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Holland Computing Center
chipathlon
Commits
faac4939
Commit
faac4939
authored
Jun 09, 2017
by
aknecht2
Browse files
Fixed lots of minor bugs to make sure the workflow actually generates! Running tests now.
parent
d0f38192
Changes
13
Hide whitespace changes
Inline
Side-by-side
chipathlon/conf.py
View file @
faac4939
...
...
@@ -69,8 +69,8 @@ executables = [
"chip-job-peakranger-format"
,
"chip-job-sort-peak"
,
"chip-job-zcat-peak"
,
"chip-job-zerone-
add-cols
"
,
"chip-job-hd-
add-cols
"
"chip-job-zerone-
format
"
,
"chip-job-hd-
format
"
]
# Java needs to have -Xmx specified...
...
...
chipathlon/generators/peak_call_generator.py
View file @
faac4939
...
...
@@ -161,8 +161,7 @@ class PeakCallGenerator(ModuleGenerator):
"control.bam"
:
call_pair
[
0
].
full_name
,
"signal.bam"
:
call_pair
[
1
].
full_name
}
additional_inputs
=
{}
return
(
self
.
get_markers
(
run
),
inputs
,
additional_inputs
)
return
(
self
.
get_markers
(
run
),
inputs
)
def
_hiddendomains
(
self
,
run
,
result
):
"""
...
...
@@ -178,8 +177,7 @@ class PeakCallGenerator(ModuleGenerator):
"signal.bed"
:
call_pair
[
1
].
full_name
,
"prefix"
:
result
.
prefix
}
additional_inputs
=
{}
return
(
self
.
get_markers
(
run
),
inputs
,
additional_inputs
)
return
(
self
.
get_markers
(
run
),
inputs
)
def
_pepr
(
self
,
run
,
result
):
"""
...
...
@@ -195,8 +193,7 @@ class PeakCallGenerator(ModuleGenerator):
"prefix"
:
result
.
prefix
,
"peak_type"
:
run
.
peak_type
}
additional_inputs
=
{}
return
(
self
.
get_markers
(
run
),
inputs
,
additional_inputs
)
return
(
self
.
get_markers
(
run
),
inputs
)
def
_make_call_pairs
(
self
,
run
,
result_list
):
"""
...
...
chipathlon/jobs/modules/peak_call.yaml
View file @
faac4939
...
...
@@ -337,7 +337,7 @@ peak_call:
chrom.sizes
:
param_name
:
chrom_sizes
prefix
:
type
:
string
param_name
:
prefix
outputs
:
result.bed
:
param_name
:
result_peaks
...
...
@@ -352,10 +352,10 @@ peak_call:
-
hiddendomains_format
:
inputs
:
result.bed
:
type
:
file
param_name
:
result_peaks
outputs
:
results_sorted.bed
:
type
:
file
param_name
:
full_result
final_result
:
true
-
pepr[tool]
:
-
pepr_callpeak
:
...
...
chipathlon/jobs/params/hiddendomains_callpeak.yaml
View file @
faac4939
...
...
@@ -23,11 +23,11 @@ hiddendomains_callpeak:
file_type
:
txt
control_bins
:
type
:
file
file_type
:
b
xt
file_type
:
t
xt
treatment_bins
:
type
:
file
file_type
:
txt
command
:
hidden
d
omains
command
:
hidden
D
omains
arguments
:
-
"
-B"
:
type
:
string
...
...
@@ -53,7 +53,7 @@ hiddendomains_callpeak:
has_value
:
true
default
:
"
$chrom_sizes"
-
"
-o"
:
type
:
file
type
:
string
changeable
:
false
required
:
true
has_value
:
true
...
...
chipathlon/jobs/params/hiddendomains_format.yaml
View file @
faac4939
...
...
@@ -3,7 +3,6 @@ hiddendomains_format:
result_peaks
:
type
:
file
file_type
:
bed
additional_inputs
:
null
outputs
:
full_result
:
type
:
file
...
...
chipathlon/jobs/params/pepr_callpeak.yaml
View file @
faac4939
...
...
@@ -17,7 +17,7 @@ pepr_callpeak:
pepr_params
:
type
:
file
file_type
:
txt
command
:
pep
r
command
:
PeP
r
arguments
:
-
"
-c"
:
type
:
list
...
...
@@ -38,7 +38,7 @@ pepr_callpeak:
-
$signal.bed
-
$signal.bed
-
"
-n"
:
type
:
file
type
:
string
changeable
:
true
required
:
true
has_value
:
true
...
...
chipathlon/jobs/wrappers/hiddendomains_wrapper.sh
deleted
100755 → 0
View file @
d0f38192
#!/bin/bash
.
/util/opt/lmod/lmod/init/profile
module load hiddendomains/2.3
hiddenDomains
"
$@
"
chipathlon/jobs/wrappers/pepr_wrapper.sh
deleted
100755 → 0
View file @
d0f38192
#!/bin/bash
.
/util/opt/lmod/lmod/init/profile
module load pepr/1.1
PePr
"
$@
"
chipathlon/jobs/wrappers/picard_wrapper.sh
deleted
100755 → 0
View file @
d0f38192
#!/bin/bash
#set -eu -o pipefail
#set -o pipefail
.
/util/opt/lmod/lmod/init/profile
module load picard/2.9
# Use Java installed with Anaconda to ensure correct version
java
=
"
$ENV_PREFIX
/bin/java"
# if JAVA_HOME is set (non-empty), use it. Otherwise keep "java"
if
[
!
-z
"
${
JAVA_HOME
:
=
}
"
]
;
then
if
[
-e
"
$JAVA_HOME
/bin/java"
]
;
then
java
=
"
$JAVA_HOME
/bin/java"
fi
fi
picard
"
$@
"
chipathlon/jobs/wrappers/zerone_wrapper.sh
deleted
100755 → 0
View file @
d0f38192
#!/bin/bash
.
/util/opt/lmod/lmod/init/profile
module load zerone/1.0
zerone
"
$@
"
chipathlon/workflow.py
View file @
faac4939
...
...
@@ -242,7 +242,6 @@ class Workflow(object):
# Load each yaml_job as an actual object
for
root
,
dirs
,
files
in
os
.
walk
(
"%s/%s"
%
(
os
.
path
.
dirname
(
os
.
path
.
realpath
(
__file__
)),
chipathlon
.
conf
.
job_params
)):
for
f
in
files
:
print
(
f
)
yaml_job
=
chipathlon
.
workflow_job
.
WorkflowJob
(
os
.
path
.
join
(
root
,
f
),
self
.
params
.
get
(
f
.
split
(
"."
)[
0
]),
self
.
debug
)
if
yaml_job
.
is_valid
():
if
yaml_job
.
command
in
self
.
executables
:
...
...
chipathlon/workflow_job.py
View file @
faac4939
...
...
@@ -566,9 +566,9 @@ class WorkflowJob(object):
# Need to figure out 2 things:
# 1. Should we add the argument name?
# 2. What's the correct value to add?
add_value
=
self
.
_interpolate_value
(
inputs
,
outputs
,
arg_name
,
arg_info
)
if
self
.
debug
:
print
"%s: Loading argument: %s, info: %s, value: %s"
%
(
self
,
arg_name
,
arg_info
,
add_value
)
print
"
\t
%s: Loading argument: %s, info: %s"
%
(
self
,
arg_name
,
arg_info
)
add_value
=
self
.
_interpolate_value
(
inputs
,
outputs
,
arg_name
,
arg_info
)
# Only add arguments that have a value
if
add_value
is
not
None
:
# Need to add in the arg_name and the arg_value
...
...
setup.py
View file @
faac4939
...
...
@@ -22,7 +22,9 @@ setup(
"scripts/chip-job-peakranger-format"
,
"scripts/chip-job-save-result"
,
"scripts/chip-job-sort-peak"
,
"scripts/chip-job-zcat-peak"
"scripts/chip-job-zcat-peak"
,
"scripts/chip-job-zerone-format"
,
"scripts/chip-job-hd-format"
],
install_requires
=
[
"pymongo"
,
"pyyaml"
],
zip_safe
=
False
...
...
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