Installation of Bismark

Question

[appropiate]

I am trying to install Bismark in Ubuntu 20.04. According to documentation of Bismark, "simply copy the bismark_v0.X.Y.tar.gz file into a Bismark installation folder and extract all files by typing:

tar xzf bismark_v0.X.Y.tar.gz"

As I understand it, I have extracted Bismark-0.22.3.tar.gz and got a folder named Bismark-0.22.3, which I placed in a folder named Bismark at /usr/bin, but it does not seem to work. I also tried to put Bismark-0.22.3 elsewere with same result when I try a command:

bismark_genome_preparation --path_to_aligner /usr/bin/bowtie2/ --verbose /data/genomes/homo_sapiens/GRCh38/
bismark_genome_preparation: command not found

Perl is installed and bowtie2 is at /usr/bin/

Any guidance appreciated!

Answer 1

[Pierre Lindenbaum]

not

bismark_genome_preparation --path_to_aligner (...)

but

/full/path/to/bismark_genome_preparation --path_to_aligner (...)

or have a look at the documentation about the ${PATH} variable in bash.

which I placed in a folder named Bismark at /usr/bin

won't work if bismark_genome_preparation is not itself in /usr/bin.

[appropiate]

Oh, so I should have all the executables in the extracted folder moved to /usr/bin instead of moving there the folder itself, else add the path of the folder to $PATH, correct?

[Pierre Lindenbaum]

yes, or update PATH, or use a full path.