Intall MAGIC-BLAST in Ubuntu from BASH SHELL in windows powershell.

Question

[jjvelazcoa]

I've been trying install magic blast for the ubuntu version in windows powershell by downloading the package and using the command:

sudo apt-get install magicblast

But it does not work. I get the following message:

Reading package lists... Done

Building dependency tree

Reading state information... Done

E: Unable to locate package makeblastdb

I have also tried using the ncbi-magicblast-1.5.0 command, but nothing works.

If there is someone who has managed to install it, I thank you for sharing the information.

Answer 1

[GenoMax]

You should use conda as recommended by NCBI.

conda install -c bioconda magicblast
conda activate magicblast

[jjvelazcoa]

Thanks, i did it. But i need to have magicblast running in bash powershell for my bioinformatics course.

[JC]

But i need to have magicblast running in bash powershell for my bioinformatics course.

I strongly recommend doing the curse in a Linux system, as a Docker container or VM

[GenoMax]

If you did the above then you should be able to run magicblast once you activate the conda environment. If you open a new bash shell you will need to do conda activate magicblast in that shell.

Answer 2

[Nanderson-coder]

I was able to use magicblast command in the ncbi-magicblast-1.5.0/bin/ folder using:

./magicblast

instead of only magicblast. Also use

export PATH=$PATH:/home/ncbi-magicblast-1.5.0/bin/ then you can use the regular magicblast command in any folder e.g.

magicblast -help