comparison PSM2SAM.R @ 2:757ecf27b4a9 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 969036a4673f5565185badb0d4fe513a7b784261
author galaxyp
date Mon, 25 Sep 2017 13:23:54 -0400
parents 90ecb65017a0
children 16c4cc7793e9
comparison
equal deleted inserted replaced
1:3192cb6a88f6 2:757ecf27b4a9
51 { 51 {
52 stop("failed to read header lines from bam_file") 52 stop("failed to read header lines from bam_file")
53 } 53 }
54 54
55 # load customProDB from GitHub (NOTE: downloading the zip is faster than cloning the repo with git2r or devtools::install_github) 55 # load customProDB from GitHub (NOTE: downloading the zip is faster than cloning the repo with git2r or devtools::install_github)
56 download.file("https://github.com/chambm/customProDB/archive/master.zip", "customProDB.zip", quiet=TRUE) 56 download.file("https://github.com/chambm/customProDB/archive/c57e5498392197bc598a18c26acb70d7530a921c.zip", "customProDB.zip", quiet=TRUE)
57 unzip("customProDB.zip") 57 unzip("customProDB.zip")
58 devtools::load_all("customProDB-master") 58 devtools::load_all("customProDB-c57e5498392197bc598a18c26acb70d7530a921c")
59 59
60 # load proBAMr from GitHub 60 # load proBAMr from GitHub
61 download.file("https://github.com/chambm/proBAMr/archive/master.zip", "proBAMr.zip", quiet=TRUE) 61 download.file("https://github.com/chambm/proBAMr/archive/a03edf68f51215be40717c5374f39ce67bd2e68b.zip", "proBAMr.zip", quiet=TRUE)
62 unzip("proBAMr.zip") 62 unzip("proBAMr.zip")
63 devtools::load_all("proBAMr-master") 63 devtools::load_all("proBAMr-a03edf68f51215be40717c5374f39ce67bd2e68b")
64 64
65 psmInputLength = length(idpDB_file)+length(pepXmlTab_file)+length(peptideShakerPsmReport_file) 65 psmInputLength = length(idpDB_file)+length(pepXmlTab_file)+length(peptideShakerPsmReport_file)
66 if (psmInputLength == 0) 66 if (psmInputLength == 0)
67 { 67 {
68 stop("one of the input PSM file parameters must be specified") 68 stop("one of the input PSM file parameters must be specified")