Failed install at step 6 "lib mamba Could not solve for environment specs"

[pickleton89]

I keep running into this error when running the:
curl http://data.biostarhandbook.com/install.sh | bash

6 Installing tools into bioinfo

warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
error libmamba Could not solve for environment specs
The following packages are incompatible
└─ samtools >=1.14 is not installable because there are no viable options
├─ samtools [1.14|1.15] would require
│ └─ htslib >=1.14,<1.19.0a0 , which conflicts with any installable versions previously reported;
├─ samtools [1.15|1.15.1] would require
│ └─ htslib >=1.15,<1.19.0a0 , which conflicts with any installable versions previously reported;
├─ samtools [1.15.1|1.16.1] would require
│ └─ htslib >=1.16,<1.19.0a0 , which conflicts with any installable versions previously reported;
├─ samtools [1.16.1|1.17] would require
│ └─ htslib >=1.17,<1.19.0a0 , which conflicts with any installable versions previously reported;
├─ samtools [1.17|1.18] would require
│ └─ htslib >=1.17,<1.18.0a0 , which conflicts with any installable versions previously reported;
└─ samtools 1.18 would require
└─ htslib >=1.18,<1.19.0a0 , which conflicts with any installable versions previously reported.
critical libmamba Could not solve for environment specs

I installed samtools and htslib with the following command:
micromamba install samtools
micromamba install htslib

The errors still exists.

[ialbert]

what operating system is this?

did you have conda already installed?

Sometimes if you did already have conda there the previous .condarc could be incorrect

the ~/.condarc file should only contain:

channels:
  - conda-forge
  - bioconda
channel_priority: strict

[pickleton89]

Sorry, I forgot to list that M1 MAC Sonoma 14.1. This is what was in my ~/.condarc file.

channels:

• conda-forge
• defaults
• bioconda
  offline: false
  channel_priority: strict

---

I did have a previous install of biostar materials, but wanted a reboot as my organization had got away from me.

[ialbert]

replace your .condarc with the one I showed

[ialbert]

or delete your .condarc and the installer will recreate it with the correct layout.

[ialbert]

Turns out I could also force the correct order in the install.sh so I have made the change that next time will correct the order of channels even if these previously existed in the wrong order.

You can also do it manually with:

micromamba config prepend channels bioconda
micromamba config prepend channels conda-forge

[pickleton89]

Thanks. I deleted the .condarc file as you suggested. I am currently installing, I am at step 6, and appears to be working as no error at this time.

[pickleton89]

doctor.py said that I am doing well :)

Thank you for your assistance.

[ialbert]

Thanks for the report, I fixed the install.sh so it would correct this inconsistency in the future.

[xiangyuanyu]

error libmamba Could not solve for environment specs
The following packages are incompatible
└─ samtools >=1.14 * is not installable because there are no viable options
├─ samtools [1.14|1.15] would require
│ └─ htslib >=1.14,<1.23.0a0 *, which conflicts with any installable versions previously reported;
├─ samtools [1.15|1.15.1] would require
│ └─ htslib >=1.15,<1.23.0a0 *, which conflicts with any installable versions previously reported;
├─ samtools [1.15.1|1.16.1] would require
│ └─ htslib >=1.16,<1.23.0a0 *, which conflicts with any installable versions previously reported;
├─ samtools [1.16.1|1.17|1.18] would require
│ └─ htslib >=1.17,<1.23.0a0 *, which conflicts with any installable versions previously reported;
├─ samtools 1.18 would require
│ └─ htslib >=1.18,<1.23.0a0 *, which conflicts with any installable versions previously reported;
├─ samtools 1.19 would require
│ └─ htslib >=1.19,<1.23.0a0 *, which conflicts with any installable versions previously reported;
├─ samtools [1.19.1|1.19.2] would require
│ └─ htslib >=1.19.1,<1.23.0a0 *, which conflicts with any installable versions previously reported;
├─ samtools 1.20 would require
│ └─ htslib >=1.20,<1.23.0a0 *, which conflicts with any installable versions previously reported;
├─ samtools 1.21 would require
│ └─ htslib >=1.21,<1.23.0a0 *, which conflicts with any installable versions previously reported;
├─ samtools 1.22 would require
│ └─ htslib >=1.22,<1.23.0a0 *, which conflicts with any installable versions previously reported;
└─ samtools 1.22.1 would require
└─ htslib >=1.22.1,<1.23.0a0 *, which conflicts with any installable versions previously reported.
critical libmamba Could not solve for environment specs

yumnera@Mac ~
$ cat ~/.condarc
channels:

• conda-forge
• bioconda
  channel_priority: strict
  I met with similar issue, but after I check the condarc, and find out the correct order. I am using Mac os 15.0, M2 chip. I wonder if you could help me solve that question, thank you!

[ialbert]

This sounds like you have an M processor-based micromamba rather than the Intel-based micromamba.

Even on M type processor you have to run the Intel based micromamba.

By default the install script will install the correct version but if you already had micromamba or conda installed issues might arise.

[xiangyuanyu]

So how should I uninstall them and reset the new envir?

[ialbert]

yes, the enviroment needs to be Intel based, please follow the instructions in the book, it describes all steps in detail