Installation Problems

[ShevchenkoAlla]

Hi,
I am tring to install metawrap on the new server in a few ways - like in the instructions

conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda
conda config --add channels ursky

Unix/Linux only

mamba install --only-deps -c ursky metawrap-mg

conda install --only-deps -c ursky metawrap-mg also works, but much slower

OR

mamba install biopython blas=2.5 blast=2.6.0 bmtagger bowtie2 bwa checkm-genome fastqc kraken=1.1 kraken=2.0 krona=2.7 matplotlib maxbin2 megahit metabat2 pandas prokka quast r-ggplot2 r-recommended salmon samtools=1.9 seaborn spades trim-galore

Note: this last solution is more universal, but you may need to manually install concoct=1.0 and pplacer.

and

Bioconda installation (not recommended):

conda install -y mamba
mamba install -y -c bioconda metawrap

or conda install -y -c bioconda metawrap

But, I got issues

First it wanted me to accept some channels,

conda create -y -n metawrap-env python=2.7

CondaToSNonInteractiveError: Terms of Service have not been accepted for the following channels. Please accept or remove them before proceeding:
- https://repo.anaconda.com/pkgs/main
- https://repo.anaconda.com/pkgs/r

To accept these channels' Terms of Service, run the following commands:
conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/main
conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/r

For information on safely removing channels from your conda configuration,
please see the official documentation:

https://www.anaconda.com/docs/tools/working-with-conda/channels

I did that,
But still got some errors,

LibMambaUnsatisfiableError: Encountered problems while solving:

• nothing provides bcftools needed by metawrap-mg-0.8-py27pl5_0

Could not solve for environment specs
The following packages are incompatible
└─ metawrap-mg =* * is not installable because there are no viable options
├─ metawrap-mg [0.8|0.8.2|...|1.0.3] would require
│ └─ bcftools =* *, which does not exist (perhaps a missing channel);
├─ metawrap-mg [1.0.4|1.0.5|...|1.1.7] would require
│ └─ bcftools =1.6 *, which does not exist (perhaps a missing channel);
└─ metawrap-mg [1.1.8|1.2|...|1.3.2] would require
└─ biopython =1.68 *, which does not exist (perhaps a missing channel).

After

install biopython blas=2.5 blast=2.6.0 bmtagger bowtie2 bwa checkm-genome fastqc kraken=1.1 kraken=2.0 krona=2.7 matplotlib maxbin2 megahit metabat2 pandas prokka quast r-ggplot2 r-recommended salmon samtools=1.9 seaborn spades trim-galore

Note: this last solution is more universal, but you may need to manually install concoct=1.0 and pplacer.

conda install biopython blas=2.5 blast=2.6.0 bmtagger bowtie2 bwa checkm-genome fastqc kraken=1.1 kraken=2.0 krona=2.7 matplotlib maxbin2 megahit metabat2 pandas prokka quast r-ggplot2 r-recommended salmon samtools=1.9 seaborn spades trim-galore
2 channel Terms of Service accepted
Channels:

• ursky
• conda-forge
• defaults
  Platform: linux-64
  Collecting package metadata (repodata.json): done
  Solving environment: failed

LibMambaUnsatisfiableError: Encountered problems while solving:

• unsupported request
• unsupported request
• unsupported request
• unsupported request
• unsupported request
• unsupported request
• unsupported request
• unsupported request
• nothing provides perl-lwp-simple needed by maxbin2-2.2.5-0
• unsupported request
• unsupported request
• unsupported request
• unsupported request
• unsupported request
• unsupported request
• unsupported request

Could not solve for environment specs
The following packages are incompatible
├─ blast =2.6.0 * does not exist (perhaps a typo or a missing channel);
├─ bmtagger =* * does not exist (perhaps a typo or a missing channel);
├─ bowtie2 =* * does not exist (perhaps a typo or a missing channel);
├─ bwa =* * does not exist (perhaps a typo or a missing channel);
├─ checkm-genome =* * does not exist (perhaps a typo or a missing channel);
├─ fastqc =* * does not exist (perhaps a typo or a missing channel);
├─ kraken =1.1,=2.0 * does not exist (perhaps a typo or a missing channel);
├─ krona =2.7 * does not exist (perhaps a typo or a missing channel);
├─ maxbin2 =* * is not installable because it requires
│ └─ perl-lwp-simple =* , which does not exist (perhaps a missing channel);
├─ megahit = * does not exist (perhaps a typo or a missing channel);
├─ prokka =* * does not exist (perhaps a typo or a missing channel);
├─ quast =* * does not exist (perhaps a typo or a missing channel);
├─ salmon =* * does not exist (perhaps a typo or a missing channel);
├─ samtools =1.9 * does not exist (perhaps a typo or a missing channel);
├─ spades =* * does not exist (perhaps a typo or a missing channel);
└─ trim-galore =* * does not exist (perhaps a typo or a missing channel).

(metawrap-env) [shevch_alla@m01 shevch_alla]$

I have found the issue here, wich says don't use old version... (#548)
Can anyone provide detailed instructions?

Are there any correct way to install metawrap now?

Thanks,

Best,

Alla

[yqy6611]

This is an outdated pipeline. Revising the original scripts manually and fitting latest dependancies are inevitable.

[ShevchenkoAlla]

This is an outdated pipeline. Revising the original scripts manually and fitting latest dependancies are inevitable.

Thanks,
I guess I will figure this out on my own....

[willboulton]

Most of the original installation instructions seemed to work fine, at least for me. I did the following (on a Centos-based HPC system):

mamba create -n metawrap_env python=2.7 && mamba activate metawrap_env
git clone https://github.com/bxlab/metaWRAP.git
mamba install biopython blas=2.5 blast=2.6.0 bmtagger bowtie2 bwa checkm-genome fastqc kraken=1.1 kraken2=2.0 krona=2.7 matplotlib maxbin2 megahit metabat2 pandas prokka quast r-ggplot2 r-recommended salmon samtools=1.9 seaborn spades trim-galore

So note I changed the 2nd kraken to kraken2 ... i have yet to test whether metawrap itself will run because of this, or if it will error, but the installation went through just fine.

[ShevchenkoAlla]

Most of the original installation instructions seemed to work fine, at least for me. I did the following (on a Centos-based HPC system):

mamba create -n metawrap_env python=2.7 && mamba activate metawrap_env git clone https://github.com/bxlab/metaWRAP.git mamba install biopython blas=2.5 blast=2.6.0 bmtagger bowtie2 bwa checkm-genome fastqc kraken=1.1 kraken2=2.0 krona=2.7 matplotlib maxbin2 megahit metabat2 pandas prokka quast r-ggplot2 r-recommended salmon samtools=1.9 seaborn spades trim-galore

So note I changed the 2nd kraken to kraken2 ... i have yet to test whether metawrap itself will run because of this, or if it will error, but the installation went through just fine.

Thank you

But, I have the same issue using your suggestion

conda install biopython blas=2.5 blast=2.6.0 bmtagger bowtie2 bwa checkm-genome fastqc kraken=1.1 kraken2=2.0 krona=2.7 matplotlib maxbin2 megahit metabat2 pandas prokka quast r-ggplot2 r-recommended salmon samtools=1.9 seaborn spades trim-galore
2 channel Terms of Service accepted
Channels:

• ursky
• conda-forge
• defaults
  Platform: linux-64
  Collecting package metadata (repodata.json): done
  Solving environment: failed

LibMambaUnsatisfiableError: Encountered problems while solving:

• unsupported request
• unsupported request
• unsupported request
• unsupported request
• unsupported request
• unsupported request
• unsupported request
• unsupported request
• unsupported request
• nothing provides perl-lwp-simple needed by maxbin2-2.2.5-0
• unsupported request
• unsupported request
• unsupported request
• unsupported request
• unsupported request
• unsupported request
• unsupported request

Could not solve for environment specs
The following packages are incompatible
├─ blast =2.6.0 * does not exist (perhaps a typo or a missing channel);
├─ bmtagger =* * does not exist (perhaps a typo or a missing channel);
├─ bowtie2 =* * does not exist (perhaps a typo or a missing channel);
├─ bwa =* * does not exist (perhaps a typo or a missing channel);
├─ checkm-genome =* * does not exist (perhaps a typo or a missing channel);
├─ fastqc =* * does not exist (perhaps a typo or a missing channel);
├─ kraken2 =2.0 * does not exist (perhaps a typo or a missing channel);
├─ kraken =1.1 * does not exist (perhaps a typo or a missing channel);
├─ krona =2.7 * does not exist (perhaps a typo or a missing channel);
├─ maxbin2 =* * is not installable because it requires
│ └─ perl-lwp-simple =* , which does not exist (perhaps a missing channel);
├─ megahit = * does not exist (perhaps a typo or a missing channel);
├─ prokka =* * does not exist (perhaps a typo or a missing channel);
├─ quast =* * does not exist (perhaps a typo or a missing channel);
├─ salmon =* * does not exist (perhaps a typo or a missing channel);
├─ samtools =1.9 * does not exist (perhaps a typo or a missing channel);
├─ spades =* * does not exist (perhaps a typo or a missing channel);
└─ trim-galore =* * does not exist (perhaps a typo or a missing channel).

[yqy6611]

Recently I have installed dependancies on my new HPC. I just released all the restrictions of the versions and it worked as a charm. Still I removed prokka, salmon, and quast from the list and installed them into individual conda environments.