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hansenlab / RecountGenotyper

Genotype calling from Recount3 RNA-seq data.
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Specify dependency for zstdcat #10

Closed caalo closed 1 year ago

caalo commented 1 year ago

The software zstdcat is used in GetMandS() but is not a default software outside of JHPCE cluster. For computers without zstdcat, we get the following error:

> test_geno<-GetMandS(snps_gr, bigWig_path, alt_path, sample_id_rep, temp_folder)
Loading in:  /Users/clo2/Documents/RecountGenotyper/inst/extdata/test.bw 
Loading in:  test 
sh: zstdcat: command not found
Warning messages:
1: In system(paste0("zstdcat ", alt_path, " > ", temp_altFile)) :
  error in running command
2: In data.table::fread(temp_altFile, select = c(1, 2, 4)) :
  File '/var/folders/2v/0x2zqrfs0pj9nqgmdv3v8n5r0000gp/T//RtmpOkpztq~.alt.temp.csv' has size 0. Returning a NULL data.table.

Mac users can install it via brew here: https://formulae.brew.sh/formula/zstd

I recommend catching this error message and print a statement telling the user what software is missing, and/or write down the dependency in the README.

kasperdanielhansen commented 1 year ago

You can also execute something like system("zstdcat -v") and check if that runs without error to simulate an installation check (assuming that zstdcat supports -v; otherwise use another flag like -h or --help or --version)

On Fri, Sep 8, 2023 at 10:36 PM Chris Lo @.***> wrote:

The software zstdcat is used in GetMandS() but is not a default software outside of JHPCE cluster. For computers without zstdcat, we get the following error:

test_geno<-GetMandS(snps_gr, bigWig_path, alt_path, sample_id_rep, temp_folder) Loading in: /Users/clo2/Documents/RecountGenotyper/inst/extdata/test.bw Loading in: test sh: zstdcat: command not found Warning messages: 1: In system(paste0("zstdcat ", alt_path, " > ", temp_altFile)) : error in running command 2: In data.table::fread(temp_altFile, select = c(1, 2, 4)) : File '/var/folders/2v/0x2zqrfs0pj9nqgmdv3v8n5r0000gp/T//RtmpOkpztq~.alt.temp.csv' has size 0. Returning a NULL data.table.

Mac users have to install it via brew here: https://formulae.brew.sh/formula/zstd

I recommend catching this error message and print a statement telling the user what software is missing, and/or write down the dependency in the README.

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-- Best, Kasper