4 months ago by
Feedback from the developers at Gitter, summarized:
This older Samtools wrapper needs an update to use Conda to install dependencies, instead of the prior method that involved dependency packages.
Until that is done, uninstall package_samtools_1_2 and package_ncurses_5_9 and install samtools 1.2 with Conda.
The same methods would apply to other older tool wrappers that still have "dependency packages" included, and the dependency is available from Conda or there are installation problems. Many if not most commonly used tools have already been updated to use Conda, but not all. For most use cases, the most current version of a tool wrapper is the best to use, not only because of how dependencies are managed but because of bug fixes, updated tool forms, and the like introduced in the updated version.
However, Samtools is a bit different since it is not only a standalone tool suite (tools that can be used directly) but also a tool suite that is utilized by many other tools as a dependency plus has other dependencies (ncurses, etc). This effectively means that installing the exact version of Samtools that another tool is dependent on matters to achieve full functionality and to avoid errors. It is more common than not to have a few versions of key dependencies installed on a Galaxy server.
More about Conda and dependency resolution strategies:
Related Q&A at biostars.org: https://www.biostars.org/p/199705/ That thread includes help for Conda Samtools installs plus direct install of samtools/ncurses on Ubuntu that doesn't involve Conda (should you choose that alternative method).
Thanks! Jen, Galaxy team