Tutorial:installing samtools with conda - overcoming two common errors
2
7
Entering edit mode
7 months 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 • 3.5k views
ADD COMMENT
1
Entering edit mode

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

ADD REPLY
2
Entering edit mode
3 months ago
darklings ▴ 220
conda config --add channels bioconda
conda config --add channels conda-forge
conda install samtools==1.11

works for me

ADD COMMENT

Login before adding your answer.

Traffic: 1024 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6