From 2ae511c64765a32e2dd9b2336a89ff3b36164cf7 Mon Sep 17 00:00:00 2001
From: Cedric Midoux <cedric.midoux@inra.fr>
Date: Tue, 23 Feb 2021 15:22:13 +0100
Subject: [PATCH] LOGS
---
.gitignore | 4 +++-
DADA2.Rproj | 13 +++++++++++++
RunSnake.sh | 2 +-
cluster.json | 6 +++---
global.smk | 3 ++-
qsubSnake.sh | 4 ++--
6 files changed, 24 insertions(+), 8 deletions(-)
create mode 100644 DADA2.Rproj
diff --git a/.gitignore b/.gitignore
index 8d628c8..c3de72e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,5 +1,7 @@
-.log/
+LOGS/
.snakemake/
DATA/
work/
report/
+.Rproj.user
+.Rhistory
diff --git a/DADA2.Rproj b/DADA2.Rproj
new file mode 100644
index 0000000..8e3c2eb
--- /dev/null
+++ b/DADA2.Rproj
@@ -0,0 +1,13 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
diff --git a/RunSnake.sh b/RunSnake.sh
index 77636ab..b794596 100755
--- a/RunSnake.sh
+++ b/RunSnake.sh
@@ -3,7 +3,7 @@ export PYTHONPATH=''
source /usr/local/genome/Anaconda2-5.1.0/etc/profile.d/conda.sh
conda activate snakemake-5.7.4
-mkdir -p ./.log/out/ ./.log/err/
+mkdir -p LOGS/
snakemake \
--snakefile $1 \
diff --git a/cluster.json b/cluster.json
index 90ebd36..a79100f 100644
--- a/cluster.json
+++ b/cluster.json
@@ -1,9 +1,9 @@
{
"__default__" :
{
- "out" : "./.log/out/",
- "err" : "./.log/err/",
- "queue" : "short.q",
+ "out" : "LOGS/",
+ "err" : "LOGS/",
+ "queue" : "maiage.q",
"cluster" : ""
}
}
diff --git a/global.smk b/global.smk
index cff37ee..3818bb9 100644
--- a/global.smk
+++ b/global.smk
@@ -15,7 +15,8 @@ rule all:
"report/clusters_metrics.html",
"report/affiliations_metrics.html",
"report/abundance.biom",
- "report/abundance.tsv"
+ "report/abundance.tsv",
+ "report/tree.nwk"
include: "quality.smk"
include: "preprocess.smk"
diff --git a/qsubSnake.sh b/qsubSnake.sh
index c45cd04..7dc75b2 100755
--- a/qsubSnake.sh
+++ b/qsubSnake.sh
@@ -1,2 +1,2 @@
-mkdir -p ./.log/out/ ./.log/err/
-qsub -V -cwd -o ./.log/out/ -e ./.log/err/ -q maiage.q,long.q -N `basename $1` RunSnake.sh $1
+mkdir -p LOGS/
+qsub -V -cwd -o LOGS/ -e LOGS/ -q maiage.q,long.q -N `basename $1` RunSnake.sh $1
--
GitLab