## Claim: this is my personal trick. I recommend people to subscribe their KEGG FTP download to support the authors.
# change folder to the folder where your SPIA installed
cd /Library/Frameworks/R.framework/Versions/3.4/Resources/library/SPIA
# download all XML files for all human pathway
curl -s http://rest.kegg.jp/list/pathway/hsa | awk '{split($1,a,":"); print "curl -s http://rest.kegg.jp/get/"a[2]"/kgml -o extdata/keggxml/hsa/"a[2]".xml"}' | bash
# then switch to R console
setwd("/Library/Frameworks/R.framework/Versions/3.4/Resources/library/SPIA")
library(SPIA)
makeSPIAdata(kgml.path=system.file("extdata/keggxml/hsa",package="SPIA"),organism="hsa",out.path="./extdata")
Done!
Hello,
ReplyDeletewhen I do it in my terminal... it prints it on the top frame of the window but nothing is downloaded. I would appreciate your help.
I am using a mac os 10.11.6 and tbh I don't much about unix but I am using the terminal that comes with the mac.
Thank you,
Vivian
HI Vivian. Thanks for showing interest of my tips. Can you please copy the message from your terminal when you enter the commands? It's OK to use the terminal coming with Mac.
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