Mercurial > repos > galaxyp > custom_pro_db
comparison customProDB.R @ 6:2c7df0077d28 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 380011a7d342f3c7a2780dfa841adca1f6df1d30
| author | galaxyp |
|---|---|
| date | Fri, 22 Feb 2019 02:13:31 -0500 |
| parents | a3a66063d460 |
| children |
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| 5:a3a66063d460 | 6:2c7df0077d28 |
|---|---|
| 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/9db2223ef9932e50124b92d1bc49206af1f40fb3.zip", "customProDB.zip", quiet=TRUE) | 103 download.file("https://github.com/chambm/customProDB/archive/13cbebf9e3f26507afbbb661c9e985da2fd0840a.zip", "customProDB.zip", quiet=TRUE) |
| 104 unzip("customProDB.zip") | 104 unzip("customProDB.zip") |
| 105 devtools::load_all("customProDB-9db2223ef9932e50124b92d1bc49206af1f40fb3") | 105 devtools::load_all("customProDB-13cbebf9e3f26507afbbb661c9e985da2fd0840a") |
| 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) |