R Markdown: Can't access Bash command installed through Conda/Anaconda

Question

I'm exploring some bioinformatics data and I like to use R notebooks (i.e. Rmarkdown) when I can. Right now, I need to use a command line tool to analyze a VCF file and I would like to do it through a Bash code chunk in the Rmarkdown notebook.

The problem is that the command I want to use was installed with conda into my conda environment. The tool is bcftools. When I try to access this command, I get this error (code chunk commented out to show rmarkdown code chunk format):

#```{bash}
bcftools view -H test.vcf.gz
#```

/var/folders/9l/phf62p1s0cxgnzp4hgl7hy8h0000gn/T/RtmplzEvEh/chunk-code-6869322acde0.txt: line 3: bcftools: command not found

Whereas if I run from Terminal, I get output (using conda environment called "binfo"):

> bcftools view -H test.vcf.gz | head -n 3
chr10   78484538    .   A   C   .   PASS    DP=57;SOMATIC;SS=2;SSC=16;GPV=1;SPV=0.024109    GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:34:33:0:0%:0,33,0,0   0/1:.:23:19:4:17.39%:1,18,0,4
chr12   4333138 .   G   T   .   PASS    DP=119;SOMATIC;SS=2;SSC=14;GPV=1;SPV=0.034921   GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:72:71:1:1.39%:71,0,1,0    0/1:.:47:42:5:10.64%:42,0,5,0
chr15   75086860    .   C   T   .   PASS    DP=28;SOMATIC;SS=2;SSC=18;GPV=1;SPV=0.013095    GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:15:15:0:0%:4,11,0,0   0/1:.:13:8:5:38.46%:5,3,1,4
(binfo)

So, how do I access tools installed with conda/in my conda env from an R notebook/Rmarkdown bash code chunk? I searched for quite a while and could not find anyone talking about running conda commands in a shell chunk in Rmarkdown. Any help would be appreciated because I like the R notebook format for exploratory analysis.

Answer 1

Passing Arguments to Engines

If your Conda is properly configured to work in bash, then you can use engine.opts to tell bash to launch in login mode (i.e., source your .bash_profile (Mac) or .bashrc (Linux)):

bash

```{bash engine.opts='-l'}
bcftools view -H test.vcf.gz
```

zsh

If working with zsh (e.g., Mac OS 10.15 Catalina users), then the interactive flag, --interactive|-i is what you want (Credit: @Leo).

```{zsh engine.opts='-i'}
bcftools view -H test.vcf.gz
```

Again, this presumes you've previously run conda init zsh to set up Conda to work with the shell.

Note on Reproducibility

Since reproducibility is usually a concern in scientific work, I will add that you may want to do something to capture the state of your Conda environment. For example, if you are working in version control, then commit a conda env export > environment.yaml. Another option would be to output that info directly at the end of the Rmd, like what is usually done with sessionInfo(). That is,

```{bash engine.opts='-l', comment=NA}
conda env export
```

where the comment=NA is so that the output can be cleanly copied from the rendered version.