mito3.6 can't not install normally.
xiekunwhy opened this issue · comments
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
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
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
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
Which platform are you trying to install MitoZ on?
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.
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
../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
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.
../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.
Docker and Singularity versions should ultimately solve the installation problem.