Skip to content
GitLab
Menu
Projects
Groups
Snippets
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
jlopez
RPACIB
Commits
711d5101
Commit
711d5101
authored
Jul 11, 2018
by
jlopez
Browse files
Add new tools & fix bugs
parent
9d0f89b2
Changes
3
Hide whitespace changes
Inline
Side-by-side
container.yaml
View file @
711d5101
...
@@ -4,7 +4,8 @@ containers: [
...
@@ -4,7 +4,8 @@ containers: [
,{
name
:
"
bamtools"
,
version
:
"
2.4.0"
,
description
:
"
C++
API
&
command-line
toolkit
for
working
with
BAM
data"
,
documentation
:
"
https://github.com/pezmaster31/bamtools/wiki"
,
install
:
[
"
conda
install
bamtools=2.4.0"
]
}
,{
name
:
"
bamtools"
,
version
:
"
2.4.0"
,
description
:
"
C++
API
&
command-line
toolkit
for
working
with
BAM
data"
,
documentation
:
"
https://github.com/pezmaster31/bamtools/wiki"
,
install
:
[
"
conda
install
bamtools=2.4.0"
]
}
,{
name
:
"
bcftools"
,
version
:
"
1.5"
,
description
:
"
Bcftools
is
a
program
for
variant
calling
and
manipulating
VCFs
and
BCFs"
,
documentation
:
"
https://samtools.github.io/bcftools/"
,
install
:
[
"
conda
install
bcftools=1.5"
]
}
,{
name
:
"
bcftools"
,
version
:
"
1.5"
,
description
:
"
Bcftools
is
a
program
for
variant
calling
and
manipulating
VCFs
and
BCFs"
,
documentation
:
"
https://samtools.github.io/bcftools/"
,
install
:
[
"
conda
install
bcftools=1.5"
]
}
,{
name
:
"
bedtools"
,
version
:
"
2.25.0"
,
description
:
"
a
powerful
toolset
for
genome
arithmetic"
,
documentation
:
"
http://quinlanlab.org/tutorials/bedtools/bedtools.html"
,
install
:
[
"
conda
install
bedtools=2.25.0"
]
}
,{
name
:
"
bedtools"
,
version
:
"
2.25.0"
,
description
:
"
a
powerful
toolset
for
genome
arithmetic"
,
documentation
:
"
http://quinlanlab.org/tutorials/bedtools/bedtools.html"
,
install
:
[
"
conda
install
bedtools=2.25.0"
]
}
,{
name
:
"
bior_annotate"
,
version
:
"
2.1.1"
,
description
:
"
"
,
documentation
:
"
"
,
install
:
[]
}
,{
name
:
"
bedtools"
,
version
:
"
2.27.1"
,
description
:
"
a
powerful
toolset
for
genome
arithmetic"
,
documentation
:
"
http://quinlanlab.org/tutorials/bedtools/bedtools.html"
,
install
:
[
"
conda
install
bedtools=2.27.1"
]
}
#,{ name: "bior_annotate", version: "2.1.1", description: "", documentation: "", install: [] }
,{
name
:
"
blast"
,
version
:
"
2.2.31"
,
description
:
"
basic
local
alignment
search
tool"
,
documentation
:
"
http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome"
,
install
:
[
"
conda
install
blast=2.2.31"
]
}
,{
name
:
"
blast"
,
version
:
"
2.2.31"
,
description
:
"
basic
local
alignment
search
tool"
,
documentation
:
"
http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome"
,
install
:
[
"
conda
install
blast=2.2.31"
]
}
,{
name
:
"
bowtie"
,
version
:
"
1.1.2"
,
description
:
"
an
ultrafast
memory-efficient
short
read
aligner"
,
documentation
:
"
http://bowtie-bio.sourceforge.net/manual.shtml"
,
install
:
[
"
conda
install
bowtie=1.1.2"
]
}
,{
name
:
"
bowtie"
,
version
:
"
1.1.2"
,
description
:
"
an
ultrafast
memory-efficient
short
read
aligner"
,
documentation
:
"
http://bowtie-bio.sourceforge.net/manual.shtml"
,
install
:
[
"
conda
install
bowtie=1.1.2"
]
}
,{
name
:
"
bowtie2"
,
version
:
"
2.2.8"
,
description
:
"
an
ultrafast
memory-efficient
short
read
aligner"
,
documentation
:
"
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml"
,
install
:
[
"
conda
install
bowtie2=2.2.8"
]
}
,{
name
:
"
bowtie2"
,
version
:
"
2.2.8"
,
description
:
"
an
ultrafast
memory-efficient
short
read
aligner"
,
documentation
:
"
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml"
,
install
:
[
"
conda
install
bowtie2=2.2.8"
]
}
...
@@ -15,6 +16,8 @@ containers: [
...
@@ -15,6 +16,8 @@ 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
:
"
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
:
"
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
:
"
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
:
"
CNVnator"
,
version
:
"
0.3.3"
,
description
:
"
an
approach
to
discover,
genotype,
and
characterize
typical
and
atypical
CNVs
from
family
and
population
genome
sequencing."
,
documentation
:
"
https://github.com/abyzovlab/CNVnator"
,
install
:
[
"
cd
/opt/biotools/
;
wget
--quiet
https://root.cern.ch/download/root_v6.10.08.Linux-ubuntu16-x86_64-gcc5.4.tar.gz
;
tar
zxf
root_v6.10.08.Linux-ubuntu16-x86_64-gcc5.4.tar.gz"
,
"
export
ROOTSYS=/opt/biotools/root"
,
"
export
LD_LIBRARY_PATH=
\"
$ROOTSYS/lib:$LD_LIBRARY_PATH
\"
"
,
"
echo
'export
ROOTSYS=/opt/biotools/root'
>>
$SINGULARITY_ENVIRONMENT"
,
"
echo
'export
LD_LIBRARY_PATH=
\"
$ROOTSYS/lib:$LD_LIBRARY_PATH
\"
'
>>
$SINGULARITY_ENVIRONMENT"
,
"
cd
/opt/biotools/
;
wget
https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2
-O
bcftools.tar.bz2
;
tar
-xjvf
bcftools.tar.bz2
;
cd
bcftools-1.3.1/
;
make
;
make
prefix=/usr/local/bin
install"
,
"
ln
-s
/usr/local/bin/bin/bcftools
/usr/bin/bcftools
"
,
"
cd
/opt/biotools/
;
wget
--quiet
https://github.com/abyzovlab/CNVnator/releases/download/v0.3.3/CNVnator_v0.3.3.zip
;
unzip
CNVnator_v0.3.3.zip
;
cd
CNVnator_v0.3.3/src/samtools/htslib-1.3.1/
;
make
;
make
install
;
cd
../
;
make
;
make
install
;
cd
../
;
make"
,
"
ln
-s
/opt/biotools/CNVnator_v0.3.3/src/cnvnator
/opt/biotools/bin/cnvnator"
]
}
,{
name
:
"
cnv-seq"
,
version
:
"
1.0"
,
description
:
"
CNV-seq,
a
new
method
to
detect
copy
number
variation
using
high-throughput
sequencing"
,
documentation
:
"
http://tiger.dbs.nus.edu.sg/cnv-seq/"
,
install
:
[
"
cd
/opt/biotools/
;
wget
http://tiger.dbs.nus.edu.sg/cnv-seq/cnv-seq.tar.gz;
tar
-xvf
cnv-seq.tar.gz;
ln
-s
/opt/biotools/cnv-seq/cnv-seq.pl
bin/cnv-seq"
]}
,{
name
:
"
cross-species-scaffolding"
,
version
:
"
0.1"
,
description
:
"
Generate
in
silico
mate-pair
reads
from
single-/paired-end
reads
of
your
organism
of
interest"
,
documentation
:
"
https://github.com/thackl/cross-species-scaffolding"
,
install
:
[
"
cd
/opt/biotools;
rm
-rf
cross-species-scaffolding;
git
clone
https://github.com/thackl/cross-species-scaffolding.git
;
cd
cross-species-scaffolding;
mkdir
samples;
make
util/bcftools;
make
util/samtools;
make
dependencies;"
],
env
:
"
export
PATH=/opt/biotools/cross-species-scaffolding/bin:/opt/biotools/cross-species-scaffolding/util/samtools:$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
;
cd
cross-species-scaffolding;
mkdir
samples;
make
util/bcftools;
make
util/samtools;
make
dependencies;"
],
env
:
"
export
PATH=/opt/biotools/cross-species-scaffolding/bin:/opt/biotools/cross-species-scaffolding/util/samtools:$PATH"
}
,{
name
:
"
crux"
,
version
:
"
2.1"
,
description
:
"
a
software
toolkit
for
tandem
mass
spectrometry
analysis"
,
documentation
:
"
http://cruxtoolkit.sourceforge.net/"
,
install
:
[]
}
,{
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
:
"
1.10.4"
,
description
:
"
graphical
user
interface
for
de
novo
sequencing
of
tandem
mass
spectra"
,
documentation
:
"
https://github.com/compomics/denovogui"
,
install
:
[]
}
...
@@ -55,6 +58,8 @@ containers: [
...
@@ -55,6 +58,8 @@ containers: [
,{
name
:
"
proteinprophet"
,
version
:
"
201510131012"
,
description
:
"
Protein
inference
for
MS/MS
analysis"
,
documentation
:
"
http://proteinprophet.sourceforge.net/"
,
install
:
[]
}
,{
name
:
"
proteinprophet"
,
version
:
"
201510131012"
,
description
:
"
Protein
inference
for
MS/MS
analysis"
,
documentation
:
"
http://proteinprophet.sourceforge.net/"
,
install
:
[]
}
,{
name
:
"
proteowizard"
,
version
:
"
3_0_9992"
,
description
:
"
tools
and
software
libraries
that
facilitate
proteomics
data
analysis"
,
documentation
:
"
http://proteowizard.sourceforge.net/"
,
install
:
[
"
conda
install
proteowizard=3_0_9992"
]
}
,{
name
:
"
proteowizard"
,
version
:
"
3_0_9992"
,
description
:
"
tools
and
software
libraries
that
facilitate
proteomics
data
analysis"
,
documentation
:
"
http://proteowizard.sourceforge.net/"
,
install
:
[
"
conda
install
proteowizard=3_0_9992"
]
}
,{
name
:
"
raremetalworker"
,
version
:
"
4.13.7"
,
description
:
"
single
variant
analysis,
generating
summary
statistics
for
gene
level
meta
analyses"
,
documentation
:
"
http://genome.sph.umich.edu/wiki/RAREMETALWORKER"
,
install
:
[]
}
,{
name
:
"
raremetalworker"
,
version
:
"
4.13.7"
,
description
:
"
single
variant
analysis,
generating
summary
statistics
for
gene
level
meta
analyses"
,
documentation
:
"
http://genome.sph.umich.edu/wiki/RAREMETALWORKER"
,
install
:
[]
}
,{
name
:
"
repeatmasker"
,
version
:
"
4.0.6"
,
description
:
"
RepeatMasker
is
a
program
that
screens
DNA
sequences
for
interspersed
repeats
and
low
complexity
DNA
sequences."
,
documentation
:
"
http://www.repeatmasker.org/"
,
install
:
[
"
conda
install
-c
bioconda
repeatmasker=4.0.6;
mkdir
/share;
ln
-s
/opt/conda/share/RepeatMasker
/share/RepeatMasker"
]}
#,{ name: "root", version: "6.04", description: "", documentation: "", install: ["conda install -c nlesc root=6.04"]}
,{
name
:
"
saintq"
,
version
:
"
0.0.2"
,
description
:
"
assigning
confidence
scores
to
protein-protein
interactions
based
on
quantitative
proteomics"
,
documentation
:
"
http://saint-apms.sourceforge.net/Main.html"
,
install
:
[]
}
,{
name
:
"
saintq"
,
version
:
"
0.0.2"
,
description
:
"
assigning
confidence
scores
to
protein-protein
interactions
based
on
quantitative
proteomics"
,
documentation
:
"
http://saint-apms.sourceforge.net/Main.html"
,
install
:
[]
}
,{
name
:
"
samtools"
,
version
:
"
1.2"
,
description
:
"
Tools
for
manipulating
next-generation
sequencing
data"
,
documentation
:
"
https://github.com/samtools/samtools"
,
install
:
[
"
conda
install
samtools=1.2"
]
}
,{
name
:
"
samtools"
,
version
:
"
1.2"
,
description
:
"
Tools
for
manipulating
next-generation
sequencing
data"
,
documentation
:
"
https://github.com/samtools/samtools"
,
install
:
[
"
conda
install
samtools=1.2"
]
}
,{
name
:
"
samtools"
,
version
:
"
1.3"
,
description
:
"
Tools
for
manipulating
next-generation
sequencing
data"
,
documentation
:
"
https://github.com/samtools/samtools"
,
install
:
[
"
conda
install
samtools=1.3"
]
}
,{
name
:
"
samtools"
,
version
:
"
1.3"
,
description
:
"
Tools
for
manipulating
next-generation
sequencing
data"
,
documentation
:
"
https://github.com/samtools/samtools"
,
install
:
[
"
conda
install
samtools=1.3"
]
}
...
@@ -75,6 +80,8 @@ containers: [
...
@@ -75,6 +80,8 @@ containers: [
,{
name
:
"
toppas"
,
version
:
"
1.11.1-3"
,
description
:
"
a
graphical
workflow
editor
for
the
analysis
of
high-throughput
proteomics
data"
,
documentation
:
"
http://open-ms.sourceforge.net/workflow-integration/toppasworkflows/"
,
install
:
[]
}
,{
name
:
"
toppas"
,
version
:
"
1.11.1-3"
,
description
:
"
a
graphical
workflow
editor
for
the
analysis
of
high-throughput
proteomics
data"
,
documentation
:
"
http://open-ms.sourceforge.net/workflow-integration/toppasworkflows/"
,
install
:
[]
}
,{
name
:
"
TPMCalculator"
,
version
:
"
0.0.1"
,
description
:
"
This
program
calculates
the
TPM
(Transcript
per
Millions)
values
for
the
exons
and
introns
from
NGS
RNA-Seq
aligned
reads
(BAM
files)"
,
documentation
:
"
https://github.com/r78v10a07/TPMCalculator"
,
install
:
[]
}
,{
name
:
"
TPMCalculator"
,
version
:
"
0.0.1"
,
description
:
"
This
program
calculates
the
TPM
(Transcript
per
Millions)
values
for
the
exons
and
introns
from
NGS
RNA-Seq
aligned
reads
(BAM
files)"
,
documentation
:
"
https://github.com/r78v10a07/TPMCalculator"
,
install
:
[]
}
,{
name
:
"
tpp"
,
version
:
"
5.0"
,
description
:
"
a
collection
of
integrated
tools
for
MS/MS
proteomics"
,
documentation
:
"
http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP"
,
install
:
[]
}
,{
name
:
"
tpp"
,
version
:
"
5.0"
,
description
:
"
a
collection
of
integrated
tools
for
MS/MS
proteomics"
,
documentation
:
"
http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP"
,
install
:
[]
}
,{
name
:
"
trf"
,
version
:
"
4.09"
,
description
:
"
Tandem
Repeats
Finder
is
a
program
to
locate
and
display
tandem
repeats
in
DNA
sequences."
,
documentation
:
"
https://tandem.bu.edu/trf/trf.html"
,
install
:
[
"
conda
install
-c
bioconda
trf=4.09"
]}
,{
name
:
"
trimmomatic"
,
version
:
"
0.36"
,
description
:
"
Trimmomatic
performs
a
variety
of
useful
trimming
tasks
for
illumina
paired-end
and
single
ended
data.The
selection
of
trimming
steps
and
their
associated
parameters
are
supplied
on
the
command
line."
,
documentation
:
"
http://www.usadellab.org/cms/?page=trimmomatic"
,
install
:
[
"
conda
install
-c
bioconda
trimmomatic=0.36"
]
}
,{
name
:
"
vcftools"
,
version
:
"
0.1.14"
,
description
:
"
A
set
of
tools
written
in
Perl
and
C++
for
working
with
VCF
files,
such
as
those
generated
by
the
1000
Genomes
Project"
,
documentation
:
"
https://github.com/vcftools/vcftools|https://vcftools.github.io/index.html"
,
install
:
[
"
conda
install
vcftools=0.1.14"
]
}
,{
name
:
"
vcftools"
,
version
:
"
0.1.14"
,
description
:
"
A
set
of
tools
written
in
Perl
and
C++
for
working
with
VCF
files,
such
as
those
generated
by
the
1000
Genomes
Project"
,
documentation
:
"
https://github.com/vcftools/vcftools|https://vcftools.github.io/index.html"
,
install
:
[
"
conda
install
vcftools=0.1.14"
]
}
,{
name
:
"
vcftools"
,
version
:
"
0.1.15"
,
description
:
"
A
set
of
tools
written
in
Perl
and
C++
for
working
with
VCF
files,
such
as
those
generated
by
the
1000
Genomes
Project"
,
documentation
:
"
https://github.com/vcftools/vcftools|https://vcftools.github.io/index.html"
,
install
:
[
"
conda
install
vcftools=0.1.15"
]
}
,{
name
:
"
vcftools"
,
version
:
"
0.1.15"
,
description
:
"
A
set
of
tools
written
in
Perl
and
C++
for
working
with
VCF
files,
such
as
those
generated
by
the
1000
Genomes
Project"
,
documentation
:
"
https://github.com/vcftools/vcftools|https://vcftools.github.io/index.html"
,
install
:
[
"
conda
install
vcftools=0.1.15"
]
}
,{
name
:
"
velvet"
,
version
:
"
1.2.10"
,
description
:
"
Short
read
de
novo
assembler
using
de
Bruijn
graphs"
,
documentation
:
"
https://www.zfmk.de/dateien/atoms/files/aliscore_v.2.0_manual_0.pdf"
,
install
:
[
"
conda
install
velvet=1.2.10"
]
}
,{
name
:
"
velvet"
,
version
:
"
1.2.10"
,
description
:
"
Short
read
de
novo
assembler
using
de
Bruijn
graphs"
,
documentation
:
"
https://www.zfmk.de/dateien/atoms/files/aliscore_v.2.0_manual_0.pdf"
,
install
:
[
"
conda
install
velvet=1.2.10"
]
}
...
...
pages/pages_def_home.R
View file @
711d5101
...
@@ -33,7 +33,9 @@ tabHome = fluidPage(align="left",
...
@@ -33,7 +33,9 @@ tabHome = fluidPage(align="left",
textInput
(
"imageName"
,
"Image Name"
,
""
),
textInput
(
"imageName"
,
"Image Name"
,
""
),
br
(),
br
(),
selectizeInput
(
'fromTemplate'
,
'From:'
,
choices
=
c
(
`ubuntu:16.04`
=
'ubuntu:16.04'
,
`r-base`
=
'r-base'
),
selected
=
"r-base"
,
multiple
=
FALSE
),
#selectizeInput('fromTemplate', 'From:', choices = c(`ubuntu:16.04` = 'ubuntu:16.04', `r-base` = 'r-base'), selected = "r-base", multiple = FALSE),
selectizeInput
(
'fromTemplate'
,
'From:'
,
choices
=
c
(
`ubuntu:16.04`
=
'ubuntu:16.04'
),
selected
=
"ubuntu:16.04"
,
multiple
=
FALSE
),
br
(),
br
(),
radioButtons
(
"containerType"
,
"Container type:"
,
choices
=
list
(
"Singularity"
=
"singularity"
,
"Docker"
=
"docker"
),
selected
=
"singularity"
),
radioButtons
(
"containerType"
,
"Container type:"
,
choices
=
list
(
"Singularity"
=
"singularity"
,
"Docker"
=
"docker"
),
selected
=
"singularity"
),
br
(),
br
(),
...
...
server/opt_home.R
View file @
711d5101
...
@@ -79,6 +79,8 @@ createEnv <- function(result) {
...
@@ -79,6 +79,8 @@ createEnv <- function(result) {
if
(
!
is.null
(
input
$
dtbiocontainer_rows_all
))
{
if
(
!
is.null
(
input
$
dtbiocontainer_rows_all
))
{
result
<-
paste
(
result
,
"\texport PATH=/opt/conda/bin:$PATH"
,
sep
=
"\n"
)
result
<-
paste
(
result
,
"\texport PATH=/opt/conda/bin:$PATH"
,
sep
=
"\n"
)
result
<-
paste
(
result
,
"\texport PATH=/opt/biotools/bin:$PATH"
,
sep
=
"\n"
)
result
<-
paste
(
result
,
"\texport PATH=/opt/biotools/bin:$PATH"
,
sep
=
"\n"
)
result
<-
paste
(
result
,
"\texport ROOTSYS=/opt/biotools/root"
,
sep
=
"\n"
)
result
<-
paste
(
result
,
"\texport LD_LIBRARY_PATH='$LD_LIBRARY_PATH:$ROOTSYS/lib'"
,
sep
=
"\n"
)
result
<-
createPathBiocontainer
(
result
)
result
<-
createPathBiocontainer
(
result
)
}
}
...
@@ -103,6 +105,9 @@ createEnv <- function(result) {
...
@@ -103,6 +105,9 @@ createEnv <- function(result) {
if
(
!
is.null
(
input
$
dtbiocontainer_rows_all
))
{
if
(
!
is.null
(
input
$
dtbiocontainer_rows_all
))
{
result
<-
paste
(
result
,
"RUN export PATH=/opt/conda/bin:$PATH"
,
sep
=
"\n"
)
result
<-
paste
(
result
,
"RUN export PATH=/opt/conda/bin:$PATH"
,
sep
=
"\n"
)
result
<-
paste
(
result
,
"RUN export PATH=/opt/biotools/bin:$PATH"
,
sep
=
"\n"
)
result
<-
paste
(
result
,
"RUN export PATH=/opt/biotools/bin:$PATH"
,
sep
=
"\n"
)
result
<-
paste
(
result
,
"RUN export ROOTSYS=/opt/biotools/root"
,
sep
=
"\n"
)
result
<-
paste
(
result
,
"RUN export LD_LIBRARY_PATH='$LD_LIBRARY_PATH:$ROOTSYS/lib'"
,
sep
=
"\n"
)
result
<-
createPathBiocontainer
(
result
)
result
<-
createPathBiocontainer
(
result
)
}
}
}
}
...
@@ -390,7 +395,7 @@ createBiocontainer <- function(result, haveR) {
...
@@ -390,7 +395,7 @@ createBiocontainer <- function(result, haveR) {
result
<-
paste0
(
result
,
"\n"
)
result
<-
paste0
(
result
,
"\n"
)
result
<-
paste
(
result
,
"\tapt-get install -y autotools-dev automake cmake curl grep sed dpkg fuse git zip openjdk-8-jre build-essential pkg-config python python-dev python-pip bzip2 ca-certificates libglib2.0-0 libxext6 libsm6 libxrender1 mercurial subversion zlib1g-dev"
,
sep
=
"\n"
)
result
<-
paste
(
result
,
"\tapt-get install -y autotools-dev automake cmake curl grep sed dpkg fuse git zip openjdk-8-jre build-essential pkg-config python python-dev python-pip bzip2 ca-certificates libglib2.0-0 libxext6 libsm6 libxrender1 mercurial subversion zlib1g-dev
libncurses5-dev libncursesw5-dev
"
,
sep
=
"\n"
)
result
<-
paste
(
result
,
"\tapt-get update"
,
sep
=
"\n"
)
result
<-
paste
(
result
,
"\tapt-get update"
,
sep
=
"\n"
)
result
<-
paste0
(
result
,
"\n"
)
result
<-
paste0
(
result
,
"\n"
)
...
@@ -439,7 +444,7 @@ createBiocontainer <- function(result, haveR) {
...
@@ -439,7 +444,7 @@ createBiocontainer <- function(result, haveR) {
result
<-
paste0
(
result
,
"\n"
)
result
<-
paste0
(
result
,
"\n"
)
result
<-
paste
(
result
,
"RUN apt-get install -y autotools-dev automake cmake curl grep sed dpkg fuse git zip openjdk-8-jre build-essential pkg-config python python-dev python-pip bzip2 ca-certificates libglib2.0-0 libxext6 libsm6 libxrender1 mercurial subversion zlib1g-dev"
,
sep
=
"\n"
)
result
<-
paste
(
result
,
"RUN apt-get install -y autotools-dev automake cmake curl grep sed dpkg fuse git zip openjdk-8-jre build-essential pkg-config python python-dev python-pip bzip2 ca-certificates libglib2.0-0 libxext6 libsm6 libxrender1 mercurial subversion zlib1g-dev
libncurses5-dev libncursesw5-dev
"
,
sep
=
"\n"
)
result
<-
paste
(
result
,
"RUN apt-get update"
,
sep
=
"\n"
)
result
<-
paste
(
result
,
"RUN apt-get update"
,
sep
=
"\n"
)
result
<-
paste0
(
result
,
"\n"
)
result
<-
paste0
(
result
,
"\n"
)
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a 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