User: Jim Hester

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Jim Hester10
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Posts by Jim Hester

<prev • 3 results • page 1 of 1 • next >
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Comment: C: Recommended way to use BiocInstaller / BiocManager in packages on CRAN?
... CRAN does allow you to have BiocInstaller in Suggests, this is what I am doing in devtools, and did not receive this note from Prof. Ripley for devtools. However this means all packages that wish to support R < 3.5 need to include code to conditionally use either BiocManager or BiocInstaller dep ...
written 12 months ago by Jim Hester10
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Comment: C: How to automate a process on the command line for 1500 genes?
... I forgot bash doesn't support nested substitutions like zsh. In bash you have to do it in two steps, for file in *gff;do temp=${file##aa_bb_cc_dd_} gene=${temp%.gff} echo program.sh $file ../../../unchanged_file.txt $gene $file $gene.bed done I have updated my answer appropriately, if i ...
written 4.2 years ago by Jim Hester10
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Answer: A: How to automate a process on the command line for 1500 genes?
... Note you can do this using R as well, the system() function can call any 'command line' program.  Remove the echo from the examples to actually call program.sh gffs <- list.files(pattern="gff$", full.names = TRUE) lapply(gffs, function(file) { gene <- gsub(".*aa_bb_cc_dd_(.*).gff$", "\\1 ...
written 4.3 years ago by Jim Hester10

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Scholar 4.1 years ago, created an answer that has been accepted. For A: How to automate a process on the command line for 1500 genes?

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