v18 gene expression

Author: brettbj

.drone.sec

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+eyJhbGciOiJSU0EtT0FFUCIsImVuYyI6IkExMjhHQ00ifQ.s4vyZap4533o0ytFth_U2t6C2PSsK0YkdI05DwowiUS5_n2btcw7oIg6lOc4h-pIAUsxRwZ6fW5OaJ-30IukOitS1y4m0m2kG4SN9FDVhtsICyhMEft3R7r32DJFpo-gw2ryZ9RLSFMFEfFjfJKgC3v587M4A36U0IlwjgsgO5dkVP9HNxVUKVPpGo3kVPjLp34dkwCp2B4ZPC-Rb3VRe9UwwA9Tb9zijX-RsTm0xYft8-28_6XLhO_bbG7mbCh_dddnuEO35ETl_xm__UOV9SNOghOWzNRSgljV4NjOSkigJ0W47kTCXU3d9hnwxovRFL7DRm9cWSTWLP-WlHVm_w.3s2vMZibqKq0bwJC.YjyyItUW-j_s2MQv-SKucEHB3XwnouCdAP4OxLTYP6MBXkdKnWqwIQdFBl7LmqyhC8ajpV3IWtdgzKDmhGGtaDsSz_6RiaFd.SGVrjmJi-MkwRbnOXb4wFA

.drone.yml

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+build:
+  image: brettbj/continuous_analysis_brainarray_v18
+  commands:
+    - git status
+    - tar -xvf /data/GSE47664_RAW.tar 
+    - Rscript r_script.r
+
+    - cd /drone/src/github.com/greenelab/continuous_analysis_brainarray
+    - mkdir -p results
+    - mv output.csv results/output.csv
+    - mv truncated_output.csv results/truncated_output.csv
+
+    - git config user.email "[email protected]"
+    - git config user.name "Brett Beaulieu-Jones"
+    - git config --global push.default simple
+    - git remote set-url origin https://github.com/greenelab/continuous_analysis_brainarray.git
+
+    - git checkout master
+    - git remote set-url origin https://brettbj:[email protected]/greenelab/continuous_analysis_brainarray.git
+    - git fetch
+    - git branch --set-upstream-to=origin/master master
+    - git pull
+    - git add results
+    - git commit -a -m "Drone Build [skip ci] [ci skip]"
+    - git push 
+
+branches:
+  - staging
+

r_script.r

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+packageVersion("hgu133plus2hsentrezgcdf")
+library(affy)
+CELs.entrezgene = ReadAffy(cdfname="hgu133plus2hsentrezgcdf")
+eset.entrezgene = rma(CELs.entrezgene)
+rma.exprs <- exprs(eset.entrezgene)
+
+library(multtest)
+
+groups=c(1, 1, 1, 0, 0, 0)
+stats=mt.teststat(rma.exprs, groups, test="t")
+rawp=2*(1-pnorm(abs(stats)))
+adjp=p.adjust(rawp, method="bonferroni")
+arraysRMAstats=cbind(rma.exprs[-1,0], adjp)
+trunc_stats = head(arraysRMAstats, n=100)
+
+write.table(trunc_stats, file="truncated_output.csv", sep=",", col.names = FALSE)
+write.table(arraysRMAstats, file="output.csv", sep=",", col.names = FALSE)

v18/Dockerfile

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+FROM ubuntu:14.04
+MAINTAINER Brett Beaulieu-Jones
+
+RUN apt-get update
+
+RUN apt-get -y install r-base r-recommended r-base-dev
+RUN apt-get -y install wget
+
+RUN Rscript -e 'source("http://bioconductor.org/biocLite.R"); biocLite(c("multtest", "affy", "AnnotationDbi"))'
+
+RUN mkdir -p /data/
+RUN wget -q http://mbni.org/customcdf/18.0.0/entrezg.download/hgu133plus2hsentrezgcdf_18.0.0.tar.gz -P /data
+RUN R CMD INSTALL /data/hgu133plus2hsentrezgcdf_18.0.0.tar.gz 
+
+RUN wget -q ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE47nnn/GSE47664/suppl/GSE47664_RAW.tar -P /data
+

v19/Dockerfile

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+FROM ubuntu:14.04
+MAINTAINER Brett Beaulieu-Jones
+
+RUN apt-get update
+
+RUN apt-get -y install r-base r-recommended r-base-dev
+RUN apt-get -y install wget
+
+RUN Rscript -e 'source("http://bioconductor.org/biocLite.R"); biocLite(c("multtest", "affy", "AnnotationDbi"))'
+
+RUN mkdir -p /data/
+RUN wget -q http://mbni.org/customcdf/19.0.0/entrezg.download/hgu133plus2hsentrezgcdf_19.0.0.tar.gz -P /data
+RUN R CMD INSTALL /data/hgu133plus2hsentrezgcdf_19.0.0.tar.gz 
+
+RUN wget -q ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE47nnn/GSE47664/suppl/GSE47664_RAW.tar -P /data
+

v20/Dockerfile

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+FROM ubuntu:14.04
+MAINTAINER Brett Beaulieu-Jones
+
+RUN apt-get update
+
+RUN apt-get -y install r-base r-recommended r-base-dev
+RUN apt-get -y install wget
+
+RUN Rscript -e 'source("http://bioconductor.org/biocLite.R"); biocLite(c("multtest", "affy", "AnnotationDbi"))'
+
+RUN mkdir -p /data/
+RUN wget -q http://mbni.org/customcdf/20.0.0/entrezg.download/hgu133plus2hsentrezgcdf_20.0.0.tar.gz -P /data
+RUN R CMD INSTALL /data/hgu133plus2hsentrezgcdf_20.0.0.tar.gz 
+
+RUN wget -q ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE47nnn/GSE47664/suppl/GSE47664_RAW.tar -P /data
+