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biopet.biopet
Commits
eb97957f
Commit
eb97957f
authored
Sep 11, 2015
by
Peter van 't Hof
Browse files
Tools split into new modules, core and utils are compileable now
parent
f4b5230c
Changes
253
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public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp
View file @
eb97957f
#import(nl.lumc.sasc.biopet.
core
.summary.Summary)
#import(nl.lumc.sasc.biopet.
utils
.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
...
...
public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamMetricsFront.ssp
View file @
eb97957f
#import(nl.lumc.sasc.biopet.
core
.summary.Summary)
#import(nl.lumc.sasc.biopet.
utils
.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
<%@ var summary: Summary %>
<%@ var rootPath: String %>
...
...
public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamStats.ssp
View file @
eb97957f
#import(nl.lumc.sasc.biopet.
core
.summary.Summary)
#import(nl.lumc.sasc.biopet.
utils
.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
<%@ var summary: Summary %>
<%@ var sampleId: Option[String] %>
...
...
public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bammetricsInputFile.ssp
View file @
eb97957f
#import(nl.lumc.sasc.biopet.
core
.summary.Summary)
#import(nl.lumc.sasc.biopet.
utils
.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(java.io.File)
<%@ var summary: Summary %>
...
...
public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp
View file @
eb97957f
#import(nl.lumc.sasc.biopet.utils.IoUtils)
#import(nl.lumc.sasc.biopet.
core
.summary.Summary)
#import(nl.lumc.sasc.biopet.
utils
.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(org.apache.commons.io.FileUtils)
#import(java.io.File)
...
...
public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp
View file @
eb97957f
#import(nl.lumc.sasc.biopet.utils.IoUtils)
#import(nl.lumc.sasc.biopet.
core
.summary.Summary)
#import(nl.lumc.sasc.biopet.
utils
.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(org.apache.commons.io.FileUtils)
#import(java.io.File)
...
...
public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp
View file @
eb97957f
#import(nl.lumc.sasc.biopet.
core
.summary.Summary)
#import(nl.lumc.sasc.biopet.
utils
.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
...
...
public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp
View file @
eb97957f
#import(nl.lumc.sasc.biopet.
core
.summary.Summary)
#import(nl.lumc.sasc.biopet.
utils
.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
...
...
public/biopet-core/pom.xml
View file @
eb97957f
...
...
@@ -42,6 +42,11 @@
<artifactId>
gatk-queue
</artifactId>
<version>
3.4
</version>
</dependency>
<dependency>
<groupId>
org.broadinstitute.gatk
</groupId>
<artifactId>
gatk-queue-extensions-public
</artifactId>
<version>
3.4
</version>
</dependency>
<dependency>
<groupId>
org.scalatra.scalate
</groupId>
<artifactId>
scalate-core_2.10
</artifactId>
...
...
public/biopet-core/src/main/resources/log4j.properties
0 → 100644
View file @
eb97957f
#
# Biopet is built on top of GATK Queue for building bioinformatic
# pipelines. It is mainly intended to support LUMC SHARK cluster which is running
# SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
# should also be able to execute Biopet tools and pipelines.
#
# Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
#
# Contact us at: sasc@lumc.nl
#
# A dual licensing mode is applied. The source code within this project that are
# not part of GATK Queue is freely available for non-commercial use under an AGPL
# license; For commercial users or users who do not want to follow the AGPL
# license, please contact us to obtain a separate license.
#
# Set root logger level to DEBUG and its only appender to A1.
log4j.rootLogger
=
INFO, A1
# A1 is set to be a ConsoleAppender.
log4j.appender.A1
=
org.apache.log4j.ConsoleAppender
log4j.appender.A1.Target
=
System.err
# A1 uses PatternLayout.
log4j.appender.A1.layout
=
org.apache.log4j.PatternLayout
log4j.appender.A1.layout.ConversionPattern
=
%-5p [%d] [%C{1}] - %m%n
\ No newline at end of file
public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/License.txt
0 → 100644
View file @
eb97957f
Biopet is built on top of GATK Queue for building bioinformatic
pipelines. It is mainly intended to support LUMC SHARK cluster which is running
SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
should also be able to execute Biopet tools and pipelines.
Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
Contact us at: sasc@lumc.nl
A dual licensing mode is applied. The source code within this project that are
not part of GATK Queue is freely available for non-commercial use under an AGPL
license; For commercial users or users who do not want to follow the AGPL
license, please contact us to obtain a separate license.
\ No newline at end of file
public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/executables.ssp
0 → 100644
View file @
eb97957f
#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
<%@ var summary: Summary %>
<%@ var rootPath: String %>
<%@ var sampleId: Option[String] = None %>
<%@ var libId: Option[String] = None %>
<%@ var pipeline: String = summary.getValue("meta", "pipeline_name").getOrElse("").toString %>
#{
val executables = summary.getValue(sampleId, libId, pipeline, "executables").getOrElse(Map()).asInstanceOf[Map[String, Map[String, Any]]]
}#
<table class="table">
<thead>
<tr>
<th>Name</th>
<th>Version</th>
</tr>
</thead>
<tbody>
#for (name <- executables.keySet.toList.sorted)
<tr>
<td>${name}</td>
#{
val version = executables(name).get("version") match {
case Some(x) if x != None => x.toString
case _ => "N/A"
}
}#
<td>${version}</td>
</tr>
#end
</tbody>
</table>
\ No newline at end of file
public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap-theme.min.css
0 → 100644
View file @
eb97957f
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:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
startColorstr
=
'#ff337ab7'
,
endColorstr
=
'#ff2e6da4'
,
GradientType
=
0
);
background-repeat
:
repeat-x
}
.navbar-default
{
background-image
:
-webkit-linear-gradient
(
top
,
#fff
0
,
#f8f8f8
100%
);
background-image
:
-o-linear-gradient
(
top
,
#fff
0
,
#f8f8f8
100%
);
background-image
:
-webkit-gradient
(
linear
,
left
top
,
left
bottom
,
from
(
#fff
),
to
(
#f8f8f8
));
background-image
:
linear-gradient
(
to
bottom
,
#fff
0
,
#f8f8f8
100%
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
startColorstr
=
'#ffffffff'
,
endColorstr
=
'#fff8f8f8'
,
GradientType
=
0
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
enabled
=
false
);
background-repeat
:
repeat-x
;
border-radius
:
4px
;
-webkit-box-shadow
:
inset
0
1px
0
rgba
(
255
,
255
,
255
,
.15
),
0
1px
5px
rgba
(
0
,
0
,
0
,
.075
);
box-shadow
:
inset
0
1px
0
rgba
(
255
,
255
,
255
,
.15
),
0
1px
5px
rgba
(
0
,
0
,
0
,
.075
)}
.navbar-default
.navbar-nav
>
.active
>
a
,
.navbar-default
.navbar-nav
>
.open
>
a
{
background-image
:
-webkit-linear-gradient
(
top
,
#dbdbdb
0
,
#e2e2e2
100%
);
background-image
:
-o-linear-gradient
(
top
,
#dbdbdb
0
,
#e2e2e2
100%
);
background-image
:
-webkit-gradient
(
linear
,
left
top
,
left
bottom
,
from
(
#dbdbdb
),
to
(
#e2e2e2
));
background-image
:
linear-gradient
(
to
bottom
,
#dbdbdb
0
,
#e2e2e2
100%
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
startColorstr
=
'#ffdbdbdb'
,
endColorstr
=
'#ffe2e2e2'
,
GradientType
=
0
);
background-repeat
:
repeat-x
;
-webkit-box-shadow
:
inset
0
3px
9px
rgba
(
0
,
0
,
0
,
.075
);
box-shadow
:
inset
0
3px
9px
rgba
(
0
,
0
,
0
,
.075
)}
.navbar-brand
,
.navbar-nav
>
li
>
a
{
text-shadow
:
0
1px
0
rgba
(
255
,
255
,
255
,
.25
)}
.navbar-inverse
{
background-image
:
-webkit-linear-gradient
(
top
,
#3c3c3c
0
,
#222
100%
);
background-image
:
-o-linear-gradient
(
top
,
#3c3c3c
0
,
#222
100%
);
background-image
:
-webkit-gradient
(
linear
,
left
top
,
left
bottom
,
from
(
#3c3c3c
),
to
(
#222
));
background-image
:
linear-gradient
(
to
bottom
,
#3c3c3c
0
,
#222
100%
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
startColorstr
=
'#ff3c3c3c'
,
endColorstr
=
'#ff222222'
,
GradientType
=
0
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
enabled
=
false
);
background-repeat
:
repeat-x
}
.navbar-inverse
.navbar-nav
>
.active
>
a
,
.navbar-inverse
.navbar-nav
>
.open
>
a
{
background-image
:
-webkit-linear-gradient
(
top
,
#080808
0
,
#0f0f0f
100%
);
background-image
:
-o-linear-gradient
(
top
,
#080808
0
,
#0f0f0f
100%
);
background-image
:
-webkit-gradient
(
linear
,
left
top
,
left
bottom
,
from
(
#080808
),
to
(
#0f0f0f
));
background-image
:
linear-gradient
(
to
bottom
,
#080808
0
,
#0f0f0f
100%
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
startColorstr
=
'#ff080808'
,
endColorstr
=
'#ff0f0f0f'
,
GradientType
=
0
);
background-repeat
:
repeat-x
;
-webkit-box-shadow
:
inset
0
3px
9px
rgba
(
0
,
0
,
0
,
.25
);
box-shadow
:
inset
0
3px
9px
rgba
(
0
,
0
,
0
,
.25
)}
.navbar-inverse
.navbar-brand
,
.navbar-inverse
.navbar-nav
>
li
>
a
{
text-shadow
:
0
-1px
0
rgba
(
0
,
0
,
0
,
.25
)}
.navbar-fixed-bottom
,
.navbar-fixed-top
,
.navbar-static-top
{
border-radius
:
0
}
@media
(
max-width
:
767px
){
.navbar
.navbar-nav
.open
.dropdown-menu
>
.active
>
a
,
.navbar
.navbar-nav
.open
.dropdown-menu
>
.active
>
a
:focus
,
.navbar
.navbar-nav
.open
.dropdown-menu
>
.active
>
a
:hover
{
color
:
#fff
;
background-image
:
-webkit-linear-gradient
(
top
,
#337ab7
0
,
#2e6da4
100%
);
background-image
:
-o-linear-gradient
(
top
,
#337ab7
0
,
#2e6da4
100%
);
background-image
:
-webkit-gradient
(
linear
,
left
top
,
left
bottom
,
from
(
#337ab7
),
to
(
#2e6da4
));
background-image
:
linear-gradient
(
to
bottom
,
#337ab7
0
,
#2e6da4
100%
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
startColorstr
=
'#ff337ab7'
,
endColorstr
=
'#ff2e6da4'
,
GradientType
=
0
);
background-repeat
:
repeat-x
}}
.alert
{
text-shadow
:
0
1px
0
rgba
(
255
,
255
,
255
,
.2
);
-webkit-box-shadow
:
inset
0
1px
0
rgba
(
255
,
255
,
255
,
.25
),
0
1px
2px
rgba
(
0
,
0
,
0
,
.05
);
box-shadow
:
inset
0
1px
0
rgba
(
255
,
255
,
255
,
.25
),
0
1px
2px
rgba
(
0
,
0
,
0
,
.05
)}
.alert-success
{
background-image
:
-webkit-linear-gradient
(
top
,
#dff0d8
0
,
#c8e5bc
100%
);
background-image
:
-o-linear-gradient
(
top
,
#dff0d8
0
,
#c8e5bc
100%
);
background-image
:
-webkit-gradient
(
linear
,
left
top
,
left
bottom
,
from
(
#dff0d8
),
to
(
#c8e5bc
));
background-image
:
linear-gradient
(
to
bottom
,
#dff0d8
0
,
#c8e5bc
100%
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
startColorstr
=
'#ffdff0d8'
,
endColorstr
=
'#ffc8e5bc'
,
GradientType
=
0
);
background-repeat
:
repeat-x
;
border-color
:
#b2dba1
}
.alert-info
{
background-image
:
-webkit-linear-gradient
(
top
,
#d9edf7
0
,
#b9def0
100%
);
background-image
:
-o-linear-gradient
(
top
,
#d9edf7
0
,
#b9def0
100%
);
background-image
:
-webkit-gradient
(
linear
,
left
top
,
left
bottom
,
from
(
#d9edf7
),
to
(
#b9def0
));
background-image
:
linear-gradient
(
to
bottom
,
#d9edf7
0
,
#b9def0
100%
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
startColorstr
=
'#ffd9edf7'
,
endColorstr
=
'#ffb9def0'
,
GradientType
=
0
);
background-repeat
:
repeat-x
;
border-color
:
#9acfea
}
.alert-warning
{
background-image
:
-webkit-linear-gradient
(
top
,
#fcf8e3
0
,
#f8efc0
100%
);
background-image
:
-o-linear-gradient
(
top
,
#fcf8e3
0
,
#f8efc0
100%
);
background-image
:
-webkit-gradient
(
linear
,
left
top
,
left
bottom
,
from
(
#fcf8e3
),
to
(
#f8efc0
));
background-image
:
linear-gradient
(
to
bottom
,
#fcf8e3
0
,
#f8efc0
100%
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
startColorstr
=
'#fffcf8e3'
,
endColorstr
=
'#fff8efc0'
,
GradientType
=
0
);
background-repeat
:
repeat-x
;
border-color
:
#f5e79e
}
.alert-danger
{
background-image
:
-webkit-linear-gradient
(
top
,
#f2dede
0
,
#e7c3c3
100%
);
background-image
:
-o-linear-gradient
(
top
,
#f2dede
0
,
#e7c3c3
100%
);
background-image
:
-webkit-gradient
(
linear
,
left
top
,
left
bottom
,
from
(
#f2dede
),
to
(
#e7c3c3
));
background-image
:
linear-gradient
(
to
bottom
,
#f2dede
0
,
#e7c3c3
100%
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
startColorstr
=
'#fff2dede'
,
endColorstr
=
'#ffe7c3c3'
,
GradientType
=
0
);
background-repeat
:
repeat-x
;
border-color
:
#dca7a7
}
.progress
{
background-image
:
-webkit-linear-gradient
(
top
,
#ebebeb
0
,
#f5f5f5
100%
);
background-image
:
-o-linear-gradient
(
top
,
#ebebeb
0
,
#f5f5f5
100%
);
background-image
:
-webkit-gradient
(
linear
,
left
top
,
left
bottom
,
from
(
#ebebeb
),
to
(
#f5f5f5
));
background-image
:
linear-gradient
(
to
bottom
,
#ebebeb
0
,
#f5f5f5
100%
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
startColorstr
=
'#ffebebeb'
,
endColorstr
=
'#fff5f5f5'
,
GradientType
=
0
);
background-repeat
:
repeat-x
}
.progress-bar
{
background-image
:
-webkit-linear-gradient
(
top
,
#337ab7
0
,
#286090
100%
);
background-image
:
-o-linear-gradient
(
top
,
#337ab7
0
,
#286090
100%
);
background-image
:
-webkit-gradient
(
linear
,
left
top
,
left
bottom
,
from
(
#337ab7
),
to
(
#286090
));
background-image
:
linear-gradient
(
to
bottom
,
#337ab7
0
,
#286090
100%
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
startColorstr
=
'#ff337ab7'
,
endColorstr
=
'#ff286090'
,
GradientType
=
0
);
background-repeat
:
repeat-x
}
.progress-bar-success
{
background-image
:
-webkit-linear-gradient
(
top
,
#5cb85c
0
,
#449d44
100%
);
background-image
:
-o-linear-gradient
(
top
,
#5cb85c
0
,
#449d44
100%
);
background-image
:
-webkit-gradient
(
linear
,
left
top
,
left
bottom
,
from
(
#5cb85c
),
to
(
#449d44
));
background-image
:
linear-gradient
(
to
bottom
,
#5cb85c
0
,
#449d44
100%
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
startColorstr
=
'#ff5cb85c'
,
endColorstr
=
'#ff449d44'
,
GradientType
=
0
);
background-repeat
:
repeat-x
}
.progress-bar-info
{
background-image
:
-webkit-linear-gradient
(
top
,
#5bc0de
0
,
#31b0d5
100%
);
background-image
:
-o-linear-gradient
(
top
,
#5bc0de
0
,
#31b0d5
100%
);
background-image
:
-webkit-gradient
(
linear
,
left
top
,
left
bottom
,
from
(
#5bc0de
),
to
(
#31b0d5
));
background-image
:
linear-gradient
(
to
bottom
,
#5bc0de
0
,
#31b0d5
100%
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
startColorstr
=
'#ff5bc0de'
,
endColorstr
=
'#ff31b0d5'
,
GradientType
=
0
);
background-repeat
:
repeat-x
}
.progress-bar-warning
{
background-image
:
-webkit-linear-gradient
(
top
,
#f0ad4e
0
,
#ec971f
100%
);
background-image
:
-o-linear-gradient
(
top
,
#f0ad4e
0
,
#ec971f
100%
);
background-image
:
-webkit-gradient
(
linear
,
left
top
,
left
bottom
,
from
(
#f0ad4e
),
to
(
#ec971f
));
background-image
:
linear-gradient
(
to
bottom
,
#f0ad4e
0
,
#ec971f
100%
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
startColorstr
=
'#fff0ad4e'
,
endColorstr
=
'#ffec971f'
,
GradientType
=
0
);
background-repeat
:
repeat-x
}
.progress-bar-danger
{
background-image
:
-webkit-linear-gradient
(
top
,
#d9534f
0
,
#c9302c
100%
);
background-image
:
-o-linear-gradient
(
top
,
#d9534f
0
,
#c9302c
100%
);
background-image
:
-webkit-gradient
(
linear
,
left
top
,
left
bottom
,
from
(
#d9534f
),
to
(
#c9302c
));
background-image
:
linear-gradient
(
to
bottom
,
#d9534f
0
,
#c9302c
100%
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
startColorstr
=
'#ffd9534f'
,
endColorstr
=
'#ffc9302c'
,
GradientType
=
0
);
background-repeat
:
repeat-x
}
.progress-bar-striped
{
background-image
:
-webkit-linear-gradient
(
45deg
,
rgba
(
255
,
255
,
255
,
.15
)
25%
,
transparent
25%
,
transparent
50%
,
rgba
(
255
,
255
,
255
,
.15
)
50%
,
rgba
(
255
,
255
,
255
,
.15
)
75%
,
transparent
75%
,
transparent
);
background-image
:
-o-linear-gradient
(
45deg
,
rgba
(
255
,
255
,
255
,
.15
)
25%
,
transparent
25%
,
transparent
50%
,
rgba
(
255
,
255
,
255
,
.15
)
50%
,
rgba
(
255
,
255
,
255
,
.15
)
75%
,
transparent
75%
,
transparent
);
background-image
:
linear-gradient
(
45deg
,
rgba
(
255
,
255
,
255
,
.15
)
25%
,
transparent
25%
,
transparent
50%
,
rgba
(
255
,
255
,
255
,
.15
)
50%
,
rgba
(
255
,
255
,
255
,
.15
)
75%
,
transparent
75%
,
transparent
)}
.list-group
{
border-radius
:
4px
;
-webkit-box-shadow
:
0
1px
2px
rgba
(
0
,
0
,
0
,
.075
);
box-shadow
:
0
1px
2px
rgba
(
0
,
0
,
0
,
.075
)}
.list-group-item.active
,
.list-group-item.active
:focus
,
.list-group-item.active
:hover
{
text-shadow
:
0
-1px
0
#286090
;
background-image
:
-webkit-linear-gradient
(
top
,
#337ab7
0
,
#2b669a
100%
);
background-image
:
-o-linear-gradient
(
top
,
#337ab7
0
,
#2b669a
100%
);
background-image
:
-webkit-gradient
(
linear
,
left
top
,
left
bottom
,
from
(
#337ab7
),
to
(
#2b669a
));
background-image
:
linear-gradient
(
to
bottom
,
#337ab7
0
,
#2b669a
100%
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
startColorstr
=
'#ff337ab7'
,
endColorstr
=
'#ff2b669a'
,
GradientType
=
0
);
background-repeat
:
repeat-x
;
border-color
:
#2b669a
}
.list-group-item.active
.badge
,
.list-group-item.active
:focus
.badge
,
.list-group-item.active
:hover
.badge
{
text-shadow
:
none
}
.panel
{
-webkit-box-shadow
:
0
1px
2px
rgba
(
0
,
0
,
0
,
.05
);
box-shadow
:
0
1px
2px
rgba
(
0
,
0
,
0
,
.05
)}
.panel-default
>
.panel-heading
{
background-image
:
-webkit-linear-gradient
(
top
,
#f5f5f5
0
,
#e8e8e8
100%
);
background-image
:
-o-linear-gradient
(
top
,
#f5f5f5
0
,
#e8e8e8
100%
);
background-image
:
-webkit-gradient
(
linear
,
left
top
,
left
bottom
,
from
(
#f5f5f5
),
to
(
#e8e8e8
));
background-image
:
linear-gradient
(
to
bottom
,
#f5f5f5
0
,
#e8e8e8
100%
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
startColorstr
=
'#fff5f5f5'
,
endColorstr
=
'#ffe8e8e8'
,
GradientType
=
0
);
background-repeat
:
repeat-x
}
.panel-primary
>
.panel-heading
{
background-image
:
-webkit-linear-gradient
(
top
,
#337ab7
0
,
#2e6da4
100%
);
background-image
:
-o-linear-gradient
(
top
,
#337ab7
0
,
#2e6da4
100%
);
background-image
:
-webkit-gradient
(
linear
,
left
top
,
left
bottom
,
from
(
#337ab7
),
to
(
#2e6da4
));
background-image
:
linear-gradient
(
to
bottom
,
#337ab7
0
,
#2e6da4
100%
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
startColorstr
=
'#ff337ab7'
,
endColorstr
=
'#ff2e6da4'
,
GradientType
=
0
);
background-repeat
:
repeat-x
}
.panel-success
>
.panel-heading
{
background-image
:
-webkit-linear-gradient
(
top
,
#dff0d8
0
,
#d0e9c6
100%
);
background-image
:
-o-linear-gradient
(
top
,
#dff0d8
0
,
#d0e9c6
100%
);
background-image
:
-webkit-gradient
(
linear
,
left
top
,
left
bottom
,
from
(
#dff0d8
),
to
(
#d0e9c6
));
background-image
:
linear-gradient
(
to
bottom
,
#dff0d8
0
,
#d0e9c6
100%
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
startColorstr
=
'#ffdff0d8'
,
endColorstr
=
'#ffd0e9c6'
,
GradientType
=
0
);
background-repeat
:
repeat-x
}
.panel-info
>
.panel-heading
{
background-image
:
-webkit-linear-gradient
(
top
,
#d9edf7
0
,
#c4e3f3
100%
);
background-image
:
-o-linear-gradient
(
top
,
#d9edf7
0
,
#c4e3f3
100%
);
background-image
:
-webkit-gradient
(
linear
,
left
top
,
left
bottom
,
from
(
#d9edf7
),
to
(
#c4e3f3
));
background-image
:
linear-gradient
(
to
bottom
,
#d9edf7
0
,
#c4e3f3
100%
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
startColorstr
=
'#ffd9edf7'
,
endColorstr
=
'#ffc4e3f3'
,
GradientType
=
0
);
background-repeat
:
repeat-x
}
.panel-warning
>
.panel-heading
{
background-image
:
-webkit-linear-gradient
(
top
,
#fcf8e3
0
,
#faf2cc
100%
);
background-image
:
-o-linear-gradient
(
top
,
#fcf8e3
0
,
#faf2cc
100%
);
background-image
:
-webkit-gradient
(
linear
,
left
top
,
left
bottom
,
from
(
#fcf8e3
),
to
(
#faf2cc
));
background-image
:
linear-gradient
(
to
bottom
,
#fcf8e3
0
,
#faf2cc
100%
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
startColorstr
=
'#fffcf8e3'
,
endColorstr
=
'#fffaf2cc'
,
GradientType
=
0
);
background-repeat
:
repeat-x
}
.panel-danger
>
.panel-heading
{
background-image
:
-webkit-linear-gradient
(
top
,
#f2dede
0
,
#ebcccc
100%
);
background-image
:
-o-linear-gradient
(
top
,
#f2dede
0
,
#ebcccc
100%
);
background-image
:
-webkit-gradient
(
linear
,
left
top
,
left
bottom
,
from
(
#f2dede
),
to
(
#ebcccc
));
background-image
:
linear-gradient
(
to
bottom
,
#f2dede
0
,
#ebcccc
100%
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
startColorstr
=
'#fff2dede'
,
endColorstr
=
'#ffebcccc'
,
GradientType
=
0
);
background-repeat
:
repeat-x
}
.well
{
background-image
:
-webkit-linear-gradient
(
top
,
#e8e8e8
0
,
#f5f5f5
100%
);
background-image
:
-o-linear-gradient
(
top
,
#e8e8e8
0
,
#f5f5f5
100%
);
background-image
:
-webkit-gradient
(
linear
,
left
top
,
left
bottom
,
from
(
#e8e8e8
),
to
(
#f5f5f5
));
background-image
:
linear-gradient
(
to
bottom
,
#e8e8e8
0
,
#f5f5f5
100%
);
filter
:
progid
:
DXImageTransform
.
Microsoft
.
gradient
(
startColorstr
=
'#ffe8e8e8'
,
endColorstr
=
'#fff5f5f5'
,
GradientType
=
0
);
background-repeat
:
repeat-x
;
border-color
:
#dcdcdc
;
-webkit-box-shadow
:
inset
0
1px
3px
rgba
(
0
,
0
,
0
,
.05
),
0
1px
0
rgba
(
255
,
255
,
255
,
.1
);
box-shadow
:
inset
0
1px
3px
rgba
(
0
,
0
,
0
,
.05
),
0
1px
0
rgba
(
255
,
255
,
255
,
.1
)}
\ No newline at end of file
public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap.min.css
0 → 100644
View file @
eb97957f
This diff is collapsed.
Click to expand it.
public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap_dashboard.css
0 → 100644
View file @
eb97957f
/*
* Base structure
*/
/* Move down content because we have a fixed navbar that is 50px tall */
body
{
padding-top
:
50px
;
}
/*
* Global add-ons
*/
.sub-header
{
padding-bottom
:
10px
;
border-bottom
:
1px
solid
#eee
;
}
/*
* Top navigation
* Hide default border to remove 1px line.
*/
.navbar-fixed-top
{
border
:
0
;
}
/*
* Sidebar
*/
/* Hide for mobile, show later */
.sidebar
{
display
:
none
;
}
@media
(
min-width
:
768px
)
{
.sidebar
{
position
:
fixed
;
top
:
51px
;
bottom
:
0
;
left
:
0
;
z-index
:
1000
;
display
:
block
;
padding
:
20px
;
overflow-x
:
hidden
;
overflow-y
:
auto
;
/* Scrollable contents if viewport is shorter than content. */
background-color
:
#f5f5f5
;
border-right
:
1px
solid
#eee
;
}
}
/* Sidebar navigation */
.nav-sidebar
{
margin-right
:
-21px
;
/* 20px padding + 1px border */
margin-bottom
:
20px
;
margin-left
:
-20px
;
}
.nav-sidebar
>
li
>
a
{
padding-right
:
20px
;
padding-left
:
20px
;
}
.nav-sidebar
>
.active
>
a
,
.nav-sidebar
>
.active
>
a
:hover
,
.nav-sidebar
>
.active
>
a
:focus
{
color
:
#fff
;
background-color
:
#428bca
;
}
/*
* Main content
*/
.main
{
padding
:
20px
;
}
@media
(
min-width
:
768px
)
{
.main
{
padding-right
:
40px
;
padding-left
:
40px
;
}
}
.main
.page-header
{
margin-top
:
0
;
}
/*
* Placeholder dashboard ideas
*/
.placeholders
{
margin-bottom
:
30px
;
text-align
:
center
;
}
.placeholders
h4
{
margin-bottom
:
0
;
}
.placeholder
{
margin-bottom
:
20px
;
}
.placeholder
img
{
display
:
inline-block
;
border-radius
:
50%
;
}
/*
* dropdown menu
*/
.dropdown-submenu
{
position
:
relative
;
}
.dropdown-submenu
>
.dropdown-menu
{
top
:
0
;
left
:
100%
;
margin-top
:
-6px
;
margin-left
:
-1px
;
-webkit-border-radius
:
0
6px
6px
6px
;
-moz-border-radius
:
0
6px
6px
6px
;
border-radius
:
0
6px
6px
6px
;
}
.dropdown-submenu
:hover
>
.dropdown-menu
{
display
:
block
;
}
.dropdown-submenu
>
a
:after
{
display
:
block
;
content
:
" "
;
float
:
right
;
width
:
0
;
height
:
0
;
border-color
:
transparent
;
border-style
:
solid
;
border-width
:
5px
0
5px
5px
;
border-left-color
:
#cccccc
;
margin-top
:
5px
;
margin-right
:
-10px
;
}
.dropdown-submenu
:hover
>
a
:after
{
border-left-color
:
#ffffff
;
}
.dropdown-submenu
.pull-left
{
float
:
none
;
}
.dropdown-submenu.pull-left
>
.dropdown-menu
{
left
:
-100%
;
margin-left
:
10px
;
-webkit-border-radius
:
6px
0
6px
6px
;
-moz-border-radius
:
6px
0
6px
6px
;
border-radius
:
6px
0
6px
6px
;
}
.root
:hover
>
.dropdown-menu
{
display
:
block
;
}
\ No newline at end of file
public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/sortable-theme-bootstrap.css
0 → 100644
View file @
eb97957f
/* line 2, ../sass/_sortable.sass */
table
[
data-sortable
]
{
border-collapse
:
collapse
;
border-spacing
:
0
;
}
/* line 6, ../sass/_sortable.sass */
table
[
data-sortable
]
th
{
vertical-align
:
bottom
;
font-weight
:
bold
;
}
/* line 10, ../sass/_sortable.sass */
table
[
data-sortable
]
th
,
table
[
data-sortable
]
td
{
text-align
:
left
;
padding
:
10px
;
}
/* line 14, ../sass/_sortable.sass */
table
[
data-sortable
]
th
:not
([
data-sortable
=
"false"
])
{
-webkit-user-select
:
none
;
-moz-user-select
:
none
;
-ms-user-select
:
none
;
-o-user-select
:
none
;
user-select
:
none
;
-webkit-tap-highlight-color
:
rgba
(
0
,
0
,
0
,
0
);
-webkit-touch-callout
:
none
;
cursor
:
pointer
;
}
/* line 26, ../sass/_sortable.sass */
table
[
data-sortable
]
th
:after
{
content
:
""
;
visibility
:
hidden
;
display
:
inline-block
;
vertical-align
:
inherit
;
height
:
0
;
width
:
0
;
border-width
:
5px
;
border-style
:
solid
;
border-color
:
transparent
;
margin-right
:
1px
;
margin-left
:
10px
;
float
:
right
;
}
/* line 40, ../sass/_sortable.sass */
table
[
data-sortable
]
th
[
data-sorted
=
"true"
]
:after
{
visibility
:
visible
;
}
/* line 43, ../sass/_sortable.sass */
table
[
data-sortable
]
th
[
data-sorted-direction
=
"descending"
]
:after
{
border-top-color
:
inherit
;
margin-top
:
8px
;
}
/* line 47, ../sass/_sortable.sass */
table
[
data-sortable
]
th
[
data-sorted-direction
=
"ascending"
]
:after
{
border-bottom-color
:
inherit
;
margin-top
:
3px
;
}
/* line 5, ../sass/sortable-theme-bootstrap.sass */
table
[
data-sortable
]
.sortable-theme-bootstrap
{
font-family
:
"Helvetica Neue"
,
Helvetica
,
Arial
,
sans-serif
;
font-size
:
14px
;
line-height
:
20px
;
color
:
#333333
;
background
:
white
;
}
/* line 12, ../sass/sortable-theme-bootstrap.sass */
table
[
data-sortable
]
.sortable-theme-bootstrap
thead
th
{
border-bottom
:
2px
solid
#e0e0e0
;
}
/* line 15, ../sass/sortable-theme-bootstrap.sass */
table
[
data-sortable
]
.sortable-theme-bootstrap
tbody
td
{
border-top
:
1px
solid
#e0e0e0
;
}
/* line 18, ../sass/sortable-theme-bootstrap.sass */
table
[
data-sortable
]
.sortable-theme-bootstrap
th
[
data-sorted
=
"true"
]
{
color
:
#3a87ad
;
background
:
#d9edf7
;
border-bottom-color
:
#bce8f1
;
}
/* line 23, ../sass/sortable-theme-bootstrap.sass */
table
[
data-sortable
]
.sortable-theme-bootstrap
th
[
data-sorted
=
"true"
][
data-sorted-direction
=
"descending"
]
:after
{
border-top-color
:
#3a87ad
;
}
/* line 26, ../sass/sortable-theme-bootstrap.sass */
table
[
data-sortable
]
.sortable-theme-bootstrap
th
[
data-sorted
=
"true"
][
data-sorted-direction
=
"ascending"
]
:after
{
border-bottom-color
:
#3a87ad
;
}
/* line 31, ../sass/sortable-theme-bootstrap.sass */
table
[
data-sortable
]
.sortable-theme-bootstrap.sortable-theme-bootstrap-striped
tbody
>
tr
:nth-child
(
odd
)
>
td
{
background-color
:
#f9f9f9
;
}
\ No newline at end of file
public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/fonts/glyphicons-halflings-regular.ttf
0 → 100644
View file @
eb97957f
File added
public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/fonts/glyphicons-halflings-regular.woff
0 → 100644
View file @
eb97957f
File added
public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/fonts/glyphicons-halflings-regular.woff2
0 → 100644
View file @
eb97957f
File added
public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/js/bootstrap.min.js
0 → 100644
View file @
eb97957f
This diff is collapsed.
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