Commit 6d2ae08c authored by Holger Brandl's avatar Holger Brandl
Browse files

updated rnaseq template

parent eb3eb91a
# todo define project name
export project=<<PROJECTNAME>>
# TODO define project name
export project="TODO define project name"
# screen -R ${project}
## madmax
if [ -n "$LSF_SERVERDIR" ]; then
if [ "$HOSTNAME"=="falcon1" ]; then
export baseDir="/projects/bioinfo/holger/projects/${project}"
export PROJECT_SCRIPTS="/projects/bioinfo/holger/scripts/${project}"
export NGS_TOOLS="/projects/bioinfo/scripts/ngs_tools/dev"
......@@ -12,10 +12,9 @@ fi
## bioinfo
if [ $(hostname) == "bioinformatics-srv1" ]; then
#<<<todo define paths on bioinfo>>>
#export baseDir=/home/brandl/mnt/chip-seq_study/ChIPSeq_March_2015/data
#export PROJECT_SCRIPTS=/home/brandl/mnt/chip-seq_study/ChIPSeq_March_2015/scripts
export NGS_TOOLS="/home/brandl/mnt/mack/bioinfo/scripts/ngs_tools/dev"
export baseDir=/net/mack/lustre/projects/bioinfo/holger/projects/${project}
export PROJECT_SCRIPTS==/net/mack/lustre/projects/bioinfo/holger/scripts/${project}
export NGS_TOOLS=/net/mack/lustre/projects/bioinfo/scripts/ngs_tools/dev
fi
......@@ -23,9 +22,9 @@ source ${NGS_TOOLS}/dge_workflow/dge_utils.sh
export PATH=${NGS_TOOLS}/dge_workflow:$PATH
## todo define igenome to be used
## TODO define igenome to be used
## igenome=/projects/bioinfo/igenomes/Canis_familiaris/Ensembl/CanFam3.1
igenome=<<<<TBD>>>>
#igenome=<<<<TBD>>>>
########################################################################################################################
### Fetch the data
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment