Metagenomic-analysis Pipeline
Error with `conda install` command
```
(MetagenomicAnalysis) parallels@ubuntu-linux-20-04-desktop:~/software/metagenomic-analysis$ conda install -y \
> snakemake ruamel.yaml biopython \
> 'r=4.1' r-ggplot2 r-optparse r-scales \
```
This yields the following error, due to conflicts:
```
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: |
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed
UnsatisfiableError: The following specifications were found to be incompatible with each other:
Output in format: Requested package -> Available versions
Package krb5 conflicts for:
r=4.1 -> r-base[version='>=4.1,<4.2.0a0'] -> krb5[version='>=1.19.1,<1.20.0a0']
r-ggplot2 -> r-base[version='>=4.0,<4.1.0a0'] -> krb5[version='>=1.16.4,<1.17.0a0|>=1.17.1,<1.18.0a0|>=1.19.1,<1.20.0a0']
r-scales -> r-base[version='>=4.0,<4.1.0a0'] -> krb5[version='>=1.16.4,<1.17.0a0|>=1.17.1,<1.18.0a0|>=1.19.1,<1.20.0a0']
r-optparse -> r-base[version='>=4.0,<4.1.0a0'] -> krb5[version='>=1.16.4,<1.17.0a0|>=1.17.1,<1.18.0a0|>=1.19.1,<1.20.0a0']
Package xz conflicts for:
biopython -> python[version='>=3.8,<3.9.0a0'] -> xz[version='>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0']
r-scales -> r-base[version='>=4.0,<4.1.0a0'] -> xz[version='>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0']
r=4.1 -> r-base[version='>=4.1,<4.2.0a0'] -> xz[version='>=5.2.5,<5.3.0a0']
r-ggplot2 -> r-base[version='>=4.0,<4.1.0a0'] -> xz[version='>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0']
r-optparse -> r-base[version='>=4.0,<4.1.0a0'] -> xz[version='>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0']
ruamel.yaml -> python[version='>=3.9,<3.10.0a0'] -> xz[version='>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0']
python=3.7 -> xz[version='>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0']
Package libblas conflicts for:
biopython -> numpy -> libblas[version='>=3.8.0,<4.0a0']
r-ggplot2 -> r-base[version='>=4.0,<4.1.0a0'] -> libblas[version='>=3.8.0,<4.0a0']
r-optparse -> r-base[version='>=4.0,<4.1.0a0'] -> libblas[version='>=3.8.0,<4.0a0']
r=4.1 -> r-base[version='>=4.1,<4.2.0a0'] -> libblas[version='>=3.8.0,<4.0a0']
r-scales -> r-base[version='>=4.0,<4.1.0a0'] -> libblas[version='>=3.8.0,<4.0a0']
Package pypy3.6 conflicts for:
biopython -> pypy3.6[version='>=7.3.2|>=7.3.3']
ruamel.yaml -> python[version='>=3.6,<3.7.0a0'] -> pypy3.6[version='7.3.*|7.3.0.*|7.3.1.*|7.3.2.*|7.3.3.*']
snakemake -> google-crc32c -> pypy3.6[version='>=7.3.1|>=7.3.2|>=7.3.3']
biopython -> numpy -> pypy3.6[version='7.3.*|7.3.0.*|7.3.1.*|7.3.2.*|7.3.3.*|>=7.3.1']
ruamel.yaml -> pypy3.6[version='>=7.3.1|>=7.3.2|>=7.3.3']
Package numpy conflicts for:
snakemake -> networkx[version='>=2.0'] -> numpy[version='>=1.16.3,<2.0a0|>=1.16.4,<2.0a0|>=1.16.5,<2.0a0|>=1.16.6,<2.0a0|>=1.17.5,<2.0a0|>=1.19|>=1.19.5,<2.0a0|>=1.19.4,<2.0a0|>=1.18.5,<2.0a0|>=1.19.2,<2.0a0']
biopython -> numpy
Package wheel conflicts for:
python=3.7 -> pip -> wheel
snakemake -> dropbox[version='>=7.2.1'] -> wheel
Package ld_impl_linux-aarch64 conflicts for:
ruamel.yaml -> python[version='>=3.9,<3.10.0a0'] -> ld_impl_linux-aarch64[version='>=2.34|>=2.36.1']
biopython -> python[version='>=3.8,<3.9.0a0'] -> ld_impl_linux-aarch64[version='>=2.34|>=2.36.1']
python=3.7 -> ld_impl_linux-aarch64[version='>=2.34']
python=3.7 -> binutils_impl_linux-aarch64 -> ld_impl_linux-aarch64[version='2.33.1|2.34|2.34|2.34|2.34|2.34|2.34|2.35|2.35.1|2.35.1|2.35.1|2.35.1|2.36.1',build='h326052a_8|h326052a_8|h281f86e_8|h281f86e_9|h36823c2_0|h36823c2_1|h02ad14f_1|h02ad14f_2|h02ad14f_1|h02ad14f_0|h71b2515_9|h326052a_7|h326052a_6|h326052a_5']
Package libstdcxx-ng conflicts for:
ruamel.yaml -> python[version='>=3.9,<3.10.0a0'] -> libstdcxx-ng[version='>=7.3.0|>=7.5.0|>=9.3.0']
r-ggplot2 -> r-base[version='>=4.0,<4.1.0a0'] -> libstdcxx-ng[version='>=7.3.0|>=7.5.0|>=9.3.0']
python=3.7 -> libstdcxx-ng[version='>=7.3.0|>=7.5.0|>=9.3.0']
r-optparse -> r-base[version='>=4.0,<4.1.0a0'] -> libstdcxx-ng[version='>=7.3.0|>=7.5.0|>=9.3.0']
biopython -> python[version='>=3.8,<3.9.0a0'] -> libstdcxx-ng[version='>=7.3.0|>=7.5.0|>=9.3.0']
r-scales -> r-base[version='>=4.0,<4.1.0a0'] -> libstdcxx-ng[version='>=7.3.0|>=7.5.0|>=9.3.0']
r=4.1 -> r-base[version='>=4.1,<4.2.0a0'] -> libstdcxx-ng[version='>=9.3.0']
snakemake -> pandas -> libstdcxx-ng[version='>=7.3.0|>=7.5.0|>=9.3.0']
Package setuptools conflicts for:
ruamel.yaml -> setuptools
snakemake -> dropbox[version='>=7.2.1'] -> setuptools
python=3.7 -> pip -> setuptools
Package r-scales conflicts for:
r-ggplot2 -> r-scales[version='>=0.5.0']
r-scales
Package libgfortran4 conflicts for:
r-optparse -> r-base[version='>=3.6,<3.7.0a0'] -> libgfortran4[version='>=7.5.0']
r-ggplot2 -> r-base[version='>=3.6,<3.7.0a0'] -> libgfortran4[version='>=7.5.0']
r-scales -> r-base[version='>=3.6,<3.7.0a0'] -> libgfortran4[version='>=7.5.0']
Package tzdata conflicts for:
ruamel.yaml -> python[version='>=3.9,<3.10.0a0'] -> tzdata
biopython -> python[version='>=3.9,<3.10.0a0'] -> tzdata
Package r-base conflicts for:
r=4.1 -> r-base[version='>=4.1,<4.2.0a0']
r=4.1 -> r-recommended -> r-base[version='>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=4.0,<4.1.0a0|>=3.5.1,<3.5.2.0a0']
Package r-mass conflicts for:
r=4.1 -> r-recommended -> r-mass
r-ggplot2 -> r-mass
```