created another environment called "kb", where I installed Kallisto-bustools

This is known to work well. What about installing bustools in the same env as Kallisto?

Alternatively you can create a new conda environment

conda create --name kba
conda activate kba
conda install -c bioconda kallisto
conda install conda-build
conda skeleton pypi kb_python
conda build kb_python
conda install --use-local kb_python
kb count \
pbmc_1k_v3_S1_mergedLanes_R1.fastq.gz pbmc_1k_v3_S1_mergedLanes_R2.fastq.gz \
-i Homo_sapiens.GRCh38.cdna.all.index \
-x 10XV3 \
-g t2g.txt \
-t 8 \
--cellranger

If the above doesn't work you simply delete the env

conda deactivate
conda env remove --name kba

Okay skeleton didn't work. The last option is to use Docker. There is a Docker file of kallisto https://pachterlab.github.io/kallisto/download It's a bit weird it's not in the Docker repo. The Docker builder file is https://github.com/cyverse/docker-builds/blob/master/kallisto/Dockerfile

I assume most people know how to use a Docker file.

created another environment called "kb", where I installed Kallisto-bustools

This is known to work well. What about installing bustools in the same env as Kallisto?

Alternatively you can create a new conda environment

conda create --name kba
conda activate kba
conda install -c bioconda kallisto
conda install conda-build
conda skeleton pypi kb_python
conda build kb_python
conda install --use-local kb_python
kb count \
pbmc_1k_v3_S1_mergedLanes_R1.fastq.gz pbmc_1k_v3_S1_mergedLanes_R2.fastq.gz \
-i Homo_sapiens.GRCh38.cdna.all.index \
-x 10XV3 \
-g t2g.txt \
-t 8 \
--cellranger

If the above doesn't work you simply delete the env

conda deactivate
conda env remove --name kba

Okay skeleton didn't work. The last option is to use Docker. There is a Docker file of kallisto https://pachterlab.github.io/kallisto/download It's a bit weird it's not in the Docker repo. The Docker builder file is https://github.com/cyverse/docker-builds/blob/master/kallisto/Dockerfile

I assume most people know how to use a Docker file. If not, i.e. you want a tutorial, then please post as a separate question (quite alot of text to explain).

created another environment called "kb", where I installed Kallisto-bustools

This is known to work well. What about installing bustools in the same env as Kallisto?

Alternatively you can create a new conda environment

conda create --name kba
conda activate kba
conda install -c bioconda kallisto
conda install conda-build
conda skeleton pypi kb_python
conda build kb_python
conda install --use-local kb_python
kb count \
pbmc_1k_v3_S1_mergedLanes_R1.fastq.gz pbmc_1k_v3_S1_mergedLanes_R2.fastq.gz \
-i Homo_sapiens.GRCh38.cdna.all.index \
-x 10XV3 \
-g t2g.txt \
-t 8 \
--cellranger

If the above doesn't work you simply delete the env

conda deactivate
conda env remove --name kba

created another environment called "kb", where I installed Kallisto-bustools

This is known to work well. What about installing bustools in the same env as Kallisto?

Alternatively you can create a new conda environment

conda create --name kba
conda activate kba
conda install -c bioconda kallisto
conda install conda-build
conda skeleton pypi kb_python
conda build kb_python
conda install --use-local kb_python
kb count \
pbmc_1k_v3_S1_mergedLanes_R1.fastq.gz pbmc_1k_v3_S1_mergedLanes_R2.fastq.gz \
-i Homo_sapiens.GRCh38.cdna.all.index \
-x 10XV3 \
-g t2g.txt \
-t 8 \
--cellranger

If the above doesn't work you simply delete the env

conda deactivate
conda env remove --name kba

Okay skeleton didn't work. The last option is to use Docker. There is a Docker file of kallisto https://pachterlab.github.io/kallisto/download It's a bit weird it's not in the Docker repo. The Docker builder file is https://github.com/cyverse/docker-builds/blob/master/kallisto/Dockerfile

I assume most people know how to use a Docker file.