problems installing samtools and bcftools simultaneously

Question

[florsuqueli]

Hello! I am having problems with SAMtools and BCFtools. When I installed samtools, bcftools is automatically uninstalled and vice versa.

I tried these instructions:

 git clone --branch=develop git://github.com/samtools/htslib.git
    git clone --branch=develop git://github.com/samtools/bcftools.git
    git clone --branch=develop git://github.com/samtools/samtools.git
    cd bcftools; make
    cd ../samtools; make

published in https://github.com/samtools/bcftools/wiki/HOWTOs#install , but the problem persist.

Would you help me?

[IP]

What is the error message?

[florsuqueli]

When I run the command sudo apt install bcftools the answer is (this is not an error message):

Paquetes sugeridos:
  python-numpy python-matplotlib texlive-latex-recommended
Los siguientes paquetes se ELIMINARÁN:
  samtools
Se instalarán los siguientes paquetes NUEVOS:
  bcftools
0 actualizados, 1 nuevos se instalarán, 1 para eliminar y 7 no actualizados.
Se necesita descargar 275 kB de archivos.
Se liberarán 537 kB después de esta operación.
¿Desea continuar? [S/n]

[Devon Ryan]

Why would you sudo apt install bcftools? You've just compiled the most recent version, make install prefix=something instead.

[florsuqueli]

Thanks Devon it works perfectly

Answer 1

[Istvan Albert]

If you follow the instructions at

https://github.com/samtools/bcftools/wiki/HOWTOs#install

then you will have bcftools and samtools installed into their respective directories.

Nothing could possibly be uninstalled.

When you run apt-get then you are running a different tool altogether a package manager that has nothing to do with installation above. It appears that you are installing incompatible packages hence it gets uninstalled.

[florsuqueli]

I could install both softwares using:

cd samtools-1.x    
./configure --prefix=/where/to/install
make
make install

These didn't show error messages, but, when i tried

samtools mpileup -uf ref.fa aln.bam | bcftools view -cg - | vcfutils.pl vcf2fq > cns.fq

This message appears:

El programa «vcfutils.pl» no está instalado. Puede instalarlo escribiendo: sudo apt install bcftools

El programa «bcftools» puede encontrarse en los siguientes paquetes: * bcftools * samtools Intente: sudo apt install <paquete seleccionado=""> El programa «samtools» no está instalado. Puede instalarlo escribiendo: sudo apt install samtools

What do you suggest?

[Devon Ryan]

You'll get better support in general with English error messages. Anyway, make sure that bcftools is in your PATH.