Tutorial:installing samtools with conda - overcoming two common errors
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14
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2.3 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 Tutorial • 20k 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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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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23 months ago
darklings ▴ 480
conda config --add channels bioconda
conda config --add channels conda-forge
conda install samtools==1.11

works for me

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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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2
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19 months ago
ATpoint 66k

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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19 months ago
BioRyder ▴ 220

conda install -c bioconda samtools openssl=1.0

this will solve the problem.

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