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Use GATK R Library (gsalib), Location and is a tarball available?

siemienisiemieni University of MichiganMember

I am trying to locate the gsalib R library. I am trying to run BaseRecalibrator and unable to generate the PDF due to a missing library. In your post#822 dated October 22, you stated that to download the source file from the download web page. Unfortunately, only the binaries are available from the download web page. Is there any way I can get the compressed tar file to install into our R version.

Thanks,
Dave S.

DEBUG 10:51:50,826 RScriptExecutor - Executing:
DEBUG 10:51:50,826 RScriptExecutor - Rscript
DEBUG 10:51:50,827 RScriptExecutor - -e
DEBUG 10:51:50,827 RScriptExecutor - tempLibDir = '/tmp/Rlib.2413693695421144674';source('/tmp/BQSR.6592442160016929358.R');
DEBUG 10:51:50,827 RScriptExecutor - /tmp/BQSR494718537711837890.csv
DEBUG 10:51:50,827 RScriptExecutor - /home/ginsburg_lab/club_house/run_214_analysis_3/test_sampe_sort_nodups_CovarTable_recal_plot.grp
DEBUG 10:51:50,827 RScriptExecutor - /home/ginsburg_lab/club_house/run_214_analysis_3/test_sampe_sort_nodups_CovarTable_recal.pdf
Loading required package: methods
Loading required package: gtools
Loading required package: gdata
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.

gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.

Attaching package: ‘gdata’

The following object(s) are masked from ‘package:stats’:

nobs

The following object(s) are masked from ‘package:utils’:

object.size

Loading required package: caTools
Loading required package: bitops
Loading required package: grid
Loading required package: KernSmooth
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Loading required package: MASS

Attaching package: ‘gplots’

The following object(s) are masked from ‘package:stats’:

lowess

Loading required package: plyr

Attaching package: ‘reshape’

The following object(s) are masked from ‘package:plyr’:

rename, round_any

Error in library(gsalib) : there is no package called ‘gsalib’

Answers

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