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jlopez
RPACIB
Commits
e67ec0ef
Commit
e67ec0ef
authored
Jun 13, 2018
by
jlopez
Browse files
Add export bioinfotools
parent
b2d566e5
Changes
3
Hide whitespace changes
Inline
Side-by-side
R/helper_functions.R
View file @
e67ec0ef
...
...
@@ -86,5 +86,32 @@ getInstallToolPackageBioContainer <- function(tool, containerType) {
}
getInstallToolEnvBioContainer
<-
function
(
tool
,
containerType
)
{
data
<-
allBIOCONTAINER
size
<-
length
(
data
)
intalls
<-
""
for
(
tools
in
data
)
{
splitB
<-
strsplit
(
tool
,
"%"
)
name
<-
splitB
[[
1
]][
1
]
version
<-
splitB
[[
1
]][
2
]
if
(
tools
$
name
==
name
)
{
if
(
tools
$
version
==
version
)
{
if
(
is.null
(
tools
$
env
))
{
return
(
FALSE
)
}
else
{
return
(
tools
$
env
)
}
}
}
}
return
(
FALSE
)
}
container.yaml
View file @
e67ec0ef
...
...
@@ -15,7 +15,7 @@ containers: [
,{
name
:
"
cava"
,
version
:
"
1.1.1"
,
description
:
"
lightweight,
fast
and
flexible
NGS
variant
annotation
tool"
,
documentation
:
"
http://www.well.ox.ac.uk/cava"
,
install
:
[]
}
,{
name
:
"
clustal-omega"
,
version
:
"
1.2.1-1"
,
description
:
"
general
purpose
multiple
sequence
alignment
program
for
proteins"
,
documentation
:
"
http://www.clustal.org/omega/#Documentation"
,
install
:
[
"
apt-get
install
clustalo"
]
}
,{
name
:
"
comet"
,
version
:
"
1.1.0"
,
description
:
"
an
open
source
tandem
mass
spectrometry
sequence
database
search
tool"
,
documentation
:
"
http://comet-ms.sourceforge.net/parameters/parameters_2016010/"
,
install
:
[
"
conda
install
-c
auto
comet=1.1.0"
]
}
,{
name
:
"
cross-species-scaffolding"
,
version
:
"
0.1"
,
description
:
"
Generate
in
silico
mate-pair
reads
from
single-/paired-end
reads
of
your
organism
of
interest"
,
documentation
:
"
https://github.com/thackl/cross-species-scaffolding"
,
install
:
[
"
cd
/opt/biotools;
rm
-rf
cross-species-scaffolding;
git
clone
https://github.com/thackl/cross-species-scaffolding.git
;
apt-get
-y
install
samtools;
cd
cross-species-scaffolding;
mkdir
samples;
make
dependencies;"
],
env
:
"
export
PATH=
'
/opt/biotools/cross-species-scaffolding/bin
'
:$PATH"
}
,{
name
:
"
cross-species-scaffolding"
,
version
:
"
0.1"
,
description
:
"
Generate
in
silico
mate-pair
reads
from
single-/paired-end
reads
of
your
organism
of
interest"
,
documentation
:
"
https://github.com/thackl/cross-species-scaffolding"
,
install
:
[
"
cd
/opt/biotools;
rm
-rf
cross-species-scaffolding;
git
clone
https://github.com/thackl/cross-species-scaffolding.git
;
apt-get
-y
install
samtools;
cd
cross-species-scaffolding;
mkdir
samples;
make
dependencies;"
],
env
:
"
export
PATH=/opt/biotools/cross-species-scaffolding/bin:$PATH"
}
,{
name
:
"
crux"
,
version
:
"
2.1"
,
description
:
"
a
software
toolkit
for
tandem
mass
spectrometry
analysis"
,
documentation
:
"
http://cruxtoolkit.sourceforge.net/"
,
install
:
[]
}
,{
name
:
"
denovogui"
,
version
:
"
1.10.4"
,
description
:
"
graphical
user
interface
for
de
novo
sequencing
of
tandem
mass
spectra"
,
documentation
:
"
https://github.com/compomics/denovogui"
,
install
:
[]
}
,{
name
:
"
denovogui"
,
version
:
"
1.5.2"
,
description
:
"
graphical
user
interface
for
de
novo
sequencing
of
tandem
mass
spectra"
,
documentation
:
"
https://github.com/compomics/denovogui"
,
install
:
[]
}
...
...
@@ -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
:
"
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
:
"
gatk"
,
version
:
"
3.8"
,
description
:
"
The
full
Genome
Analysis
Toolkit
(GATK)
framework,
license
restricted."
,
documentation
:
"
"
,
install
:
[
"
conda
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
:
"
gatk4"
,
version
:
"
4.0"
,
description
:
"
The
full
Genome
Analysis
Toolkit
(GATK)
framework,
license
restricted."
,
documentation
:
"
"
,
install
:
[
"
c
onda
install
-c
bioconda
gatk4"
]
}
,{
name
:
"
gcta"
,
version
:
"
1.24.7"
,
description
:
"
"
,
documentation
:
"
"
,
install
:
[
"
conda
install
-c
biobuilds
gcta=1.26.0"
]
}
,{
name
:
"
htslib"
,
version
:
"
1.8"
,
description
:
"
"
,
documentation
:
"
"
,
install
:
[
"
conda
install
htslib=1.8"
]
}
,{
name
:
"
jbrowse"
,
version
:
"
1.12.1"
,
description
:
"
"
,
documentation
:
"
"
,
install
:
[
"
conda
install
jbrowse=1.12.1"
]
}
...
...
@@ -63,7 +63,7 @@ containers: [
,{
name
:
"
soapec"
,
version
:
"
2.03"
,
description
:
"
A
correction
tool
for
SOAPdenovo"
,
documentation
:
"
http://soap.genomics.org.cn/soapdenovo.html"
,
install
:
[
"
conda
install
soapec=2.03"
]
}
,{
name
:
"
spades"
,
version
:
"
3.11.1"
,
description
:
"
Tools
(written
in
C
using
htslib)
for
manipulating
next-generation
sequencing
data"
,
documentation
:
"
http://bioinf.spbau.ru/spades"
,
install
:
[
"
conda
install
spades=3.11.1"
]
}
,{
name
:
"
spectra-cluster-cli"
,
version
:
"
1.0.1"
,
description
:
"
PRIDE
Cluster
algorithm
to
cluster
heterogeneous
mass
spectra"
,
documentation
:
"
https://github.com/spectra-cluster/spectra-cluster-cli"
,
install
:
[
"
conda
install
spectra-cluster-cli=1.0.1"
]
}
,{
name
:
"
sra-tools"
,
version
:
"
latest"
,
description
:
"
"
,
documentation
:
"
"
,
installation
:
[
"
cd
/opt/biotools;
wget
--output-document
sratoolkit.tar.gz
http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-ubuntu64.tar.gz;
tar
-vxzf
sratoolkit.tar.gz;
rm
sratoolkit.tar.gz;
mv
sratoolkit.*-ubuntu64
sratoolkit"
],
env
:
"
export
PATH=
'
$PATH
'
:$PWD/sratoolkit/bin"
]
}
,{
name
:
"
sra-tools"
,
version
:
"
latest"
,
description
:
"
"
,
documentation
:
"
"
,
installation
:
[
"
cd
/opt/biotools;
wget
--output-document
sratoolkit.tar.gz
http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-ubuntu64.tar.gz;
tar
-vxzf
sratoolkit.tar.gz;
rm
sratoolkit.tar.gz;
mv
sratoolkit.*-ubuntu64
sratoolkit"
],
env
:
"
export
PATH=$PATH:$PWD/sratoolkit/bin"
}
,{
name
:
"
stacks"
,
version
:
"
1.44"
,
description
:
"
Stacks
was
developed
to
work
with
restriction
enzyme-based
data,
such
as
RAD-seq,
for
the
purpose
of
building
genetic
maps
and
conducting
population"
,
documentation
:
"
http://catchenlab.life.illinois.edu/stacks/"
,
install
:
[
"
conda
install
stacks=1.44"
]
}
,{
name
:
"
stacks"
,
version
:
"
2.0"
,
description
:
"
Stacks
was
developed
to
work
with
restriction
enzyme-based
data,
such
as
RAD-seq,
for
the
purpose
of
building
genetic
maps
and
conducting
population"
,
documentation
:
"
http://catchenlab.life.illinois.edu/stacks/"
,
install
:
[
"
wget
http://catchenlab.life.illinois.edu/stacks/source/stacks-2.0.tar.gz
\\
"
,
"
&&
tar
-zxvf
stacks-2.0.tar.gz
-C
/opt/biotools/bin/
\\
"
,
"
&&
cd
/opt/biotools/bin/stacks-2.0/
\\
"
,
"
&&
./configure
\\
"
,
"
&&
make
\\
"
,
"
&&
make
install"
]}
,{
name
:
"
tandem"
,
version
:
"
10-12-01-1"
,
description
:
"
software
that
can
match
tandem
mass
spectra
with
peptide
sequences"
,
documentation
:
"
http://www.thegpm.org/tandem/"
,
install
:
[]
}
...
...
server/opt_home.R
View file @
e67ec0ef
...
...
@@ -79,7 +79,11 @@ createEnv <- function(result) {
if
(
!
is.null
(
input
$
dtbiocontainer_rows_all
))
{
result
<-
paste
(
result
,
"\texport PATH=/opt/conda/bin:$PATH"
,
sep
=
"\n"
)
result
<-
paste
(
result
,
"\texport PATH=/opt/biotools/bin:$PATH"
,
sep
=
"\n"
)
result
<-
createPathBiocontainer
(
result
)
}
}
else
{
if
(
input
$
rtemplate
==
"none"
||
input
$
fromTemplate
==
"r-base"
)
{
...
...
@@ -99,6 +103,7 @@ createEnv <- function(result) {
if
(
!
is.null
(
input
$
dtbiocontainer_rows_all
))
{
result
<-
paste
(
result
,
"RUN export PATH=/opt/conda/bin:$PATH"
,
sep
=
"\n"
)
result
<-
paste
(
result
,
"RUN export PATH=/opt/biotools/bin:$PATH"
,
sep
=
"\n"
)
result
<-
createPathBiocontainer
(
result
)
}
}
...
...
@@ -345,6 +350,47 @@ createBioconductorPackage <- function(result) {
return
(
result
)
}
createPathBiocontainer
<-
function
(
result
)
{
print
(
"PATH"
)
if
(
input
$
containerType
==
"singularity"
)
{
selectBioTool
<-
input
$
selectedBiocontainer
for
(
tool
in
selectBioTool
){
print
(
tool
)
to
<-
getInstallToolEnvBioContainer
(
tool
,
input
$
containerType
)
print
(
to
)
if
(
is.character
(
to
))
{
result
<-
paste0
(
result
,
"\n\t"
,
to
)
}
}
}
else
{
selectBioTool
<-
input
$
selectedBiocontainer
for
(
tool
in
selectBioTool
){
to
<-
getInstallToolEnvBioContainer
(
tool
,
input
$
containerType
)
if
(
is.character
(
to
))
{
result
<-
paste0
(
result
,
"\nRUN "
,
to
)
}
}
}
print
(
result
)
return
(
result
)
}
#' Use for create Biocontainer content
createBiocontainer
<-
function
(
result
,
haveR
)
{
...
...
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