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biopet.biopet
Commits
76381e8c
Commit
76381e8c
authored
Apr 27, 2016
by
Peter van 't Hof
Browse files
Remove protected executable
parent
e19b18ba
Changes
2
Hide whitespace changes
Inline
Side-by-side
protected/biopet-protected-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutableProtected.scala
deleted
100644 → 0
View file @
e19b18ba
/**
* Due to the license issue with GATK, this part of Biopet can only be used inside the
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package
nl.lumc.sasc.biopet
import
nl.lumc.sasc.biopet.utils.
{
BiopetExecutable
,
MainCommand
}
object
BiopetExecutableProtected
extends
BiopetExecutable
{
def
pipelines
:
List
[
MainCommand
]
=
BiopetExecutablePublic
.
publicPipelines
:::
List
(
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
gatk
.
Shiva
)
def
tools
=
BiopetExecutablePublic
.
tools
}
\ No newline at end of file
public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutablePublic.scala
View file @
76381e8c
...
...
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet
import
nl.lumc.sasc.biopet.utils.
{
BiopetExecutable
,
MainCommand
}
object
BiopetExecutablePublic
extends
BiopetExecutable
{
def
p
ublicP
ipelines
:
List
[
MainCommand
]
=
List
(
def
pipelines
:
List
[
MainCommand
]
=
List
(
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
flexiprep
.
Flexiprep
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
mapping
.
Mapping
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
mapping
.
MultisampleMapping
,
...
...
@@ -34,12 +34,9 @@ object BiopetExecutablePublic extends BiopetExecutable {
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
gears
.
Gears
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
gwastest
.
GwasTest
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
shiva
.
ShivaVariantcalling
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
basty
.
Basty
)
def
pipelines
:
List
[
MainCommand
]
=
List
(
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
basty
.
Basty
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
shiva
.
Shiva
)
:::
publicPipelines
)
def
tools
:
List
[
MainCommand
]
=
BiopetToolsExecutable
.
tools
}
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