download and unpack bcftools

Question

[kris10brandt]

Having problems with downloading and unpacking bcftools. Edited version # (1.2 and 1.4) and edited tar command info (jxvf, jxf, -xjvf, xjvf, xvzf) and got the error message. Also tried tar command -cfjv where it did not give an error message, however the file did not execute.

example below:

$ curl -OL https://github.com/samtools/bcftools/release/download/1.2/bcftools-1.2.tar.bz2 % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 9 0 9 0 0 28 0 --:--:-- --:--:-- --:--:-- 28

$ tar jxf bcftools-1.2.tar.bz2 tar: Unrecognized archive format tar: Error exit delayed from previous errors.

[GenoMax]

Try tar -axf bcftools-1.2.tar.bz2 otherwise bunzip2 bcftools-1.2.tar.bz2 followed by tar -xvf bcftools-1.2.tar (if you are using macOS). You are downloading source code so you will need to compile the program before you can execute it. Take a look at the INSTALL file for instructions on how to compile/install in source folder.

Answer 1

[h.mon]

You are downloading from the wrong address, so your file contains just "Not Found" - try cat bcftools-1.2.tar.bz2. Here is the correct address:

https://github.com/samtools/bcftools/releases/download/1.2/bcftools-1.2.tar.bz2

There is a missing s in /releases/. Your unpacking command should work after you download from the right place.