Tutorial:installing samtools with conda - overcoming two common errors

Question

[lavinia.gordon]

Posting this here to help others.

Question - trying to install samtools with conda and encountering this error:

samtools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory

or this error:

samtools: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory

This seems to resolve both errors (or at least it worked for me):

conda install "samtools>=1.10"

Note the use of ", they are important.

[dr.douglas.rhoads]

In Ubuntu 20.04 in a Windows WSL2 VM tried the conda install -c bioconda "samtools>=1.10" and got a bunch of "Package conflicts for:" zlib, libstdcxx-ng, libgcc-ng, and ncurses

[rtagett]

This is the only solution that worked for me, trying to install samtools into a named conda environment. Other variations generated conflicts.

Answer 1

[darklings]

conda config --add channels bioconda
conda config --add channels conda-forge
conda install samtools==1.11

works for me

[Sael]

Thanks a lot ! Worked for me on Ubuntu 20.04

[sbruzual]

Thank you so much darklings

[Anastasiia]

worked for Ubuntu 20.04.3 Thanks!

I had an error: samtools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory tried to install libcrypto, but failed.

[Verónica]

Thank you so so much! I tried many ways and this one finally worked on a Python 2.7 environment

Answer 2

[ATpoint]

The order of channels should be (in file $HOME/.condarc)

channels:
  - conda-forge
  - bioconda
  - defaults

This should then take care of the dependencies and correct versions.

Answer 3

[BioRyder]

conda install -c bioconda samtools openssl=1.0

this will solve the problem.