Question: Ubuntu 18.04. Samtools missing tool dependencies
0
gravatar for alexshakhin
11 weeks ago by
Russia/Podolsk/vij.edu.ru
alexshakhin0 wrote:

I am working with local Galaxy (Ubuntu 18.04 lts - Galaxy 17.09/18.01/18.05). When I try to install the program samtools (iuc) I'm getting:

Error installing tool dependency ncurses version 5.9: 'ascii' codec can't encode character u'\u2018' in position 268: ordinal not in range(128)).

In Ubuntu 16.04 - it worked properly!

ADD COMMENTlink modified 9 weeks ago • written 11 weeks ago by alexshakhin0

Hello,

I asked the developers for help at the IUC Gitter channel. They want to know what version of Samtools you are installing.

I would strongly recommend joining the conversation there to troubleshoot the problem faster: https://gitter.im/galaxy-iuc/iuc?at=5b104099e26c847ac8a84f7d

Or, you can post back the version here and I can ping them again.

Thanks, Jen, Galaxy team

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by Jennifer Hillman Jackson25k

I tried to installed samtool_filter2 https://toolshed.g2.bx.psu.edu/repository?repository_id=c65cb5859e66a330 it requires dependency package_ncurses_5_9 (Owner: iuc) https://toolshed.g2.bx.psu.edu/repository?repository_id=5b54d0cc17d543c1&changeset_revision=335ebf512407. This works in MacOS 10.13.4, Ubuntu 16.04, most likely with Centos 7. But in Ubuntu 17.10/18.04, openSUSE 42.3, Fedora 27, dependency ncurses 5.9 is not installed. Perhaps this is due to the fact that in the Ubuntu 17.10/18.04 default version ncurses 6.0 is installed on system (I can't install also the version 5.9 to the system). Because of this, all programs that have this dependency do not work.

https://ibb.co/efS4Cd

https://ibb.co/joKHXd

https://ibb.co/iZRxXd

ADD REPLYlink written 11 weeks ago by alexshakhin0

Thanks for the extra info. I updated the developers, please follow or join the conversation here: https://gitter.im/galaxy-iuc/iuc?at=5b11a05b52e35117cdfd77e7

My guess is that you could directly install these dependencies and add them to your PATH, but let's see what the developers recommend.

ADD REPLYlink written 11 weeks ago by Jennifer Hillman Jackson25k
1
gravatar for Nicola Soranzo
10 weeks ago by
Norwich, UK
Nicola Soranzo70 wrote:

samtools_filter2 has been updated on the Tool Shed to use Conda dependencies, in particular it now requires Samtools 1.8.

This should solve your install problem.

Cheers, Nicola

ADD COMMENTlink written 10 weeks ago by Nicola Soranzo70
0
gravatar for Jennifer Hillman Jackson
11 weeks ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

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

ADD COMMENTlink written 11 weeks ago by Jennifer Hillman Jackson25k
0
gravatar for alexshakhin
9 weeks ago by
Russia/Podolsk/vij.edu.ru
alexshakhin0 wrote:

Thanks Jen, Nicola! Now everything works!

ADD COMMENTlink written 9 weeks ago by alexshakhin0
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