Mercurial > repos > galaxyp > custom_pro_db

comparison customProDB.R @ 5:a3a66063d460 draft

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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 19:33:53 -0400
parents bc08158abf77
children 2c7df0077d28
comparison
equal deleted inserted replaced
4:bc08158abf77 5:a3a66063d460
98 bamLink = "input.bam" 98 bamLink = "input.bam"
99 file.symlink(bam_file, bamLink) 99 file.symlink(bam_file, bamLink)
100 file.symlink(bai_file, paste(bamLink, ".bai", sep="")) 100 file.symlink(bai_file, paste(bamLink, ".bai", sep=""))
101 101
102 # load customProDB from GitHub (NOTE: downloading the zip is faster than cloning the repo with git2r or devtools::install_github) 102 # load customProDB from GitHub (NOTE: downloading the zip is faster than cloning the repo with git2r or devtools::install_github)
103 download.file("https://github.com/chambm/customProDB/archive/c57e5498392197bc598a18c26acb70d7530a921c.zip", "customProDB.zip", quiet=TRUE) 103 download.file("https://github.com/chambm/customProDB/archive/9db2223ef9932e50124b92d1bc49206af1f40fb3.zip", "customProDB.zip", quiet=TRUE)
104 unzip("customProDB.zip") 104 unzip("customProDB.zip")
105 devtools::load_all("customProDB-c57e5498392197bc598a18c26acb70d7530a921c") 105 devtools::load_all("customProDB-9db2223ef9932e50124b92d1bc49206af1f40fb3")
106 106
107 easyRun(bamFile=bamLink, vcfFile=vcf_file, annotation_path=getwd(), 107 easyRun(bamFile=bamLink, vcfFile=vcf_file, annotation_path=getwd(),
108 rpkm_cutoff=rpkmCutoff, outfile_path=".", outfile_name="output", 108 rpkm_cutoff=rpkmCutoff, outfile_path=".", outfile_name="output",
109 nov_junction=FALSE, INDEL=outputIndels, 109 nov_junction=FALSE, INDEL=outputIndels,
110 lablersid=labelrsid, COSMIC=use_cosmic) 110 lablersid=labelrsid, COSMIC=use_cosmic)