Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
fceb39a9
Commit
fceb39a9
authored
Nov 19, 2015
by
Peter van 't Hof
Browse files
Fixed license headers
parent
d5fbab5b
Changes
49
Hide whitespace changes
Inline
Side-by-side
public/biopet-core/pom.xml
View file @
fceb39a9
<?xml version="1.0" encoding="UTF-8"?>
<!--
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.
-->
<project
xmlns=
"http://maven.apache.org/POM/4.0.0"
xmlns:xsi=
"http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation=
"http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"
>
...
...
public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap_dashboard.css
View file @
fceb39a9
/**
* 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.
*/
/*
* Base structure
*/
...
...
public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/sortable-theme-bootstrap.css
View file @
fceb39a9
/**
* 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.
*/
/* line 2, ../sass/_sortable.sass */
table
[
data-sortable
]
{
border-collapse
:
collapse
;
...
...
public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/js/sortable.min.js
View file @
fceb39a9
/*
* 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.
*/
/*! sortable.js 0.5.0 */
(
function
(){
var
a
,
b
,
c
,
d
,
e
,
f
;
a
=
"
table[data-sortable]
"
,
c
=
/^-
?[
£$¤
]?[\d
,.
]
+%
?
$/
,
f
=
/^
\s
+|
\s
+$/g
,
e
=
"
ontouchstart
"
in
document
.
documentElement
,
b
=
e
?
"
touchstart
"
:
"
click
"
,
d
=
{
init
:
function
(){
var
b
,
c
,
e
,
f
,
g
;
for
(
c
=
document
.
querySelectorAll
(
a
),
g
=
[],
e
=
0
,
f
=
c
.
length
;
f
>
e
;
e
++
)
b
=
c
[
e
],
g
.
push
(
d
.
initTable
(
b
));
return
g
},
initTable
:
function
(
a
){
var
b
,
c
,
e
,
f
,
g
;
if
(
1
===
a
.
tHead
.
rows
.
length
&&
"
true
"
!==
a
.
getAttribute
(
"
data-sortable-initialized
"
)){
for
(
a
.
setAttribute
(
"
data-sortable-initialized
"
,
"
true
"
),
e
=
a
.
querySelectorAll
(
"
th
"
),
b
=
f
=
0
,
g
=
e
.
length
;
g
>
f
;
b
=++
f
)
c
=
e
[
b
],
"
false
"
!==
c
.
getAttribute
(
"
data-sortable
"
)
&&
d
.
setupClickableTH
(
a
,
c
,
b
);
return
a
}},
setupClickableTH
:
function
(
a
,
c
,
e
){
var
f
;
return
f
=
d
.
getColumnType
(
a
,
e
),
c
.
addEventListener
(
b
,
function
(){
var
b
,
g
,
h
,
i
,
j
,
k
,
l
,
m
,
n
,
o
,
p
,
q
,
r
,
s
,
t
,
u
;
for
(
j
=
"
true
"
===
this
.
getAttribute
(
"
data-sorted
"
),
k
=
this
.
getAttribute
(
"
data-sorted-direction
"
),
b
=
j
?
"
ascending
"
===
k
?
"
descending
"
:
"
ascending
"
:
f
.
defaultSortDirection
,
m
=
this
.
parentNode
.
querySelectorAll
(
"
th
"
),
n
=
0
,
q
=
m
.
length
;
q
>
n
;
n
++
)
c
=
m
[
n
],
c
.
setAttribute
(
"
data-sorted
"
,
"
false
"
),
c
.
removeAttribute
(
"
data-sorted-direction
"
);
for
(
this
.
setAttribute
(
"
data-sorted
"
,
"
true
"
),
this
.
setAttribute
(
"
data-sorted-direction
"
,
b
),
l
=
a
.
tBodies
[
0
],
h
=
[],
t
=
l
.
rows
,
o
=
0
,
r
=
t
.
length
;
r
>
o
;
o
++
)
g
=
t
[
o
],
h
.
push
([
d
.
getNodeValue
(
g
.
cells
[
e
]),
g
]);
for
(
j
?
h
.
reverse
():
h
.
sort
(
f
.
compare
),
u
=
[],
p
=
0
,
s
=
h
.
length
;
s
>
p
;
p
++
)
i
=
h
[
p
],
u
.
push
(
l
.
appendChild
(
i
[
1
]));
return
u
})},
getColumnType
:
function
(
a
,
b
){
var
e
,
f
,
g
,
h
,
i
;
for
(
i
=
a
.
tBodies
[
0
].
rows
,
g
=
0
,
h
=
i
.
length
;
h
>
g
;
g
++
)
if
(
e
=
i
[
g
],
f
=
d
.
getNodeValue
(
e
.
cells
[
b
]),
""
!==
f
&&
f
.
match
(
c
))
return
d
.
types
.
numeric
;
return
d
.
types
.
alpha
},
getNodeValue
:
function
(
a
){
return
a
?
null
!==
a
.
getAttribute
(
"
data-value
"
)?
a
.
getAttribute
(
"
data-value
"
):
"
undefined
"
!=
typeof
a
.
innerText
?
a
.
innerText
.
replace
(
f
,
""
):
a
.
textContent
.
replace
(
f
,
""
):
""
},
types
:{
numeric
:{
defaultSortDirection
:
"
descending
"
,
compare
:
function
(
a
,
b
){
var
c
,
d
;
return
c
=
parseFloat
(
a
[
0
].
replace
(
/
[^
0-9.-
]
/g
,
""
)),
d
=
parseFloat
(
b
[
0
].
replace
(
/
[^
0-9.-
]
/g
,
""
)),
isNaN
(
c
)
&&
(
c
=
0
),
isNaN
(
d
)
&&
(
d
=
0
),
d
-
c
}},
alpha
:{
defaultSortDirection
:
"
ascending
"
,
compare
:
function
(
a
,
b
){
var
c
,
d
;
return
c
=
a
[
0
].
toLowerCase
(),
d
=
b
[
0
].
toLowerCase
(),
c
===
d
?
0
:
d
>
c
?
-
1
:
1
}}}},
setTimeout
(
d
.
init
,
0
),
window
.
Sortable
=
d
}).
call
(
this
);
\ No newline at end of file
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetFifoPipe.scala
View file @
fceb39a9
/**
* 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.
*/
package
nl.lumc.sasc.biopet.core
import
java.io.File
...
...
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala
View file @
fceb39a9
/**
* 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.
*/
package
nl.lumc.sasc.biopet.core
import
java.io.File
...
...
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala
View file @
fceb39a9
/**
* 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.
*/
package
nl.lumc.sasc.biopet.core
import
nl.lumc.sasc.biopet.utils.config.Configurable
...
...
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommandFunction.scala
View file @
fceb39a9
/**
* 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.
*/
package
nl.lumc.sasc.biopet.core
import
nl.lumc.sasc.biopet.FullVersion
...
...
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Version.scala
View file @
fceb39a9
/**
* 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.
*/
package
nl.lumc.sasc.biopet.core
import
java.io.File
...
...
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala
View file @
fceb39a9
/**
* 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.
*/
package
nl.lumc.sasc.biopet.core
import
java.io.
{
File
,
PrintWriter
}
...
...
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/CheckChecksum.scala
View file @
fceb39a9
/**
* 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.
*/
package
nl.lumc.sasc.biopet.core.extensions
import
java.io.File
...
...
public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/BiopetPipeTest.scala
View file @
fceb39a9
/**
* 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.
*/
package
nl.lumc.sasc.biopet.core
import
org.scalatest.Matchers
...
...
public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/CommandLineResourcesTest.scala
View file @
fceb39a9
/**
* 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.
*/
package
nl.lumc.sasc.biopet.core
import
nl.lumc.sasc.biopet.utils.config.
{
Config
,
Configurable
}
...
...
public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/PipelineCommandTest.scala
View file @
fceb39a9
/**
* 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.
*/
package
nl.lumc.sasc.biopet.core
import
nl.lumc.sasc.biopet.utils.config.Config
...
...
public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/SampleLibraryTagTest.scala
View file @
fceb39a9
/**
* 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.
*/
package
nl.lumc.sasc.biopet.core
import
nl.lumc.sasc.biopet.utils.config.
{
Config
,
Configurable
}
...
...
public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/ToolCommandTest.scala
View file @
fceb39a9
/**
* 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.
*/
package
nl.lumc.sasc.biopet.core
import
org.scalatest.Matchers
...
...
public/biopet-extensions/pom.xml
View file @
fceb39a9
<?xml version="1.0" encoding="UTF-8"?>
<!--
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.
-->
<project
xmlns=
"http://maven.apache.org/POM/4.0.0"
xmlns:xsi=
"http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation=
"http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"
>
...
...
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsMerge.scala
View file @
fceb39a9
/**
* 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.
*/
package
nl.lumc.sasc.biopet.extensions.bcftools
import
java.io.File
...
...
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BuildBamIndex.scala
View file @
fceb39a9
/**
* 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.
*/
package
nl.lumc.sasc.biopet.extensions.picard
import
java.io.File
...
...
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala
View file @
fceb39a9
/**
* 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.
*/
package
nl.lumc.sasc.biopet.extensions.samtools
import
java.io.File
...
...
Prev
1
2
3
Next
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment