From e7214d8a8ff1d9ac3c850224a4c4ae43a5c733d7 Mon Sep 17 00:00:00 2001
From: Paul Harrison <paul.harrison@monash.edu>
Date: Fri, 6 Oct 2017 14:23:46 +1100
Subject: [PATCH] Fix R problem with empty data

---
 .gitignore                    |  2 ++
 nesoni/nesoni-r/DESCRIPTION   | 12 ++++++++++--
 nesoni/nesoni-r/R/counts.R    |  4 ++++
 nesoni/nesoni-r/R/fitnoise.R  |  6 +++---
 nesoni/reference_directory.py |  8 ++++----
 5 files changed, 23 insertions(+), 9 deletions(-)

diff --git a/.gitignore b/.gitignore
index 36e098d..2ee26d7 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,3 +6,5 @@ dist/*
 test/.state/*
 doc/_*
 nesoni.egg-info
+*.sublime-*
+
diff --git a/nesoni/nesoni-r/DESCRIPTION b/nesoni/nesoni-r/DESCRIPTION
index ff7f7ac..57eb9d3 100644
--- a/nesoni/nesoni-r/DESCRIPTION
+++ b/nesoni/nesoni-r/DESCRIPTION
@@ -5,5 +5,13 @@ Title: Nesoni R component
 Description: The R component of the Nesoni toolsuite.
 Author: Paul Harrison
 Maintainer: Paul Harrison <paul.harrison@monash.edu>
-Depends: limma, edgeR, Matrix, parallel
-Suggests: goseq, seriation, NMF
\ No newline at end of file
+Depends:
+    limma, 
+    edgeR, 
+    Matrix, 
+    parallel
+Suggests: 
+    goseq, 
+    seriation, 
+    NMF,
+    varistran
diff --git a/nesoni/nesoni-r/R/counts.R b/nesoni/nesoni-r/R/counts.R
index d7125cc..bdc705a 100644
--- a/nesoni/nesoni-r/R/counts.R
+++ b/nesoni/nesoni-r/R/counts.R
@@ -10,6 +10,10 @@ read.counts <- function(filename, min.total=0, min.max=0, keep=NULL, norm.file=N
     
     data <- read.grouped.table(filename, require=c('Count'), default.group='Count')
     counts <- as.matrix( data$Count )
+
+    # Can happen with empty data
+    if (storage.mode(counts) == "logical")
+        storage.mode(counts) <- "numeric"
     
     gene <- data.frame(row.names=rownames(counts), locus_tag=rownames(counts))
     
diff --git a/nesoni/nesoni-r/R/fitnoise.R b/nesoni/nesoni-r/R/fitnoise.R
index 959413c..14da00a 100644
--- a/nesoni/nesoni-r/R/fitnoise.R
+++ b/nesoni/nesoni-r/R/fitnoise.R
@@ -7,9 +7,9 @@
 #
 #
 
-library(Matrix)
-library(limma)  # EList class, p.adjust
-library(parallel)
+#library(Matrix)
+#library(limma)  # EList class, p.adjust
+#library(parallel)
 
 
 ##################################
diff --git a/nesoni/reference_directory.py b/nesoni/reference_directory.py
index 3487c0c..1f9ac2d 100644
--- a/nesoni/reference_directory.py
+++ b/nesoni/reference_directory.py
@@ -214,14 +214,14 @@ def run(self):
             reference.set_annotations(annotations)
         
         with legion.Stage() as stage:
+            if self.genome:
+                stage.process(reference.build_genome, self.genome_select)
+            if config.apply_ifavailable_program(self.bowtie, 'bowtie2-build'):
+                stage.process(reference.build_bowtie_index)
             if config.apply_ifavailable_program(self.ls, 'gmapper-ls'):
                 stage.process(reference.build_shrimp_mmap, False)
             if config.apply_ifavailable_program(self.cs, 'gmapper-cs'):
                 stage.process(reference.build_shrimp_mmap, True)
-            if config.apply_ifavailable_program(self.bowtie, 'bowtie2-build'):
-                stage.process(reference.build_bowtie_index)
-            if self.genome:
-                stage.process(reference.build_genome, self.genome_select)
             if config.apply_ifavailable_jar(self.snpeff, 'snpEff.jar'):
                 stage.process(reference.build_snpeff)