Merge pull request #92 from drpatelh/master

Test using .Rprofile in container
nf-core · Mar 11, 2020 · 09b89d7 · 09b89d7
2 parents 3541076 + 1629267
commit 09b89d7
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Showing 4 changed files with 7 additions and 3 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -13,7 +13,6 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 * [#76](https://github.com/nf-core/atacseq/issues/76) - featureCounts coupled to DESeq2
 * [#79](https://github.com/nf-core/atacseq/issues/79) - Parallelize DESeq2
 * [#80](https://github.com/nf-core/atacseq/pull/80) - Added social preview image
-
 * Update template to tools `1.9`
 * Parameter `--skip_consensus_peaks` to skip consensus peak generation
 
@@ -22,6 +21,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 * [nf-core/chipseq#118](https://github.com/nf-core/chipseq/issues/118) - Running on with SGE
 * [nf-core/chipseq#132](https://github.com/nf-core/chipseq/issues/132) - BigWig Error: sort: cannot create temporary file in '': Read-only file system
 * [#73](https://github.com/nf-core/atacseq/issues/73) - macs_annotatePeaks.mLb.clN.summary.txt file is not created
+* [#86](https://github.com/nf-core/atacseq/issues/86) - bug in the plot_homer_annotatepeaks.r script
 * Make executables in `bin/` compatible with Python 3
 
 ### `Dependencies`

diff --git a/Dockerfile b/Dockerfile
@@ -11,3 +11,6 @@ ENV PATH /opt/conda/envs/nf-core-atacseq-1.1.1dev/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
 RUN conda env export --name nf-core-atacseq-1.1.1dev > nf-core-atacseq-1.1.1dev.yml
+
+# Instruct R processes to use this empty file instead of clashing with a local version
+RUN touch .Rprofile
diff --git a/bin/plot_homer_annotatepeaks.r b/bin/plot_homer_annotatepeaks.r
@@ -57,7 +57,7 @@ plot.feature.dat <- data.frame()
 for (idx in 1:length(HomerFiles)) {
 
     sampleid = SampleIDs[idx]
-    anno.dat <- read.table(HomerFiles[idx], sep="\t", header=TRUE,quote="")
+    anno.dat <- read.csv(HomerFiles[idx], sep="\t", header=TRUE)
     anno.dat <- anno.dat[,c("Annotation","Distance.to.TSS","Nearest.PromoterID")]
 
     ## REPLACE UNASSIGNED FEATURE ENTRIES WITH SENSIBLE VALUES

diff --git a/nextflow.config b/nextflow.config
@@ -127,9 +127,10 @@ if (!params.igenomes_ignore) {
 // Increase time available to build conda environment
 conda { createTimeout = "60 min" }
 
-// Export this variable to prevent local Python libraries from conflicting with those in the container
+// Export these variables to prevent local Python/R libraries from conflicting with those in the container
 env {
   PYTHONNOUSERSITE = 1
+  R_PROFILE_USER = "~/.Rprofile"
 }
 
 // Capture exit codes from upstream processes when piping