Re: [galaxy-dev] Manual Tool and dependency installation
Hi Ravi, in a nutshell try to install all tools locally on your computer (same architecture than your cluster). Copy over all tools and directories. Now go to every tool-directory and create a symlink from the folder where the env.sh file is located to a folder called default. For example: /usr/local/tools/samtools/0.0.19/iuc/package_asdf/34213452345/ (here is your env.sh file) to /usr/local/tools/samtools/default/ That should work, but your are loosing reproducibility and can't use different versions of the same tool. What about running Galaxy in a docker container (https://github.com/bgruening/docker-recipes/tree/master/galaxy) and hosting everything there, isolated from your webserver? Hope that helps a little bit, Bjoern Am 14.05.2014 18:43, schrieb Ravi Alla: Hi All, Due to the nature of our cluster we are not allowed to have compilers on our webserver, which is where our galaxy instance runs. Because of this tool dependencies and tools that need to be compiled fail to install through the galaxy tool shed webpage. Is there a way for me to install dependencies and tools manually? For example I am trying to install the GATK2 wrapper. This depends on samtools-0.1.19 from iuc which in turn requires ncurses-5.9. Is there instructions somewhere as to where to install these tools such that they are tied to the GATK2 wrapper? Pardon me if this is a naive question, but I am really out of sorts here. Thank you Ravi ___ 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] Manual Tool and dependency installation
Hi Ravi To start, have a look at those wiki pages: https://wiki.galaxyproject.org/Admin/Config/ToolDependencies https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies Regards, Hans-Rudolf On 05/14/2014 06:43 PM, Ravi Alla wrote: Hi All, Due to the nature of our cluster we are not allowed to have compilers on our webserver, which is where our galaxy instance runs. Because of this tool dependencies and tools that need to be compiled fail to install through the galaxy tool shed webpage. Is there a way for me to install dependencies and tools manually? For example I am trying to install the GATK2 wrapper. This depends on samtools-0.1.19 from iuc which in turn requires ncurses-5.9. Is there instructions somewhere as to where to install these tools such that they are tied to the GATK2 wrapper? Pardon me if this is a naive question, but I am really out of sorts here. Thank you Ravi ___ 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/
[galaxy-dev] Manual Tool and dependency installation
Hi All, Due to the nature of our cluster we are not allowed to have compilers on our webserver, which is where our galaxy instance runs. Because of this tool dependencies and tools that need to be compiled fail to install through the galaxy tool shed webpage. Is there a way for me to install dependencies and tools manually? For example I am trying to install the GATK2 wrapper. This depends on samtools-0.1.19 from iuc which in turn requires ncurses-5.9. Is there instructions somewhere as to where to install these tools such that they are tied to the GATK2 wrapper? Pardon me if this is a naive question, but I am really out of sorts here. Thank you Ravi ___ 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/
