Mercurial > repos > galaxyp > custom_pro_db_annotation_data_manager

comparison data_manager/customProDB_annotation.R @ 3:9ee512decde8 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit d4b5497065b853ed094aebc9e4185e9995c5e0e0
author galaxyp
date Wed, 01 Nov 2017 19:34:06 -0400
parents 0a9ffebba65d
children
comparison
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2:0a9ffebba65d 3:9ee512decde8
88 { 88 {
89 gstop("failed to remove json params file after reading") 89 gstop("failed to remove json params file after reading")
90 }) 90 })
91 91
92 # load customProDB from GitHub (NOTE: downloading the zip is faster than cloning the repo with git2r or devtools::install_github) 92 # load customProDB from GitHub (NOTE: downloading the zip is faster than cloning the repo with git2r or devtools::install_github)
93 download.file("https://github.com/chambm/customProDB/archive/c57e5498392197bc598a18c26acb70d7530a921c.zip", "customProDB.zip", quiet=TRUE) 93 download.file("https://github.com/chambm/customProDB/archive/9db2223ef9932e50124b92d1bc49206af1f40fb3.zip", "customProDB.zip", quiet=TRUE)
94 unzip("customProDB.zip") 94 unzip("customProDB.zip")
95 devtools::load_all("customProDB-c57e5498392197bc598a18c26acb70d7530a921c") 95 devtools::load_all("customProDB-9db2223ef9932e50124b92d1bc49206af1f40fb3")
96 96
97 #suppressPackageStartupMessages(library(customProDB)) 97 #suppressPackageStartupMessages(library(customProDB))
98 options(timeout=3600) 98 options(timeout=3600)
99 99
100 # download protein and coding sequences for UCSC annotation 100 # download protein and coding sequences for UCSC annotation