Hi Robert,

Thanks for the useful report. I think I've fixed the issue in
makeGmapGenomePackage. If you grab 1.3.2 (devel) and rebuild your package,
it should work.

Michael


On Wed, May 15, 2013 at 8:59 AM, Robert Castelo <robert.castelo@upf.edu>wrote:

> hi,
>
> using the gmapR package i built the GmapGenome package from the
> Bioconductor hg19 human genome package as follows:
>
> library(gmapR)
> library(BSgenome.Hsapiens.**UCSC.hg19)
> gmapGenomePath <- file.path("./HsapGenome")
> gmapGenomeDirectory <- GmapGenomeDirectory(**gmapGenomePath, create=TRUE)
> gmapGenome <- GmapGenome(genome=Hsapiens, directory=gmapGenomeDirectory,
> name="hg19", create=TRUE)
>
> makeGmapGenomePackage(**gmapGenome=gmapGenome,
>                       version="1.0.0",
>                       maintainer="<robert.castelo@**upf.edu<robert.castelo@upf.edu>
> >",
>                       author="Robert Castelo",
>                       destDir=".",
>                       license="Artistic-2.0",
>                       pkgName="GmapGenome.Hsapiens.**UCSC.hg19")
>
> afterwards, i bundled the package from the shell with:
>
> $ R CMD build GmapGenome.Hsapiens.UCSC.hg19
>
> and i install it with
>
> $ R CMD INSTALL GmapGenome.Hsapiens.UCSC.hg19_**1.0.0.tar.gz
>
> when i try to use the package in a call to gsnap() it seems that there is
> no way to pass the *name* of the GmapGenome object to the command-line that
> works under the hoods, i.e.:
>
> library(GmapGenome.Hsapiens.**UCSC.hg19)
>
> gsnapParam <- GsnapParam(genome=GmapGenome.**Hsapiens.UCSC.hg19,
> unique_only=TRUE, nthreads=8)
>
> gsnapOutput <- gsnap(input_a=fastqs[1], input_b=NULL, params=gsnapParam)
> Error in .system_gsnap(commandLine("**gsnap")) :
>   Execution of gsnap failed, command-line: '/opt/R/R-3.0.0/lib64/R/**
> aprilLibrary/gmapR/usr/bin/**gsnap --db=GmapGenome.Hsapiens.UCSC.**hg19
> --dir=/opt/R/R-3.0.0/lib64/R/**aprilLibrary/GmapGenome.**Hsapiens.UCSC.hg19/extdata
> --nthreads=8 --npaths=1 --quiet-if-excessive --nofails
> --format=sam f.fastq > f.sam 2>&1'; last output line: ''
>
> the error is not very explanatory, but basically the command-line argument
> "--db=GmapGenome.Hsapiens.**UCSC.hg19" should have been "--db=hg19". if i
> proceed that way in command-line, then it works.
>
> i've looked at the arguments of gsnap() and GsnapParam() but found no way
> to specify the genome object *name* that it would go to the "--db"
> parameter. i guess it should be a matter for the function GsnapParam() to
> fetch the prefix of the files in
>
> list.files(system.file("**extdata", package="GmapGenome.Hsapiens.**
> UCSC.hg19"))
>  [1] "hg19.chromosome"          "hg19.chromosome.iit" "hg19.chrsubset"
>       "hg19.contig"
>  [5] "hg19.contig.iit"          "hg19.genomecomp" "hg19.ref12153gammaptrs"
>   "hg19.ref12153offsetscomp"
>  [9] "hg19.ref12153positions"   "hg19.version"
>
> and plug it into the command-line call.
>
> by the way, not related but another but i incidentally found is then one
> tries to pass one *single* end read gzipped fastq file.
>
> library(LungCancerLines)
> fastqs <- LunCancerFastqFiles()
>
> gsnapOutput <- gsnap(input_a=fastqs[1], input_b=NULL, params=gsnapParam)
> Error in if (file_ext(input_a) == "gz" && file_ext(input_b) == "gz") { :
>   missing value where TRUE/FALSE needed
>
>
> cheers,
> robert.
> ps: sessionInfo()
> R version 3.0.0 (2013-04-03)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF8       LC_NUMERIC=C LC_TIME=en_US.UTF8
>  LC_COLLATE=en_US.UTF8
>  [5] LC_MONETARY=en_US.UTF8    LC_MESSAGES=en_US.UTF8    LC_PAPER=C
>       LC_NAME=C
>  [9] LC_ADDRESS=C              LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF8
> LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> base
>
> other attached packages:
>  [1] GmapGenome.Hsapiens.UCSC.hg19_**1.0.0 LungCancerLines_0.0.8
> BSgenome.Hsapiens.UCSC.hg19_1.**3.19
>  [4] BSgenome_1.28.0                     gmapR_1.2.0       ShortRead_1.18.0
>  [7] latticeExtra_0.6-24                 RColorBrewer_1.0-5
> Rsamtools_1.12.3
> [10] lattice_0.20-15                     Biostrings_2.28.0
>  GenomicRanges_1.12.3
> [13] IRanges_1.18.1                      BiocGenerics_0.6.0
>  vimcom_0.9-8
> [16] setwidth_1.0-3                      colorout_1.0-0
>
> loaded via a namespace (and not attached):
>  [1] AnnotationDbi_1.22.5    Biobase_2.20.0          biomaRt_2.16.0
> bitops_1.0-5
>  [5] DBI_0.2-7               GenomicFeatures_1.12.1  grid_3.0.0
> hwriter_1.3
>  [9] RCurl_1.95-4.1          RSQLite_0.11.3          rtracklayer_1.20.2
>    stats4_3.0.0
> [13] tools_3.0.0             VariantAnnotation_1.6.5 XML_3.96-1.1
>  zlibbioc_1.6.0
>
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