Re: [galaxy-dev] Missing modules after upgrade to 16.01
Hi Cristian, It's up to you whether you keep it with Galaxy or not. I prefer not to modify the Galaxy clone at all so I keep it outside. More details about keeping the virtualenv separate can be found here in the documentation: https://docs.galaxyproject.org/en/master/admin/framework_dependencies.html#managing-dependencies-manually --nate On Tue, Mar 1, 2016 at 1:40 PM, C. Ch. wrote: > Hi Bjoern, > > Thanks for the tip! My problem was that galaxy assumes that the venv is in > the installation directory as a hidden folder whilst I have the virtual > environment installed at ~/venv and configured in my .bashrc to launch at > login. Why I installed it like that? I don't remember... Probably to > separate the venv from the galaxy installation. > > For the future, is it better to change my venv to reside in the galaxy > folder or is it of no importance where I keep it? > > Thanks again! > Cristian > > > Subject: Re: [galaxy-dev] Missing modules after upgrade to 16.01 > > To: tuto...@hotmail.com; galaxy-dev@lists.galaxyproject.org > > From: bjoern.gruen...@gmail.com > > Date: Tue, 1 Mar 2016 13:47:41 +0100 > > > > Hi, > > > > please have a look at this script and run it: > > > > ./scripts/common_startup.sh > > > > Also make sure you have samtools installed. > > > > Ciao, > > Bjoern > > > > Am 01.03.2016 um 13:39 schrieb C. Ch.: > > > Hi, > > > > > > I've upgraded to 16.01 and have error messages indicating missing > > > modules. This produces problems while setting the metadata. The > > > processes run, the results are there but the history entry is in red. > > > > > > How can I trigger the installation of all the modules that galaxy needs > > > with the new pip based mechanism? > > > > > > Thanks for the help! > > > Cristian > > > > > > > > > ___ > > > 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: > > > https://lists.galaxyproject.org/ > > > > > > 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: > https://lists.galaxyproject.org/ > > 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Missing modules after upgrade to 16.01
Hi Bjoern, Thanks for the tip! My problem was that galaxy assumes that the venv is in the installation directory as a hidden folder whilst I have the virtual environment installed at ~/venv and configured in my .bashrc to launch at login. Why I installed it like that? I don't remember... Probably to separate the venv from the galaxy installation. For the future, is it better to change my venv to reside in the galaxy folder or is it of no importance where I keep it? Thanks again!Cristian > Subject: Re: [galaxy-dev] Missing modules after upgrade to 16.01 > To: tuto...@hotmail.com; galaxy-dev@lists.galaxyproject.org > From: bjoern.gruen...@gmail.com > Date: Tue, 1 Mar 2016 13:47:41 +0100 > > Hi, > > please have a look at this script and run it: > > ./scripts/common_startup.sh > > Also make sure you have samtools installed. > > Ciao, > Bjoern > > Am 01.03.2016 um 13:39 schrieb C. Ch.: > > Hi, > > > > I've upgraded to 16.01 and have error messages indicating missing > > modules. This produces problems while setting the metadata. The > > processes run, the results are there but the history entry is in red. > > > > How can I trigger the installation of all the modules that galaxy needs > > with the new pip based mechanism? > > > > Thanks for the help! > > Cristian > > > > > > ___ > > 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: > > https://lists.galaxyproject.org/ > > > > 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Missing modules after upgrade to 16.01
Hi, please have a look at this script and run it: ./scripts/common_startup.sh Also make sure you have samtools installed. Ciao, Bjoern Am 01.03.2016 um 13:39 schrieb C. Ch.: > Hi, > > I've upgraded to 16.01 and have error messages indicating missing > modules. This produces problems while setting the metadata. The > processes run, the results are there but the history entry is in red. > > How can I trigger the installation of all the modules that galaxy needs > with the new pip based mechanism? > > Thanks for the help! > Cristian > > > ___ > 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: > https://lists.galaxyproject.org/ > > 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Missing modules after upgrade to 16.01
Hi, I've upgraded to 16.01 and have error messages indicating missing modules. This produces problems while setting the metadata. The processes run, the results are there but the history entry is in red. How can I trigger the installation of all the modules that galaxy needs with the new pip based mechanism? Thanks for the help!Cristian ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
