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bioinfo
ngs_tools
Commits
6d2ae08c
Commit
6d2ae08c
authored
Mar 02, 2017
by
Holger Brandl
Browse files
updated rnaseq template
parent
eb3eb91a
Changes
1
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Inline
Side-by-side
dge_workflow/dge_star_template.sh
View file @
6d2ae08c
#
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
...
...
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