mito3.6 can't not install normally.

[xiekunwhy]

Hi,

I can't not install mito3.6 using conda normally, here are the problems

../bin/mamba create -n mitoz3.6 -c conda-forge -c bioconda mitoz=3.6

Could not solve for environment specs
Encountered problems while solving:
  - package mkl-2020.4-h726a3e6_304 requires llvm-openmp >=11.0.0, but none of the providers can be installed

The environment can't be solved, aborting the operation

../bin/mamba env create -n mitoz3.6 -f mitozEnv.yml

pkgs/main/noarch                                              No change


Looking for: ['biopython', 'blast', 'bs4', 'bwa', 'circos=0.69', 'coreutils', "ete3[version='>=3.1.2']", 'fastp', 'hmmer=3.1b2', 'html5lib', 'infernal=1.1.1', 'libgd', 'megahit', 'openjdk', 'perl-app-cpanminus', 'perl-bioperl', 'perl-clone', 'perl-config-general', 'perl-encode-locale', 'perl-list-moreutils', 'perl-math-bezier', 'perl-math-round', 'perl-math-vecstat', 'perl-module-implementation', 'perl-params-validate', 'perl-set-intspan', 'perl-statistics-basic', 'perl-statistics-descriptive', 'perl=5.32', 'pkgconfig', "python[version='>=3.6,<3.10']", 'requests', 'samtools', 'seqkit', "spades[version='>=3.15.2']", "spades[version='>=3.15.4']", 'tbl2asn', 'tiara', 'wise2']


Could not solve for environment specs
Encountered problems while solving:
  - package tiara-1.0.3-pyhd8ed1ab_0 requires pytorch >=1.7.0,<1.8.dev0, but none of the providers can be installed

The environment can't be solved, aborting the operation

Do you know how to solve these problems ?

Best,
Kun

[linzhi2013]

Hi Kun,

Have you tried mamba clean -y -a or/and conda clean -y -a before installing MitoZ?

Or you can try

mamba  env create -f  https://github.com/linzhi2013/MitoZ/releases/download/3.6/mitoz3.6.environment.yml

, which will create an environment named mitoz3.6 in your system.

then,

conda env list

to find the path of the new environment.

and then activate it:

source activate /home/gmeng/.conda/envs/mybase/envs/mitoz3.6

This method has just been documented at https://github.com/linzhi2013/MitoZ/wiki/Installation#62-installation-of-dependencies

[xiekunwhy]

Hi,

Still not working,

Yes, I have run mamba clean -y -a before installing.

mamba env create -f https://github.com/linzhi2013/MitoZ/releases/download/3.6/mitoz3.6.environment.yml not work and gives following errors,

Could not solve for environment specs
Encountered problems while solving:
  - package biopython-1.78-py38h7f8727e_0 is excluded by strict repo priority
  - package c-ares-1.19.0-h5eee18b_0 is excluded by strict repo priority
  - package libdb-6.2.32-h6a678d5_1 is excluded by strict repo priority
  - package libdeflate-1.10-h7f98852_0 is excluded by strict repo priority
  - package perl-app-cpanminus-1.7046-pl5321hd8ed1ab_0 is excluded by strict repo priority
  - package perl-extutils-makemaker-7.70-pl5321hd8ed1ab_0 is excluded by strict repo priority
  - package perl-xml-parser-2.44_01-pl5340hf309648_0 is excluded by strict repo priority
  - package tqdm-4.54.1-pyhd3eb1b0_0 is excluded by strict repo priority
  - package numpy-1.19.5-py38h8246c76_3 is excluded by strict repo priority
  - package _libgcc_mutex-0.1-conda_forge is excluded by strict repo priority
  - package _openmp_mutex-4.5-2_gnu is excluded by strict repo priority
  - package fontconfig-2.14.1-hc2a2eb6_0 is excluded by strict repo priority
  - package glib-2.70.2-h780b84a_4 is excluded by strict repo priority
  - package libgcc-ng-12.2.0-h65d4601_19 is excluded by strict repo priority
  - package libgomp-12.2.0-h65d4601_19 is excluded by strict repo priority
  - package libuuid-2.38.1-h0b41bf4_0 is excluded by strict repo priority
  - package llvm-openmp-8.0.1-hc9558a2_0 is excluded by strict repo priority
  - package urllib3-1.26.15-py38h06a4308_0 is excluded by strict repo priority
  - package zlib-1.2.13-h166bdaf_4 is excluded by strict repo priority
  - package ete3-3.1.2-pyh9f0ad1d_0 is excluded by strict repo priority

The environment can't be solved, aborting the operation

[linzhi2013]

I don't know what's wrong here. But I just tried it on a totally new Linux machine and the following commands worked for me:

$ mamba clean -y -a
$ conda clean -y -a
$ mamba create -n mitoz3.6 -c bioconda -c conda-forge mitoz=3.6

[linzhi2013]

Which platform are you trying to install MitoZ on?

[linzhi2013]

I am uploading the Conda-Pack (https://github.com/linzhi2013/MitoZ/wiki/Installation#4-conda-pack) version. If the conda method does not work for you, do not waste time on it, as I mentioned on the wiki before, conda cannot solve all dependency problems. Try on a different machine or a different installation method.

[linzhi2013]

excluded by strict repo priority

See rapidsai/cuml#4016 and try:

conda config --set channel_priority flexible
mamba  env create -f  https://github.com/linzhi2013/MitoZ/releases/download/3.6/mitoz3.6.environment.yml

[linzhi2013]

../bin/mamba create -n mitoz3.6 -c conda-forge -c bioconda mitoz=3.6

try this:

mamba create -n mitoz3.6 -c conda-forge -c bioconda python=3.8 mitoz=3.6 

[xiekunwhy]

excluded by strict repo priority

See rapidsai/cuml#4016 and try:

conda config --set channel_priority flexible
mamba  env create -f  https://github.com/linzhi2013/MitoZ/releases/download/3.6/mitoz3.6.environment.yml

this one worked.

[linzhi2013]

../bin/mamba create -n mitoz3.6 -c conda-forge -c bioconda mitoz=3.6

try this:

mamba create -n mitoz3.6 -c conda-forge -c bioconda python=3.8 mitoz=3.6 

then I do not know why, because the command mamba create -n mitoz3.6 -c conda-forge -c bioconda python=3.8 mitoz=3.6 also worked for me on another Ubuntu machine.

[linzhi2013]

Docker and Singularity versions should ultimately solve the installation problem.