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jlopez
RPACIB
Commits
b2d566e5
Commit
b2d566e5
authored
Jun 13, 2018
by
khalid
Browse files
Add recipe for GATK4
parent
ac28a6ef
Changes
1
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Inline
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container.yaml
View file @
b2d566e5
...
@@ -30,7 +30,7 @@ containers: [
...
@@ -30,7 +30,7 @@ containers: [
,{
name
:
"
frc_align"
,
version
:
"
20150723"
,
description
:
"
Computes
FRC
from
SAM/BAM
file
and
not
from
afg
files"
,
documentation
:
"
https://github.com/jts/frc_courve"
,
install
:
[]
}
,{
name
:
"
frc_align"
,
version
:
"
20150723"
,
description
:
"
Computes
FRC
from
SAM/BAM
file
and
not
from
afg
files"
,
documentation
:
"
https://github.com/jts/frc_courve"
,
install
:
[]
}
,{
name
:
"
gapcloser"
,
version
:
"
1.12"
,
description
:
"
A
novel
short-read
assembly
method
that
can
build
a
de
novo
draft
assembly
for
the
human-sized
genomes"
,
documentation
:
"
http://soap.genomics.org.cn/gapcloser.html"
,
install
:
[
"
conda
install
soapdenovo2-gapcloser=1.12"
]
}
,{
name
:
"
gapcloser"
,
version
:
"
1.12"
,
description
:
"
A
novel
short-read
assembly
method
that
can
build
a
de
novo
draft
assembly
for
the
human-sized
genomes"
,
documentation
:
"
http://soap.genomics.org.cn/gapcloser.html"
,
install
:
[
"
conda
install
soapdenovo2-gapcloser=1.12"
]
}
,{
name
:
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gatk"
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version
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3.8"
,
description
:
"
The
full
Genome
Analysis
Toolkit
(GATK)
framework,
license
restricted."
,
documentation
:
"
"
,
install
:
[
"
conda
install
gatk=3.8"
]
}
,{
name
:
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gatk"
,
version
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3.8"
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description
:
"
The
full
Genome
Analysis
Toolkit
(GATK)
framework,
license
restricted."
,
documentation
:
"
"
,
install
:
[
"
conda
install
gatk=3.8"
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}
,{
name
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gatk4"
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version
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4.0"
,
description
:
"
The
full
Genome
Analysis
Toolkit
(GATK)
framework,
license
restricted."
,
documentation
:
"
"
,
install
:
[
"
c
onda
install
gatk=3.8"
]
}
,{
name
:
"
gatk4"
,
version
:
"
4.0"
,
description
:
"
The
full
Genome
Analysis
Toolkit
(GATK)
framework,
license
restricted."
,
documentation
:
"
"
,
install
:
[
"
c
d
/opt/biotools;
apt-get
install
-y
openjdk-8-jdk;
wget
https://github.com/broadinstitute/gatk/releases/download/4.0.5.1/gatk-4.0.5.1.zip;unzip
gatk-4.0.5.1.zip;Rscript
-e
'
dependencies
=
c("
getopt"
,
"
optparse"
,
"
data.table"
,
"
ggplot2"
,
"
gplots"
,
"
gsalib"
); install.packages(dependencies)';"
],
env
:
"
export
PATH='$PATH':$PWD/gatk-4.0.5.1"
}
,{
name
:
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gcta"
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version
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1.24.7"
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description
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"
,
documentation
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"
,
install
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[
"
conda
install
-c
biobuilds
gcta=1.26.0"
]
}
,{
name
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gcta"
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version
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"
1.24.7"
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description
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"
"
,
documentation
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"
"
,
install
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[
"
conda
install
-c
biobuilds
gcta=1.26.0"
]
}
,{
name
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htslib"
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version
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1.8"
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description
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"
,
documentation
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"
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install
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[
"
conda
install
htslib=1.8"
]
}
,{
name
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"
htslib"
,
version
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"
1.8"
,
description
:
"
"
,
documentation
:
"
"
,
install
:
[
"
conda
install
htslib=1.8"
]
}
,{
name
:
"
jbrowse"
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version
:
"
1.12.1"
,
description
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"
"
,
documentation
:
"
"
,
install
:
[
"
conda
install
jbrowse=1.12.1"
]
}
,{
name
:
"
jbrowse"
,
version
:
"
1.12.1"
,
description
:
"
"
,
documentation
:
"
"
,
install
:
[
"
conda
install
jbrowse=1.12.1"
]
}
...
...
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