this is a weird error, as it fails at installing mamba, hence well before even getting to install any bioinformatics tools

this may be a mamba related issue, in which case I need to rework the installation

mamba-org/mamba#1826

from biostar-handbook.

what system is this Mac OS M1/M2?

from biostar-handbook.

I used the windows system, using ubuntu as terminal

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did you already have anaconda/miniconda installed or was it a brand new shell?

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I have installed anaconda on my computer before.

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in the same shell?

I think that is the problem here, make a new user that runs a separate environment

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I can uninstall anaconda to have a try. Thanks.

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I deleted the anaconda and had another try, still not work, showing the same errors.

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you also have to uninstall everything for the handbook

curl http://data.biostarhandbook.com/uninstall.sh | bash

then

http://data.biostarhandbook.com/install.sh | bash

maybe the best is to start with a clean Unix system. Uninstall Ubuntu and reinstall it.

It is sad though that conda itself is incapable of working corretly, the whole point of it was supposed to avoid these problems.

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I got a new problem when install step by step. At step 9:
9. Install the bioinformatics software

Activate bioinfo.

conda activate bioinfo

Install the software.

$ curl -s http://data.biostarhandbook.com/install/conda.txt | xargs mamba install -q -y
Could not solve for environment specs
The following packages are incompatible
├─ bcftools does not exist (perhaps a typo or a missing channel);
├─ bedtools does not exist (perhaps a typo or a missing channel);
├─ bioawk does not exist (perhaps a typo or a missing channel);
├─ blast 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);
├─ csvtk does not exist (perhaps a typo or a missing channel);
├─ datamash does not exist (perhaps a typo or a missing channel);
├─ emboss does not exist (perhaps a typo or a missing channel);
├─ fastp does not exist (perhaps a typo or a missing channel);
├─ fastqc does not exist (perhaps a typo or a missing channel);
├─ freebayes does not exist (perhaps a typo or a missing channel);
├─ hisat2 does not exist (perhaps a typo or a missing channel);
├─ mafft does not exist (perhaps a typo or a missing channel);
├─ minimap2 does not exist (perhaps a typo or a missing channel);
├─ parallel does not exist (perhaps a typo or a missing channel);
├─ perl-text-csv does not exist (perhaps a typo or a missing channel);
├─ samtools >=1.14 does not exist (perhaps a typo or a missing channel);
├─ seqkit does not exist (perhaps a typo or a missing channel);
├─ seqtk does not exist (perhaps a typo or a missing channel);
├─ snpeff 5.0 does not exist (perhaps a typo or a missing channel);
├─ subread does not exist (perhaps a typo or a missing channel);
├─ trimmomatic does not exist (perhaps a typo or a missing channel);
└─ ucsc-bedgraphtobigwig does not exist (perhaps a typo or a missing channel).
(bioinfo)

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sounds like the channels are not activated, as it says in the error.

In general if you get an error where nothing works that indicates a step was missed before. If you get an error where one single tool does not work then it might be some local issue. But when the whole thing fails then it means something is fundamentally not in order.

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As the auto install script died at step 7 and I started from step 7. Forgot to activate bioconda. Now, all good. Thanks very much for your help. For the original problem, it because I didn't install conda, just run the install script directly (I read the pdf version of the book which skips conda install and activate biocnda). Now, all fixed. I will read the online version of the book.

$ ~/bin/doctor.py
# Doctor! Doctor! Give me the news.
# Checking symptoms ...
# bwa           ... OK
# datamash      ... OK
# fastqc -h     ... OK
# hisat2        ... OK
# seqret -h     ... OK
# featureCounts ... OK
# efetch        ... OK
# esearch       ... OK
# samtools      ... OK
# fastq-dump    ... OK
# bowtie2       ... OK
# bcftools      ... OK
# seqtk         ... OK
# seqkit        ... OK
# bio           ... OK
# fastq-dump -X 1 -Z SRR1553591 ... OK
# You are doing well, Majesty!
(bioinfo)

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sounds like it all worked. Glad to hear. I will be closing this issue then

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