Re: [galaxy-dev] Mail is not configured for this Galaxy instance.
Hi Hans-Rudolf, Thank you very much for you help.Actually I want some more information about how to configure 'smtp_server' in universe_wsgi.ini.Could you show me some samples to have a look please? Regards, shenwiyn From: Hans-Rudolf Hotz Date: 2013-07-31 23:40 To: shenwiyn CC: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Mail is not configured for this Galaxy instance. Hi Shenwiyn You need to specify a SMTP server. Have a look at the 'smtp_server' settings in your universe_wsgi.ini file. Regards, Hans-Rudolf On 07/31/2013 04:19 PM, shenwiyn wrote: Hi everyone, In my local Galaxy,when I want to reset my Login password,some error occurre :Mail is not configured for this Galaxy instance. Please contact an administrator. Could anyone tell me some imformation about how to configure the mail for my Galaxy instance? Thank you very much. shenwiyn ___ 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] Mail is not configured for this Galaxy instance.
On 08/06/2013 08:17 AM, shenwiyn wrote: Hi Hans-Rudolf, Thank you very much for you help.Actually I want some more information about how to configure 'smtp_server' in universe_wsgi.ini.Could you show me some samples to have a look please? you need the address of your smtp server, eg: smtp_server = abcd.fmi.ch Regards, shenwiyn *From:* Hans-Rudolf Hotz mailto:h...@fmi.ch *Date:* 2013-07-31 23:40 *To:* shenwiyn mailto:shenw...@gmail.com *CC:* galaxy-dev@lists.bx.psu.edu mailto:galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] Mail is not configured for this Galaxy instance. Hi Shenwiyn You need to specify a SMTP server. Have a look at the 'smtp_server' settings in your universe_wsgi.ini file. Regards, Hans-Rudolf On 07/31/2013 04:19 PM, shenwiyn wrote: Hi everyone, In my local Galaxy,when I want to reset my Login password,some error occurre :Mail is not configured for this Galaxy instance. Please contact an administrator. Could anyone tell me some imformation about how to configure the mail for my Galaxy instance? Thank you very much. shenwiyn ___ 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] getting large files into a local instance of Galaxy
Hi Gerald Have you looked into 'Data Libraries'? http://wiki.galaxyproject.org/Admin/DataLibraries/Libraries http://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles This will allow you to access the files without data duplication. Regards, Hans-Rudolf On 08/05/2013 08:48 PM, Gerald Bothe wrote: Trying out a local instance of Galaxy. Small files can be uploaded with browse.. but this works only for files under 2Gb. Is there a folder in a local copy of galaxy-dist where I can copy a large file and have it show up in the Get Data/Upload File/Files uploaded via FTP window so that I can properly get it into the local history? Copying it directly into the database seemed not to work, it didn't show up anywhere. Gerald ___ 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
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 d...@bx.psu.edu 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 d...@bx.psu.edu 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,
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 raram...@tamu.edu 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
You are very welcome So...what happened?? Thanks --R On Tue, Aug 6, 2013 at 9:26 AM, Greg Von Kuster g...@bx.psu.edu 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 raram...@tamu.edu 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/
