From a136d04202649b74affc1603f3114e0f146ff3c5 Mon Sep 17 00:00:00 2001
From: Holger Brandl <holgerbrandl@gmail.com>
Date: Thu, 25 Feb 2016 09:32:13 +0100
Subject: [PATCH] tweaked bin-paths
---
dge_workflow/dge_utils.sh | 8 ++++----
dge_workflow/featcounts_deseq.R | 4 ++--
2 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/dge_workflow/dge_utils.sh b/dge_workflow/dge_utils.sh
index d82dfe8..2a8f67c 100755
--- a/dge_workflow/dge_utils.sh
+++ b/dge_workflow/dge_utils.sh
@@ -5,11 +5,11 @@
#source <(curl https://raw.githubusercontent.com/holgerbrandl/datautils/v1.20/bash/lsf_utils.sh 2>&1 2>/dev/null)
## enable snippet spinning
-source <(curl https://raw.githubusercontent.com/holgerbrandl/datautils/v1.20/R/spinr/spin_utils.sh 2>&1 2>/dev/null)
-export PATH=/home/brandl/bin/spinr:$PATH
+source <(curl https://raw.githubusercontent.com/holgerbrandl/datautils/v1.22/R/spinr/spin_utils.sh 2>&1 2>/dev/null)
+export PATH=/projects/bioinfo/holger/bin//spinr:$PATH
source <(curl https://raw.githubusercontent.com/holgerbrandl/datautils/v1.20/R/rendr/rendr_utils.sh 2>&1 2>/dev/null)
-export PATH=/home/brandl/bin/rendr:$PATH
+export PATH=/projects/bioinfo/holger/bin//rendr:$PATH
## define common binaries
@@ -18,7 +18,7 @@ export PATH=/projects/bioinfo/holger/bin/bowtie2-2.2.5:$PATH
export PATH=/projects/bioinfo/holger/bin/tophat-2.0.13.Linux_x86_64:$PATH
export PATH=/home/brandl/bin/cufflinks-2.2.1.Linux_x86_64:$PATH
export PATH=/sw/apps/python/current/bin:$PATH
-export PATH=/home/brandl/bin/deepTools/bin:$PATH
+export PATH=/projects/bioinfo/holger/bin/deepTools/bin:$PATH
export PATH=/projects/bioinfo/holger/bin/FastQC_0.11.2:$PATH
export PATH=/projects/bioinfo/holger/bin/bedtools2-2.25.0/bin/:$PATH
export PATH=/projects/bioinfo/holger/bin/samtools-1.3:$PATH
diff --git a/dge_workflow/featcounts_deseq.R b/dge_workflow/featcounts_deseq.R
index 157c0a7..4926141 100755
--- a/dge_workflow/featcounts_deseq.R
+++ b/dge_workflow/featcounts_deseq.R
@@ -126,8 +126,8 @@ if(!all((contrasts %>% gather %$% value %>% unique) %in% colData$condition)){
#stopifnot(all((contrasts %>% gather %$% value %>% unique) %in% colData$condition))
dds <- DESeqDataSetFromMatrix(countMatrix, colData, formula(~ condition))
-dds <- estimateSizeFactors(dds)
-dds <- estimateDispersions(dds)
+#dds <- estimateSizeFactors(dds)
+#dds <- estimateDispersions(dds)
########################################################################################################################
--
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