Mercurial > repos > galaxyp > custom_pro_db_annotation_data_manager
comparison data_manager/customProDB_annotation.R @ 3:9ee512decde8 draft default tip
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 |
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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 |