Thank you, i've solved by rebuilding the env
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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.
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
Thank you, i've solved by rebuilding the env
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