Tutorial:installing samtools with conda - overcoming two common errors
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3.7 years ago

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.

samtools conda • 36k views
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1
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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

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Hello. Can someone help with an error during installing samtools 1.2? I installed samtools with the following command:

micromamba install samtools=1.2

But then I got the error during usage of samtools:

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

My micromamba channels:

  - conda-forge
  - bioconda
channel_priority: strict

My PC: Ubuntu 22.04.2 LTS on Windows 11 Pro, 22H2 I don't have this error on a macbook.

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1
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Why are you installing an old version of samtools from 2015? Use the latest.

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0
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This is the only solution that worked for me, trying to install samtools into a named conda environment. Other variations generated conflicts.

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0
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I face this problem with bcftools. I solved it via a Docker container

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I solved my problem with libssl1.0.0 like this:

First I uninstalled samtools from my conda env, then I opened http://security.ubuntu.com/ubuntu/pool/main/o/openssl1.0/ in my browser and download last version of libssl1.0.0 for my system (for me it was libssl1.0.0_1.0.2n-1ubuntu5.13_amd64.deb) Then I just install it:

sudo gdebi ./libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb

And after that I installed samtools again. Paulo

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Thus defeating the entire purpose of conda, which is to not alter the libraries that your system needs/uses.

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0
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That's not recommended, as conda is supposed to take full care of the dependency environment. Do what is done in the accepted answer, this will work. Make a new environment and install samtools into this one, that is always a good idea to avoid cross-environment contamination and avoid overloading individual envs. By the way, what you suggest only works if you have root permission, which on e.g. a HPC will never be the case.

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16
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3.3 years ago
darklings ▴ 570
conda config --add channels bioconda
conda config --add channels conda-forge
conda install samtools==1.11

works for me

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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.

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Thanks a lot ! Worked for me on Ubuntu 20.04

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Thank you so much darklings

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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.

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

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I toggle this as "accepted answer" since it is the best way to tackle the problem. If you on top of that use mamba instead of conda it runs even faster.

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1
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2.9 years ago
BioRyder ▴ 220
conda install -c bioconda samtools openssl=1.0

this will solve the problem.

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