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HenrikBengtsson / aroma.seq

🔬 R package: aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework
https://github.com/HenrikBengtsson/aroma.seq
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REPRODUCIBILITY: Report on versions for external tools used in verbose output #42

Open HenrikBengtsson opened 7 years ago

HenrikBengtsson commented 7 years ago

In order to better promote reproducible research, aroma.seq should report on versions of external tools it uses. As a started this should be easy to add for verbose output messages, but ideally it should also add *.log files where the tool itself doesn't add such.

HenrikBengtsson commented 6 years ago

Currently we have:

> res <- capabilitiesOf(aroma.seq)
> res
    CNVkit    bowtie2        bwa  fastqDump     fastqc       gatk      htseq 
     FALSE      FALSE       TRUE      FALSE      FALSE      FALSE      FALSE 
      java       perl     picard     python   samtools sratoolkit    tophat1 
      TRUE       TRUE      FALSE       TRUE       TRUE      FALSE      FALSE 
   tophat2 
     FALSE 

> str(res)
 Named logi [1:15] FALSE FALSE TRUE FALSE FALSE FALSE ...
 - attr(*, "names")= chr [1:15] "CNVkit" "bowtie2" "bwa" "fastqDump" ...

Maybe we could add support for:

> res <- capabilitiesOf(aroma.seq, version = TRUE)
 Named logi [1:15] FALSE FALSE TRUE FALSE FALSE FALSE ...
 - attr(*, "names")= chr [1:15] "CNVkit" "bowtie2" "bwa" "fastqDump" ...
 - attr(*, "version")= chr [1:15] NA NA "0.7.12" NA ...
HenrikBengtsson commented 6 years ago

Also, report on their versions in the verbose output when they are called, e.g. in https://github.com/HenrikBengtsson/aroma.seq/blob/master/R/samtoolsMpileup.R#L47-L55