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

updated rnaseq template

parent eb3eb91a
# todo define project name # TODO define project name
export project=<<PROJECTNAME>> export project="TODO define project name"
# screen -R ${project} # screen -R ${project}
## madmax ## madmax
if [ -n "$LSF_SERVERDIR" ]; then if [ "$HOSTNAME"=="falcon1" ]; then
export baseDir="/projects/bioinfo/holger/projects/${project}" export baseDir="/projects/bioinfo/holger/projects/${project}"
export PROJECT_SCRIPTS="/projects/bioinfo/holger/scripts/${project}" export PROJECT_SCRIPTS="/projects/bioinfo/holger/scripts/${project}"
export NGS_TOOLS="/projects/bioinfo/scripts/ngs_tools/dev" export NGS_TOOLS="/projects/bioinfo/scripts/ngs_tools/dev"
...@@ -12,10 +12,9 @@ fi ...@@ -12,10 +12,9 @@ fi
## bioinfo ## bioinfo
if [ $(hostname) == "bioinformatics-srv1" ]; then if [ $(hostname) == "bioinformatics-srv1" ]; then
#<<<todo define paths on bioinfo>>> export baseDir=/net/mack/lustre/projects/bioinfo/holger/projects/${project}
#export baseDir=/home/brandl/mnt/chip-seq_study/ChIPSeq_March_2015/data export PROJECT_SCRIPTS==/net/mack/lustre/projects/bioinfo/holger/scripts/${project}
#export PROJECT_SCRIPTS=/home/brandl/mnt/chip-seq_study/ChIPSeq_March_2015/scripts export NGS_TOOLS=/net/mack/lustre/projects/bioinfo/scripts/ngs_tools/dev
export NGS_TOOLS="/home/brandl/mnt/mack/bioinfo/scripts/ngs_tools/dev"
fi fi
...@@ -23,9 +22,9 @@ source ${NGS_TOOLS}/dge_workflow/dge_utils.sh ...@@ -23,9 +22,9 @@ source ${NGS_TOOLS}/dge_workflow/dge_utils.sh
export PATH=${NGS_TOOLS}/dge_workflow:$PATH export PATH=${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=/projects/bioinfo/igenomes/Canis_familiaris/Ensembl/CanFam3.1
igenome=<<<<TBD>>>> #igenome=<<<<TBD>>>>
######################################################################################################################## ########################################################################################################################
### Fetch the data ### Fetch the data
......
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