, **kwargs ) > File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', > line 221 in decorator > return func( self, trans, *args, **kwargs ) > File > '/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', > line 561 in manage_repository > repository = suc.get_installed_tool_shed_repository( trans, repository_id ) > File '/usr/local/galaxy/galaxy-dist/lib/tool_shed/util/shed_util_common.py', > line 515 in get_installed_tool_shed_repository > return trans.sa_session.query( trans.model.ToolShedRepository ).get( > trans.security.decode_id( id ) ) > File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/security/__init__.py', > line 60 in decode_id > return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( "!" ) ) > ValueError: invalid literal for int() with base 10: 'cb73864b36ce6a1b' > > # > > How can I totally uninstall and re-install this tool? > > Thanks You seem to have found a bug in the Tool Shed, so thank you for reporting this. 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] How to Uninstall NCBI_Blast_Plus from ToolShed
People, I successfully installed NCBI_Blast_Plus from the toolshed The tool, however, failed to work giving the following error: Fatal error: Exit code 255 () Error: NCBI C++ Exception: "/usr/local/galaxy/galaxy-dist/database/tmp/tmpwL5OFq/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp", line 689: Critical: ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL pointer. I then tried uninstalling/reinstalling the tool However I now get an eternal 'installing' grey message and when I click 'manage the repo' I get: # URL: http://galaxy.tamu.edu/admin_toolshed/manage_repository?id=ff08d6222f8e14990ad98c3bdd778cf31920e6108c41c80f File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 221 in decorator return func( self, trans, *args, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 561 in manage_repository repository = suc.get_installed_tool_shed_repository( trans, repository_id ) File '/usr/local/galaxy/galaxy-dist/lib/tool_shed/util/shed_util_common.py', line 515 in get_installed_tool_shed_repository return trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( id ) ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/security/__init__.py', line 60 in decode_id return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( "!" ) ) ValueError: invalid literal for int() with base 10: 'cb73864b36ce6a1b' # How can I totally uninstall and re-install this tool? Thanks ___ 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/
