Installation of samtools on anaconda

Question

[qstefano]

Hello everyone,

I'm trying to install samtools in my anaconda environment on HPC, but running

conda install -c bioconda samtools=1.9

i get the following error:

 Package libstdcxx-ng conflicts for:
 conda-forge/linux-64::python==3.7.12=hf930737_100_cpython -> libstdcxx-ng[version='>=9.4.0']
 conda-forge/linux-64::python==3.7.12=hf930737_100_cpython -> libffi[version='>=3.4.2,<3.5.0a0'] -> libstdcxx-ng[version='>=7.3.0|>=7.5.0']

Package ncurses conflicts for:
conda-forge/linux-64::python==3.7.12=hf930737_100_cpython -> readline[version='>=8.1,<9.0a0'] -> ncurses[version='>=6.2,<7.0a0']
conda-forge/linux-64::python==3.7.12=hf930737_100_cpython -> ncurses[version='>=6.2,<6.3.0a0']

Package zlib conflicts for:
samtools=1.9 -> zlib[version='>=1.2.11,<1.3.0a0']
conda-forge/linux-64::python==3.7.12=hf930737_100_cpython -> sqlite[version='>=3.36.0,<4.0a0'] -> zlib[version='>=1.2.11,<1.3.0a0']
samtools=1.9 -> curl[version='>=7.59.0,<8.0a0'] -> zlib==1.2.11

Package libgcc-ng conflicts for:
conda-forge/linux-64::python==3.7.12=hf930737_100_cpython -> libffi[version='>=3.4.2,<3.5.0a0'] -> libgcc-ng[version='>=7.3.0|>=7.5.0|>=9.3.0']
conda-forge/linux-64::python==3.7.12=hf930737_100_cpython -> libgcc-ng[version='>=9.4.0']The following specifications were found to be incompatible with your system:

  - feature:/linux-64::__glibc==2.17=0
  - feature:|@/linux-64::__glibc==2.17=0
  - samtools=1.9 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']

So i installed samtools in another environment and it works. Is there a way to call samtools between different environments?

Thanks in advance.

Answer 1

[rpolicastro]

You should rebuild your environment using samtools in the recipe. It will automatically resolve dependencies between the different pieces of software.

I would also suggest potentially switching to mamba. Greatly speed up conda by using mamba

[qstefano]

Thank you, i've solved by rebuilding the env