Missing dependency on optparse

jbedo commented 5 years ago

PureCN has a dependency on optparse which is unstated:

$ Rscript PureCN.R
Error in library(optparse) : there is no package called ‘optparse’

lima1 commented 5 years ago

Hi Justin,

it's specified as suggested dependency, because it's not needed by the main package, "only" the command line tools.

But since the CLI is now recommended, I will add installation instructions to the Quick Vignette that automatically installs those requirements (for example: BiocManager::install("PureCN", dependencies=TRUE)).

Thanks a lot, Markus

jbedo commented 5 years ago

Thanks for the clarification.

fi1d18 commented 11 months ago

Having this already installed, I get the same error

lima1 commented 11 months ago

BiocManager::install(c("optparse", "R.utils", "TxDb.Hsapiens.UCSC.hg19.knownGene", "org.Hs.eg.db"))

Change to hg38 if necessary.

https://bioconductor.org/packages/devel/bioc/vignettes/PureCN/inst/doc/Quick.html

fi1d18 commented 11 months ago

Thanks for answering me and sorry for this weird email/request, in advance;

Please, do you have access to GDC portal?

I am trying to run mutect2 in tumor-only mode on my WES data for which I need a panel of normal (PON)

I have tried

@.***:/data/Continuum/WES/vcf$ ./gatk Mutect2 -R resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta -I PicMD.bam -O 3.mt2.vcf -tumor PicMD.targeted_sequencing.sample_name --af-of-alleles-not-in-resource 2.5e-06 --germline-resource af-only-gnomad.hg38.vcf.gz -pon somatic-hg38_1000g_pon.hg38.vcf.vcf

Which says

A USER ERROR has occurred: Cannot read file:///data/somatic-hg38_1000g_pon.hg38.vcf.vcf because no suitable codecs found

I know gatk4_mutect2_4136_pon.vcf.gz in the GDC tutorial locates here

https://gdc.cancer.gov/about-data/gdc-data-processing/gdc-reference-files

I have tried

@.***:/data/Continuum/WES/vcf$ ./gdc-client download 6c4c4a48-3589-4fc0-b1fd-ce56e88c06e4 -t token.txt

[Errno 2] No such file or directory: '/data/Continuum/WES/vcf/token.txt'

That means I have to register to GDC but postdoctoral researchers can not register

Do you have access to gatk4_mutect2_4136_pon.vcf.gz file please?

If no, do you know how to push mutect2 run with another PON?

Thanks for any help

From: Markus Riester @.> Sent: Wednesday, 16 August 2023 00:44 To: lima1/PureCN @.> Cc: Angel Izadi @.>; Comment @.> Subject: Re: [lima1/PureCN] Missing dependency on optparse (#64)

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BiocManager::install(c("optparse", "R.utils", "TxDb.Hsapiens.UCSC.hg19.knownGene", "org.Hs.eg.db"))

Change to hg38 if necessary.

https://bioconductor.org/packages/devel/bioc/vignettes/PureCN/inst/doc/Quick.html

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lima1 / PureCN

Missing dependency on optparse #64