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BICF
Astrocyte
chipseq_analysis
Commits
08d9f08a
Commit
08d9f08a
authored
Apr 17, 2020
by
Venkat Malladi
Browse files
Fix parsing of options and spacing.
parent
54b9865d
Changes
1
Hide whitespace changes
Inline
Side-by-side
workflow/scripts/plot_profile.sh
View file @
08d9f08a
...
...
@@ -18,15 +18,15 @@ raise()
}
check_tools
()
{
raise
"
raise
"
Checking for required libraries and components on this system
"
deeptools
--version
&> version_deeptools.txt
if
[
$?
-gt
0
]
then
raise
"Missing deeptools"
return
1
fi
deeptools
--version
&> version_deeptools.txt
if
[
$?
-gt
0
]
then
raise
"Missing deeptools"
return
1
fi
}
compute_matrix
()
{
...
...
@@ -34,13 +34,13 @@ compute_matrix() {
Computing matrix on
${
1
}
using
${
2
}
"
computeMatrix reference-point
\
--referencePoint
TSS
\
-S
${
1
}
\
-R
${
2
}
\
--skipZeros
\
-o
computeMatrix.gz
\
-p
max/2
computeMatrix reference-point
\
--referencePoint
TSS
\
-S
${
1
}
\
-R
${
2
}
\
--skipZeros
\
-o
computeMatrix.gz
\
-p
max/2
if
[
$?
-gt
0
]
then
...
...
@@ -54,8 +54,8 @@ plot_profile() {
Plotting profile
"
plotProfile
-m
computeMatrix.gz
\
-out
plotProfile.png
plotProfile
-m
computeMatrix.gz
\
-out
plotProfile.png
if
[
$?
-gt
0
]
then
...
...
@@ -69,7 +69,7 @@ run_main() {
# Parsing options
OPTIND
=
1
# Reset OPTIND
while
getopts
:gh opt
while
getopts
:g
:
h opt
do
case
$opt
in
g
)
gtf
=
$OPTARG
;;
...
...
@@ -84,20 +84,20 @@ run_main() {
usage
fi
bws
=
$(
ls
*
.bw
)
bws
=
$(
ls
*
.bw
)
check_tools
||
exit
1
compute_matrix
"
${
bws
}
"
"
${
gtf
}
"
||
return
1
compute_matrix
"
${
bws
}
"
"
${
gtf
}
"
||
return
1
plot_profile
||
return
1
plot_profile
||
return
1
raise
"ALL COMPLETE"
}
if
[[
"
${
BASH_SOURCE
[0]
}
"
==
"
${
0
}
"
]]
then
run_main
run_main
"
$@
"
if
[
$?
-gt
0
]
then
exit
1
...
...
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