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singleron-RD / CeleScope

Single Cell Analysis Pipelines
https://www.singleron.bio/
MIT License
89 stars 31 forks source link

Instlation versions problem #265

Open MohamedAbdalfatah opened 1 year ago

MohamedAbdalfatah commented 1 year ago

Describe the bug Hi, I'm trying ti install celescope and I found a problem during the instlation using conda

To Reproduce

 source ~/.bashrc
cd CeleScope
conda create -n celescope -y --file conda_pkgs.txt

it is return 

Retrieving notices: ...working... done
Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: |
Found conflicts! Looking for incompatible packages.                                                                                                                                                                                        failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package _openmp_mutex conflicts for:
bioconda::samtools==1.16.1 -> libgcc-ng[version='>=12'] -> _openmp_mutex[version='>=4.5']
bioconda::trust4==1.0.7 -> libgcc-ng[version='>=10.3.0'] -> _openmp_mutex[version='>=4.5']
bioconda::igblast -> libgcc-ng[version='>=12'] -> _openmp_mutex[version='>=4.5']
conda-forge::python==3.9 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5']
bioconda::subread==2.0.1 -> libgcc-ng[version='>=10.3.0'] -> _openmp_mutex[version='>=4.5']
bioconda::bcftools==1.16 -> libgcc-ng[version='>=12'] -> _openmp_mutex[version='>=4.5']

Package bzip2 conflicts for:
bioconda::igblast -> bzip2[version='>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
bioconda::bcftools==1.16 -> htslib[version='>=1.17,<1.19.0a0'] -> bzip2[version='>=1.0.8,<2.0a0']
bioconda::gatk4 -> python -> bzip2[version='>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
bioconda::snpeff -> python -> bzip2[version='>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
bioconda::samtools==1.16.1 -> htslib[version='>=1.17,<1.19.0a0'] -> bzip2[version='>=1.0.8,<2.0a0']

Package ncurses conflicts for:
bioconda::gatk4 -> python -> ncurses[version='5.9.*|5.9|>=6.1,<7.0.0a0|>=6.2,<6.3.0a0|>=6.3,<7.0a0|>=6.4,<7.0a0|>=6.2,<7.0.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0|>=6.0,<7.0a0|6.0.*']
conda-forge::python==3.9 -> ncurses[version='>=6.2,<7.0.0a0']
bioconda::igblast -> sqlite -> ncurses[version='5.9|5.9.*|>=6.1,<7.0.0a0|>=6.2,<7.0.0a0|>=6.3,<7.0a0|>=6.4,<7.0a0|>=6.2,<7.0a0']
bioconda::snpeff -> python -> ncurses[version='5.9.*|5.9|>=6.1,<7.0.0a0|>=6.2,<6.3.0a0|>=6.3,<7.0a0|>=6.4,<7.0a0|>=6.2,<7.0.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0|>=6.0,<7.0a0|6.0.*']
conda-forge::python==3.9 -> readline[version='>=8.0,<9.0a0'] -> ncurses[version='>=6.1,<7.0.0a0|>=6.3,<7.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0|>=6.4,<7.0a0']
bioconda::samtools==1.16.1 -> ncurses[version='>=6.3,<7.0a0']

Package libcurl conflicts for:
bioconda::bcftools==1.16 -> htslib[version='>=1.17,<1.19.0a0'] -> libcurl[version='>=7.83.1,<8.0a0|>=7.87.0,<8.0a0|>=8.0.1,<9.0a0|>=8.2.0,<9.0a0']
bioconda::samtools==1.16.1 -> htslib[version='>=1.17,<1.19.0a0'] -> libcurl[version='>=7.83.1,<8.0a0|>=7.87.0,<8.0a0|>=8.0.1,<9.0a0|>=8.2.0,<9.0a0']

Package libgcc-ng conflicts for:
bioconda::samtools==1.16.1 -> libgcc-ng[version='>=12']
conda-forge::gcc -> gcc_impl_linux-64=13.2.0 -> libgcc-ng[version='>=10.3.0|>=10.4.0|>=11.1.0|>=11.2.0|>=11.3.0|>=11.4.0|>=12.1.0|>=12.2.0|>=12.3.0|>=13.1.0|>=13.2.0|>=4.9|>=9.5.0|>=9.4.0|>=8.5.0']
bioconda::trust4==1.0.7 -> libgcc-ng[version='>=10.3.0']
bioconda::samtools==1.16.1 -> ncurses[version='>=6.3,<7.0a0'] -> libgcc-ng[version='>=10.3.0|>=9.4.0|>=11.2.0|>=7.5.0']
bioconda::gatk4 -> openjdk[version='>=17,<18'] -> libgcc-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.5.0|>=7.3.0|>=4.9|>=11.2.0|>=7.2.0']
bioconda::igblast -> bzip2[version='>=1.0.8,<2.0a0'] -> libgcc-ng[version='>=11.2.0|>=7.5.0|>=9.4.0|>=7.2.0']
bioconda::bcftools==1.16 -> libgcc-ng[version='>=12']
conda-forge::python==3.9 -> libffi[version='>=3.3,<3.4.0a0'] -> libgcc-ng[version='>=10.3.0|>=12|>=7.3.0|>=9.4.0|>=11.2.0|>=4.9|>=7.2.0']
bioconda::subread==2.0.1 -> libgcc-ng[version='>=10.3.0|>=9.3.0|>=7.3.0']
bioconda::trust4==1.0.7 -> libzlib[version='>=1.2.11,<1.3.0a0'] -> libgcc-ng[version='>=11.2.0|>=12|>=7.5.0|>=9.4.0|>=9.3.0|>=7.3.0|>=4.9|>=7.2.0']
bioconda::igblast -> libgcc-ng[version='>=10.3.0|>=12|>=9.3.0|>=7.3.0|>=4.9']
bioconda::bcftools==1.16 -> gsl[version='>=2.7,<2.8.0a0'] -> libgcc-ng[version='>=11.2.0|>=9.3.0|>=7.5.0|>=9.4.0|>=7.3.0|>=4.9|>=7.2.0']
bioconda::subread==2.0.1 -> libzlib[version='>=1.2.11,<1.3.0a0'] -> libgcc-ng[version='>=11.2.0|>=12|>=7.5.0|>=4.9|>=7.2.0']
conda-forge::python==3.9 -> libgcc-ng[version='>=7.5.0|>=9.3.0']
bioconda::snpeff -> openjdk[version='>=11'] -> libgcc-ng[version='>=10.3.0|>=12|>=9.3.0|>=7.5.0|>=7.3.0|>=9.4.0|>=4.9|>=11.2.0|>=7.2.0']

Package python conflicts for:
conda-forge|conda-forge::python==3.9
conda-forge::python==3.9
bioconda::snpeff -> python
bioconda::gatk4 -> python[version='2.7.*|3.5.*|3.6.*|>0']

Package libedit conflicts for:
bioconda::igblast -> sqlite -> libedit[version='>=3.1.20170329,<3.2.0a0|>=3.1.20181209,<3.2.0a0|>=3.1.20191231,<3.2.0a0']
conda-forge::python==3.9 -> sqlite[version='>=3.33.0,<4.0a0'] -> libedit[version='>=3.1.20191231,<3.2.0a0']

Package libstdcxx-ng conflicts for:
conda-forge::python==3.9 -> libffi[version='>=3.3,<3.4.0a0'] -> libstdcxx-ng[version='>=4.9|>=7.3.0|>=7.2.0']
bioconda::snpeff -> openjdk[version='>=11'] -> libstdcxx-ng[version='>=10.3.0|>=12|>=9.3.0|>=7.5.0|>=7.3.0|>=9.4.0|>=4.9|>=11.2.0|>=7.2.0']
conda-forge::gcc -> gcc_impl_linux-64=13.2.0 -> libstdcxx-ng[version='>=10.3.0|>=10.4.0|>=11.1.0|>=11.2.0|>=11.3.0|>=11.4.0|>=12.1.0|>=12.2.0|>=12.3.0|>=13.1.0|>=13.2.0|>=4.9|>=9.5.0|>=9.4.0|>=8.5.0']
conda-forge::python==3.9 -> libstdcxx-ng[version='>=7.5.0|>=9.3.0']
bioconda::igblast -> libstdcxx-ng[version='>=10.3.0|>=12|>=9.3.0|>=7.3.0']
bioconda::trust4==1.0.7 -> libstdcxx-ng[version='>=10.3.0']
bioconda::igblast -> ncbi-vdb[version='>=2.9.6'] -> libstdcxx-ng[version='>=4.9|>=7.2.0|>=7.5.0']
bioconda::gatk4 -> openjdk[version='>=17,<18'] -> libstdcxx-ng[version='>=10.3.0|>=11.2.0|>=12|>=9.3.0|>=7.5.0|>=9.4.0|>=7.3.0|>=4.9|>=7.2.0']

Package libzlib conflicts for:
bioconda::snpeff -> openjdk[version='>=11'] -> libzlib[version='1.2.11|1.2.11|1.2.11|1.2.12|1.2.12|1.2.12|1.2.12|1.2.12|1.2.13|1.2.13|>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0',build='h36c2ea0_1013|h166bdaf_0|h166bdaf_1|h166bdaf_4|hd590300_5|h166bdaf_4|h166bdaf_3|h166bdaf_2|h166bdaf_1014|h36c2ea0_1012']
conda-forge::python==3.9 -> sqlite[version='>=3.33.0,<4.0a0'] -> libzlib[version='1.2.11|1.2.11|1.2.11|1.2.12|1.2.12|1.2.12|1.2.12|1.2.12|1.2.13|1.2.13|>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0',build='h36c2ea0_1013|h166bdaf_0|h166bdaf_1|h166bdaf_4|hd590300_5|h166bdaf_4|h166bdaf_3|h166bdaf_2|h166bdaf_1014|h36c2ea0_1012']
bioconda::subread==2.0.1 -> zlib[version='>=1.2.11,<1.3.0a0'] -> libzlib[version='1.2.11|1.2.11|1.2.11|1.2.12|1.2.12|1.2.12|1.2.12|1.2.12|1.2.13',build='h36c2ea0_1013|h166bdaf_0|h166bdaf_1|h166bdaf_4|hd590300_5|h166bdaf_4|h166bdaf_3|h166bdaf_2|h166bdaf_1014|h36c2ea0_1012']
bioconda::igblast -> libzlib[version='>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0']
bioconda::samtools==1.16.1 -> libzlib[version='>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0']
bioconda::trust4==1.0.7 -> libzlib[version='>=1.2.11,<1.3.0a0']
bioconda::gatk4 -> openjdk[version='>=17,<18'] -> libzlib[version='>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0']
bioconda::subread==2.0.1 -> libzlib[version='>=1.2.11,<1.3.0a0']
bioconda::bcftools==1.16 -> libzlib[version='>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0']
bioconda::bcftools==1.16 -> zlib[version='>=1.2.13,<1.3.0a0'] -> libzlib[version='1.2.12|1.2.12|1.2.12|1.2.12|1.2.12|1.2.13',build='h166bdaf_0|h166bdaf_1|h166bdaf_4|hd590300_5|h166bdaf_4|h166bdaf_3|h166bdaf_2']
bioconda::igblast -> zlib[version='>=1.2.11,<1.3.0a0'] -> libzlib[version='1.2.11|1.2.11|1.2.11|1.2.12|1.2.12|1.2.12|1.2.12|1.2.12|1.2.13',build='h36c2ea0_1013|h166bdaf_0|h166bdaf_1|h166bdaf_4|hd590300_5|h166bdaf_4|h166bdaf_3|h166bdaf_2|h166bdaf_1014|h36c2ea0_1012']
bioconda::samtools==1.16.1 -> zlib[version='>=1.2.13,<1.3.0a0'] -> libzlib[version='1.2.12|1.2.12|1.2.12|1.2.12|1.2.12|1.2.13',build='h166bdaf_0|h166bdaf_1|h166bdaf_4|hd590300_5|h166bdaf_4|h166bdaf_3|h166bdaf_2']

Package gdbm conflicts for:
bioconda::trust4==1.0.7 -> perl -> gdbm[version='>=1.18|>=1.18,<1.19.0a0']
bioconda::igblast -> perl -> gdbm[version='>=1.18|>=1.18,<1.19.0a0']
bioconda::bcftools==1.16 -> perl -> gdbm[version='>=1.18|>=1.18,<1.19.0a0']

Package zlib conflicts for:
bioconda::igblast -> zlib[version='>=1.2.11,<1.3.0a0']
bioconda::subread==2.0.1 -> zlib[version='>=1.2.11,<1.3.0a0']
bioconda::snpeff -> openjdk[version='>=11'] -> zlib[version='1.2.*|1.2.11|>=1.2.11,<1.3.0a0|1.2.8|1.2.11.*|>=1.2.13,<1.3.0a0|>=1.2.12,<1.3.0a0']
bioconda::bcftools==1.16 -> htslib[version='>=1.17,<1.19.0a0'] -> zlib
bioconda::gatk4 -> python -> zlib[version='1.2.*|1.2.11|>=1.2.11,<1.3.0a0|1.2.8|1.2.11.*|>=1.2.13,<1.3.0a0|>=1.2.12,<1.3.0a0']
bioconda::samtools==1.16.1 -> zlib[version='>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0']
bioconda::samtools==1.16.1 -> htslib[version='>=1.17,<1.19.0a0'] -> zlib
conda-forge::python==3.9 -> sqlite[version='>=3.33.0,<4.0a0'] -> zlib[version='>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0|>=1.2.13,<2.0a0']
bioconda::snpeff -> zlib
bioconda::igblast -> libxml2[version='>=2.9.14,<2.10.0a0'] -> zlib[version='>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0|>=1.2.13,<2.0a0']
bioconda::bcftools==1.16 -> zlib[version='>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0']
conda-forge::python==3.9 -> zlib[version='>=1.2.11,<1.3.0a0']

Package openssl conflicts for:
conda-forge::python==3.9 -> openssl[version='>=1.1.1h,<1.1.2a']
bioconda::samtools==1.16.1 -> htslib[version='>=1.17,<1.19.0a0'] -> openssl[version='>=1.1.1q,<1.1.2a|>=1.1.1t,<1.1.2a|>=3.1.0,<4.0a0|>=3.1.1,<4.0a0']
bioconda::bcftools==1.16 -> htslib[version='>=1.17,<1.19.0a0'] -> openssl[version='>=1.1.1q,<1.1.2a|>=1.1.1t,<1.1.2a|>=3.1.0,<4.0a0|>=3.1.1,<4.0a0']
bioconda::gatk4 -> python -> openssl[version='1.0.*|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1f,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1k,<1.1.2a|>=1.1.1l,<1.1.2a|>=1.1.1n,<1.1.2a|>=1.1.1o,<1.1.2a|>=1.1.1q,<1.1.2a|>=1.1.1s,<1.1.2a|>=3.1.0,<4.0a0|>=3.1.1,<4.0a0|>=3.1.2,<4.0a0|>=3.0.7,<4.0a0|>=3.0.5,<4.0a0|>=3.0.3,<4.0a0|>=3.0.2,<4.0a0|>=3.0.0,<4.0a0|>=3.0.10,<4.0a0|>=1.1.1v,<1.1.2a|>=1.1.1u,<1.1.2a|>=3.0.9,<4.0a0|>=3.0.8,<4.0a0|>=1.1.1t,<1.1.2a|>=1.1.1m,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.0.2n,<1.0.3a|>=1.0.2m,<1.0.3a|>=1.0.2l,<1.0.3a']
bioconda::snpeff -> python -> openssl[version='1.0.*|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1f,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1k,<1.1.2a|>=1.1.1l,<1.1.2a|>=1.1.1n,<1.1.2a|>=1.1.1o,<1.1.2a|>=1.1.1q,<1.1.2a|>=1.1.1s,<1.1.2a|>=3.1.0,<4.0a0|>=3.1.1,<4.0a0|>=3.1.2,<4.0a0|>=3.0.7,<4.0a0|>=3.0.5,<4.0a0|>=3.0.3,<4.0a0|>=3.0.2,<4.0a0|>=3.0.0,<4.0a0|>=3.0.10,<4.0a0|>=1.1.1v,<1.1.2a|>=1.1.1u,<1.1.2a|>=3.0.9,<4.0a0|>=3.0.8,<4.0a0|>=1.1.1t,<1.1.2a|>=1.1.1m,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.0.2n,<1.0.3a|>=1.0.2m,<1.0.3a|>=1.0.2l,<1.0.3a']

Package readline conflicts for:
bioconda::snpeff -> python -> readline[version='6.2.*|7.0|>=7.0,<8.0a0|>=8.0,<9.0a0|>=8.1,<9.0a0|>=8.1.2,<9.0a0|>=8.2,<9.0a0|7.0.*|7.*']
conda-forge::python==3.9 -> readline[version='>=8.0,<9.0a0']
bioconda::igblast -> sqlite -> readline[version='6.2.*|7.0|7.0.*|>=7.0,<8.0a0|>=8.0,<9.0a0|>=8.1,<9.0a0|>=8.1.2,<9.0a0|>=8.2,<9.0a0']
bioconda::gatk4 -> python -> readline[version='6.2.*|7.0|>=7.0,<8.0a0|>=8.0,<9.0a0|>=8.1,<9.0a0|>=8.1.2,<9.0a0|>=8.2,<9.0a0|7.0.*|7.*']
conda-forge::python==3.9 -> sqlite[version='>=3.33.0,<4.0a0'] -> readline[version='>=8.1,<9.0a0|>=8.1.2,<9.0a0|>=8.2,<9.0a0']

Package xz conflicts for:
bioconda::bcftools==1.16 -> htslib[version='>=1.17,<1.19.0a0'] -> xz[version='>=5.2.6,<5.3.0a0|>=5.2.6,<6.0a0']
bioconda::samtools==1.16.1 -> htslib[version='>=1.17,<1.19.0a0'] -> xz[version='>=5.2.6,<5.3.0a0|>=5.2.6,<6.0a0']
conda-forge::python==3.9 -> xz[version='>=5.2.5,<6.0.0a0']
bioconda::gatk4 -> python -> xz[version='5.0.*|5.2.*|>=5.2.3,<6.0.0a0|>=5.2.4,<6.0.0a0|>=5.2.5,<6.0.0a0|>=5.2.6,<5.3.0a0|>=5.2.6,<6.0a0|>=5.2.6,<6.0.0a0|>=5.4.2,<6.0a0|>=5.2.10,<6.0a0|>=5.2.8,<6.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0']
bioconda::igblast -> libxml2[version='>=2.9.14,<2.10.0a0'] -> xz[version='>=5.2.3,<6.0.0a0|>=5.2.4,<6.0.0a0|>=5.2.5,<6.0.0a0|>=5.2.6,<6.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0']
bioconda::snpeff -> python -> xz[version='5.0.*|5.2.*|>=5.2.3,<6.0.0a0|>=5.2.4,<6.0.0a0|>=5.2.5,<6.0.0a0|>=5.2.6,<5.3.0a0|>=5.2.6,<6.0a0|>=5.2.6,<6.0.0a0|>=5.4.2,<6.0a0|>=5.2.10,<6.0a0|>=5.2.8,<6.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0']

Package openjdk conflicts for:
bioconda::snpeff -> java-jdk -> openjdk==8.0.112
bioconda::snpeff -> openjdk[version='>=11|>=8']

Package libnsl conflicts for:
bioconda::snpeff -> python -> libnsl[version='>=2.0.0,<2.1.0a0']
bioconda::trust4==1.0.7 -> perl -> libnsl[version='>=2.0.0,<2.1.0a0']
bioconda::gatk4 -> python -> libnsl[version='>=2.0.0,<2.1.0a0']
bioconda::bcftools==1.16 -> perl -> libnsl[version='>=2.0.0,<2.1.0a0']
bioconda::igblast -> perl -> libnsl[version='>=2.0.0,<2.1.0a0']

Package lcms2 conflicts for:
bioconda::snpeff -> openjdk[version='>=11'] -> lcms2[version='>=2.11,<3.0a0|>=2.12,<3.0a0|>=2.13.1,<3.0a0|>=2.14,<3.0a0|>=2.15,<3.0a0|>=2.9,<3.0a0']
bioconda::gatk4 -> openjdk[version='>=17,<18'] -> lcms2[version='>=2.11,<3.0a0|>=2.12,<3.0a0|>=2.13.1,<3.0a0|>=2.14,<3.0a0|>=2.15,<3.0a0|>=2.9,<3.0a0']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
  - bioconda::subread==2.0.1 -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
  - bioconda::trust4==1.0.7 -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
  - conda-forge::python==3.9 -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']

How can I deal with this? Best Mohmed

zhouyiqi91 commented 1 year ago

Hi, using mamba instead of conda will fix this problem.

conda install mamba
mamba create -n celescope -y --file conda_pkgs.txt
MohamedAbdalfatah commented 1 year ago

Thank you There is any solution to use only conda?

zhouyiqi91 commented 1 year ago

I am afraid that mamba is the only solution here. If you are worried that mamba will mess up your base conda environment or you cannot install mamba in the base environment, you can create a new environment for installation, for example

conda create -y -n mamba_install mamba
conda activate mamba_install

then install celescope

mamba create -n celescope -y --file conda_pkgs.txt