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
jlopez
RPACIB
Commits
cfcbf3b2
Commit
cfcbf3b2
authored
Apr 04, 2018
by
jlopez
Browse files
Add more biocontainer tools
parent
f24268e1
Changes
3
Hide whitespace changes
Inline
Side-by-side
container.yaml
View file @
cfcbf3b2
...
...
@@ -14,51 +14,38 @@ containers: [
,{
name
:
"
bwa"
,
version
:
"
0.7.15"
,
description
:
"
Burrow-Wheeler
Aligner
for
pairwise
alignment
between
DNA
sequences"
,
documentation
:
"
http://bio-bwa.sourceforge.net/"
,
install
:
[
"
conda
install
bwa=0.7.15"
]
}
,{
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
:
"
2015011"
,
description
:
"
an
open
source
tandem
mass
spectrometry
sequence
database
search
tool"
,
documentation
:
"
http://comet-ms.sourceforge.net/parameters/parameters_201601/"
,
install
:
[]
}
,{
name
:
"
comet"
,
version
:
"
2015012"
,
description
:
"
an
open
source
tandem
mass
spectrometry
sequence
database
search
tool"
,
documentation
:
"
http://comet-ms.sourceforge.net/parameters/parameters_201601/"
,
install
:
[]
}
,{
name
:
"
comet"
,
version
:
"
2015020"
,
description
:
"
an
open
source
tandem
mass
spectrometry
sequence
database
search
tool"
,
documentation
:
"
http://comet-ms.sourceforge.net/parameters/parameters_201601/"
,
install
:
[]
}
,{
name
:
"
comet"
,
version
:
"
2015025"
,
description
:
"
an
open
source
tandem
mass
spectrometry
sequence
database
search
tool"
,
documentation
:
"
http://comet-ms.sourceforge.net/parameters/parameters_201601/"
,
install
:
[]
}
,{
name
:
"
comet"
,
version
:
"
2016010"
,
description
:
"
an
open
source
tandem
mass
spectrometry
sequence
database
search
tool"
,
documentation
:
"
http://comet-ms.sourceforge.net/parameters/parameters_2016010/"
,
install
:
[]
}
,{
name
:
"
comet"
,
version
:
"
2016011"
,
description
:
"
an
open
source
tandem
mass
spectrometry
sequence
database
search
tool"
,
documentation
:
"
http://comet-ms.sourceforge.net/parameters/parameters_2016010/"
,
install
:
[]
}
,{
name
:
"
comet"
,
version
:
"
2016012"
,
description
:
"
an
open
source
tandem
mass
spectrometry
sequence
database
search
tool"
,
documentation
:
"
http://comet-ms.sourceforge.net/parameters/parameters_2016010/"
,
install
:
[]
}
,{
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
:
"
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
:
[]
}
,{
name
:
"
dia-umpire"
,
version
:
"
1.4256"
,
description
:
"
computational
analysis
of
data
independent
acquisition
(DIA)
mass
spectrometry-based
proteomics
data"
,
documentation
:
"
http://diaumpire.sourceforge.net"
,
install
:
[]
}
,{
name
:
"
dia-umpire"
,
version
:
"
2.1.2"
,
description
:
"
computational
analysis
of
data
independent
acquisition
(DIA)
mass
spectrometry-based
proteomics
data"
,
documentation
:
"
http://diaumpire.sourceforge.net"
,
install
:
[]
}
,{
name
:
"
dia-umpire"
,
version
:
"
2.1.3"
,
description
:
"
computational
analysis
of
data
independent
acquisition
(DIA)
mass
spectrometry-based
proteomics
data"
,
documentation
:
"
http://diaumpire.sourceforge.net"
,
install
:
[
"
conda
install
dia_umpire=2.1.3"
]
}
,{
name
:
"
DiffExpIR"
,
version
:
"
0.0.1"
,
description
:
"
Differentially
expressed
intron
retention"
,
documentation
:
"
https://github.com/r78v10a07/DiffExpIR"
,
install
:
[]
}
,{
name
:
"
discovar"
,
version
:
"
52488"
,
description
:
"
DISCOVAR
is
a
new
variant
caller"
,
documentation
:
"
http://www.broadinstitute.org/software/discovar/blog/?page_id=19"
,
install
:
[]
}
,{
name
:
"
discovardenovo"
,
version
:
"
52488"
,
description
:
"
Genome
variant
discovery
through
assembly"
,
documentation
:
"
http://www.broadinstitute.org/software/discovar/blog/?page_id=19"
,
install
:
[]
}
,{
name
:
"
discovar"
,
version
:
"
52488"
,
description
:
"
DISCOVAR
is
a
new
variant
caller"
,
documentation
:
"
http://www.broadinstitute.org/software/discovar/blog/?page_id=19"
,
install
:
[
"
conda
install
discovardenovo=52488"
]
}
,{
name
:
"
discovardenovo"
,
version
:
"
52488"
,
description
:
"
Genome
variant
discovery
through
assembly"
,
documentation
:
"
http://www.broadinstitute.org/software/discovar/blog/?page_id=19"
,
install
:
[
"
conda
install
discovardenovo=52488"
]
}
,{
name
:
"
emboss"
,
version
:
"
6.5.7"
,
description
:
"
software
analysis
package"
,
documentation
:
"
http://emboss.sourceforge.net/docs/"
,
install
:
[
"
conda
install
emboss=6.5.7"
]
}
,{
name
:
"
entrez-direct"
,
version
:
"
7.50.20171103
"
,
description
:
"
Entrez
Direct
(EDirect)
is
an
advanced
method
for
accessing
the
NCBI's
set
of
interconnected
Entrez
databases"
,
documentation
:
"
https://ncbi.github.io/magicblast/"
,
install
:
[
]
}
,{
name
:
"
fastqc"
,
version
:
"
0.11.5"
,
description
:
"
A
quality
control
tool
for
high
throughput
sequence
data."
,
documentation
:
"
http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/"
,
install
:
[]
}
,{
name
:
"
fastxtools"
,
version
:
"
0.0.14"
,
description
:
"
a
collection
of
command
line
tools
for
Short-Reads
FASTA/FASTQ
files
preprocessing"
,
documentation
:
"
http://hannonlab.cshl.edu/fastx_toolkit/commandline.html"
,
install
:
[]
}
,{
name
:
"
entrez-direct"
,
version
:
"
5.80
"
,
description
:
"
Entrez
Direct
(EDirect)
is
an
advanced
method
for
accessing
the
NCBI's
set
of
interconnected
Entrez
databases"
,
documentation
:
"
"
,
install
:
[
"
conda
install
entrez-direct=5.80"
]
}
,{
name
:
"
fastqc"
,
version
:
"
0.11.5"
,
description
:
"
A
quality
control
tool
for
high
throughput
sequence
data."
,
documentation
:
"
http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/"
,
install
:
[
"
conda
install
-c
bioconda
fastqc=0.11.5"
]
}
,{
name
:
"
fastxtools"
,
version
:
"
0.0.14"
,
description
:
"
a
collection
of
command
line
tools
for
Short-Reads
FASTA/FASTQ
files
preprocessing"
,
documentation
:
"
http://hannonlab.cshl.edu/fastx_toolkit/commandline.html"
,
install
:
[
"
conda
install
-c
biobuilds
fastx-toolkit=0.0.14"
]
}
,{
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
-r6
"
,
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
:
[]
}
,{
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
:
"
gcta"
,
version
:
"
1.24.7"
,
description
:
"
"
,
documentation
:
"
"
,
install
:
[]
}
,{
name
:
"
htslib"
,
version
:
"
1.
2.1
"
,
description
:
"
"
,
documentation
:
"
"
,
install
:
[]
}
,{
name
:
"
jbrowse"
,
version
:
"
1.1
1.6
"
,
description
:
"
"
,
documentation
:
"
"
,
install
:
[]
}
,{
name
:
"
jellyfish"
,
version
:
"
2.2.
3
"
,
description
:
"
"
,
documentation
:
"
"
,
install
:
[]
}
,{
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
:
"
1.1
2.1
"
,
description
:
"
"
,
documentation
:
"
"
,
install
:
[
"
conda
install
jbrowse=1.12.1"
]
}
,{
name
:
"
jellyfish"
,
version
:
"
2.2.
6
"
,
description
:
"
"
,
documentation
:
"
"
,
install
:
[
"
conda
install
jellyfish=2.2.6"
]
}
,{
name
:
"
magicblast"
,
version
:
"
1.3.0"
,
description
:
"
Magic-BLAST
is
a
new
tool
for
mapping
large
sets
of
next-generation
RNA
or
DNA
sequencing
runs
against
a
whole
genome
or
transcriptome"
,
documentation
:
"
https://ncbi.github.io/magicblast/"
,
install
:
[
"
wget
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/magicblast/1.3.0/ncbi-magicblast-1.3.0-x64-linux.tar.gz
-O
/tmp/ncbi-magicblast-1.3.0-x64-linux.tar.gz
\\
"
,
"
&&
tar
xzfv
/tmp/ncbi-magicblast-1.3.0-x64-linux.tar.gz
-C
/opt/biotools/bin/
\\
"
,
"
&&
cd
/opt/biotools/bin/ncbi-magicblast-1.3.0/
\\
"
,
"
&&
chmod
-R
755
/opt/biotools/bin/ncbi-magicblast-1.3.0"
,
"
&&
ln
-s
/opt/biotools/bin/ncbi-magicblast-1.3.0/bin/magicblast
/opt/biotools/bin/magicblast_1.3.0
\\
"
,
"
&&
ln
-s
/opt/biotools/bin/ncbi-magicblast-1.3.0/bin/makeblastdb
/opt/biotools/bin/makeblastdb_1.3.0
\\
"
,
"
&&
rm
-rf
/tmp/ncbi-magicblast-1.3.0-x64-linux.tar.gz"
]
}
,{
name
:
"
msamanda"
,
version
:
"
1.0.0.5242"
,
description
:
"
scoring
system
to
identify
peptides
out
of
tandem
mass
spectrometry"
,
documentation
:
"
http://ms.imp.ac.at/?goto=msamanda"
,
install
:
[]
}
,{
name
:
"
msgfp"
,
version
:
"
9949"
,
description
:
"
MS/MS
database
search
tool"
,
documentation
:
"
http://proteomics.ucsd.edu/Software/MSGFPlus/"
,
install
:
[]
}
,{
name
:
"
novor"
,
version
:
"
1b"
,
description
:
"
real-time
peptide
de
novo
sequencing"
,
documentation
:
"
http://www.rapidnovor.com/"
,
install
:
[
"
wget
https://github.com/BioDocker/software-archive/releases/download/NovoR/novor_academic_latest.zip
-O
/tmp/novor_academic_latest.zip
\\
"
,
"
&&
unzip
/tmp/novor_academic_latest.zip
-d
/opt/biotools/bin/
\\
"
,
"
&&
bash
-c
'echo
-e
\"
#!/bin/bash
\\
njava
-jar
/opt/biotools/bin/novor_v1b/lib/novor.jar
$@
\"
>
/opt/biotools/bin/novor_1b'
&&
\\
"
,
"
&&
chmod
+x
/opt/biotools/bin/novor_1b
\\
"
,
"
&&
rm
-rf
/tmp/novor_academic_latest.zip
"
]
}
,{
name
:
"
openms"
,
version
:
"
1.11.1-3"
,
description
:
"
C++
libraries
ans
tools
for
MS/MS
data
analysis"
,
documentation
:
"
http://open-ms.sourceforge.net/"
,
install
:
[]
}
,{
name
:
"
openms"
,
version
:
"
2.0.0"
,
description
:
"
C++
libraries
ans
tools
for
MS/MS
data
analysis"
,
documentation
:
"
http://open-ms.sourceforge.net/"
,
install
:
[]
}
,{
name
:
"
openms"
,
version
:
"
2.2.0"
,
description
:
"
C++
libraries
ans
tools
for
MS/MS
data
analysis"
,
documentation
:
"
http://ftp.mi.fu-berlin.de/pub/OpenMS/release2.2.0-documentation/html/index.html"
,
install
:
[]
}
,{
name
:
"
pepnovo
+
"
,
version
:
"
201
20423
"
,
description
:
"
de
novo
sequencing
of
low
precision
MS/MS
data"
,
documentation
:
"
http://proteomics.ucsd.edu/Software/PepNovo/"
,
install
:
[]
}
,{
name
:
"
pepnovo"
,
version
:
"
201
01117
"
,
description
:
"
de
novo
sequencing
of
low
precision
MS/MS
data"
,
documentation
:
"
http://proteomics.ucsd.edu/Software/PepNovo/"
,
install
:
[
"
conda
install
pepnovo=20101117"
]
}
,{
name
:
"
peptideprophet"
,
version
:
"
201510131012"
,
description
:
"
Peptide
assignment
statistics
and
validation"
,
documentation
:
"
http://peptideprophet.sourceforge.net/"
,
install
:
[]
}
,{
name
:
"
peptideshaker"
,
version
:
"
1.10.3"
,
description
:
"
interpretation
of
proteomics
identification
results"
,
documentation
:
"
http://compomics.github.io/projects/peptide-shaker.html"
,
install
:
[]
}
,{
name
:
"
peptideshaker"
,
version
:
"
1.16.16"
,
description
:
"
interpretation
of
proteomics
identification
results"
,
documentation
:
"
http://compomics.github.io/projects/peptide-shaker.html"
,
install
:
[]
}
,{
name
:
"
peptideshaker"
,
version
:
"
1.16.17"
,
description
:
"
interpretation
of
proteomics
identification
results"
,
documentation
:
"
http://compomics.github.io/projects/peptide-shaker.html"
,
install
:
[]
}
,{
name
:
"
percolator"
,
version
:
"
3.0"
,
description
:
"
Semi-supervised
learning
for
peptide
identification
from
shotgun
proteomics
datasets"
,
documentation
:
"
http://percolator.ms/"
,
install
:
[]
}
,{
name
:
"
peptideshaker"
,
version
:
"
1.16.16"
,
description
:
"
interpretation
of
proteomics
identification
results"
,
documentation
:
"
http://compomics.github.io/projects/peptide-shaker.html"
,
install
:
[
"
conda
install
peptide-shaker=1.16.16"
]
}
,{
name
:
"
peptideshaker"
,
version
:
"
1.16.17"
,
description
:
"
interpretation
of
proteomics
identification
results"
,
documentation
:
"
http://compomics.github.io/projects/peptide-shaker.html"
,
install
:
[
"
conda
install
peptide-shaker=1.16.17"
]
}
#,{ name: "percolator", version: "3.1", description: "Semi-supervised learning for peptide identification from shotgun proteomics datasets", documentation: "http://percolator.ms/", install: ["conda install boost ", "conda install tokyocabinet", "conda install percolator=3.1"] }
,{
name
:
"
pia"
,
version
:
"
1.1.0-SNAPSHOT"
,
description
:
"
Compile
PIA
XML
files
and
run
pipelines
with
this
image"
,
documentation
:
"
https://github.com/mpc-bioinformatics/pia"
,
install
:
[]
}
,{
name
:
"
pia"
,
version
:
"
1.3.0"
,
description
:
"
Compile
PIA
XML
files
and
run
analysis
pipelines
for
protein
inference
with
this
image"
,
documentation
:
"
https://github.com/julianu/pia-tutorial"
,
install
:
[]
}
,{
name
:
"
pia-web-server"
,
version
:
"
1.1.0-SNAPSHOT"
,
description
:
"
Web
server
for
PIA
-
Protein
Inference
Algorithms"
,
documentation
:
"
https://github.com/mpc-bioinformatics/pia"
,
install
:
[]
}
,{
name
:
"
picard"
,
version
:
"
1.139"
,
description
:
"
A
set
of
Java
command
line
tools
for
manipulating
high-throughput
sequencing
(HTS)
data
and
formats."
,
documentation
:
"
https://github.com/picard/picard"
,
install
:
[
"
conda
install
picard=1.139"
]
}
,{
name
:
"
picard"
,
version
:
"
1.141"
,
description
:
"
A
set
of
Java
command
line
tools
for
manipulating
high-throughput
sequencing
(HTS)
data
and
formats."
,
documentation
:
"
https://github.com/picard/picard"
,
install
:
[
"
conda
install
picard=1.141"
]
}
,{
name
:
"
picard"
,
version
:
"
2.3.0"
,
description
:
"
A
set
of
Java
command
line
tools
for
manipulating
high-throughput
sequencing
(HTS)
data
and
formats."
,
documentation
:
"
https://github.com/picard/picard"
,
install
:
[
"
conda
install
picard=2.3.0"
]
}
,{
name
:
"
picard"
,
version
:
"
2.18.1"
,
description
:
"
A
set
of
Java
command
line
tools
for
manipulating
high-throughput
sequencing
(HTS)
data
and
formats."
,
documentation
:
"
https://github.com/picard/picard"
,
install
:
[
"
conda
install
picard=2.18.1"
]
}
,{
name
:
"
progressive-cactus"
,
version
:
"
0.1"
,
description
:
"
multiple
whole-genome
alignment
package"
,
documentation
:
"
https://github.com/glennhickey/progressiveCactus"
,
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"
]
}
...
...
@@ -80,7 +67,6 @@ containers: [
,{
name
:
"
tophat"
,
version
:
"
2.1.1"
,
description
:
"
TopHat
is
a
fast
splice
junction
mapper
for
RNA-Seq
reads"
,
documentation
:
"
https://ccb.jhu.edu/software/tophat/index.shtml"
,
install
:
[
"
conda
install
tophat=2.1.1"
]
}
,{
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
:
"
tpp"
,
version
:
"
4.8"
,
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
:
"
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"
]
}
...
...
pages/pages_def_home.R
View file @
cfcbf3b2
...
...
@@ -23,14 +23,10 @@ tabHome = fluidPage(align="left",
actionButton
(
"createContainer"
,
label
=
"Create"
,
icon
(
"paper-plane"
),
style
=
"color: #fff; background-color: #337ab7; border-color: #2e6da4"
),
downloadButton
(
'downloadContainerFile'
,
label
=
"Dowload"
,
style
=
"color: #fff; background-color: #337ab7; border-color: #2e6da4"
)
)),
column
(
width
=
10
,
box
(
title
=
"
R
Packages"
,
title
=
"Packages
and tools
"
,
width
=
NULL
,
collapsible
=
TRUE
,
solidHeader
=
TRUE
,
...
...
@@ -40,16 +36,21 @@ tabHome = fluidPage(align="left",
withSpinner
(
DT
::
dataTableOutput
(
'dtrcranpackage'
),
type
=
4
,
proxy.height
=
"150px"
)
),
tabPanel
(
'Bioconductor'
,
DT
::
dataTableOutput
(
'dtrbioconductorpackage'
)),
div
(
id
=
"formBioconductor"
,
# br(),
#selectizeInput('selectedBioconductor', 'R Bioconductor selected:', choices = NULL, multiple=TRUE, options = list(maxItems = 30000)),
DT
::
dataTableOutput
(
'dtrbioconductorpackage'
))),
tabPanel
(
'Github'
,
textInput
(
"inputGithub"
,
"Package name:"
,
""
),
actionButton
(
"findGithub"
,
label
=
"Find"
,
icon
(
"paper-plane"
),
style
=
"color: #fff; background-color: #337ab7; border-color: #2e6da4"
),
div
(
id
=
"formGithub"
,
br
(),
br
(),
selectizeInput
(
'rgithubpackagelist'
,
'R Github selected:'
,
choices
=
NULL
,
multiple
=
TRUE
,
options
=
list
(
maxItems
=
30000
)),
br
(),
br
(),
DT
::
dataTableOutput
(
'dtrgithubpackage'
))),
tabPanel
(
'BioContainer tools'
,
div
(
id
=
"formContainer"
,
br
(),
selectizeInput
(
'selectedBiocontainer'
,
'Biocontainer tools selected:'
,
choices
=
NULL
,
multiple
=
TRUE
,
options
=
list
(
maxItems
=
30000
))),
DT
::
dataTableOutput
(
'dtbiocontainer'
)
)
...
...
server/opt_home.R
View file @
cfcbf3b2
...
...
@@ -165,29 +165,38 @@ createContentFile <- function() {
selectBIO
<-
allBIO
[
input
$
dtrbioconductorpackage_rows_all
,]
selectBIO
<-
selectBIO
[,
"Package"
]
sizeBIO
<-
length
(
selectBIO
)
if
(
!
is.null
(
sizeBIO
))
{
if
(
sizeBIO
<
length
(
allBIO
[,
"Package"
]))
{
if
(
sizeBIO
>=
1
)
{
result
<-
paste
(
result
,
'\tR --slave -e "source(\'https://bioconductor.org/biocLite.R\'); \\'
,
sep
=
"\n"
)
result
<-
paste
(
result
,
'\tbiocLite()"\n'
,
sep
=
"\n"
)
listRBIO
<-
'\tR --slave -e "source(\'https://bioconductor.org/biocLite.R\'); \\'
listRBIO
<-
paste0
(
listRBIO
,
"\n\tbiocLite("
)
for
(
pkg
in
1
:
sizeBIO
){
if
(
pkg
<
sizeBIO
)
{
listRBIO
<-
paste0
(
listRBIO
,
'\''
,
selectBIO
[
pkg
],
'\', '
)
}
else
{
listRBIO
<-
paste0
(
listRBIO
,
'\''
,
selectBIO
[
pkg
],
'\')"'
)
}
}
result
<-
paste
(
result
,
listRBIO
,
sep
=
"\n"
)
}
}
# if(!is.null(input$selectedBioconductor)) {
#print(input$selectedBioconductor)
sizeBIO
<-
length
(
selectBIO
)
if
(
!
is.null
(
sizeBIO
))
{
if
(
sizeBIO
<
length
(
allBIO
[,
"Package"
]))
{
if
(
sizeBIO
>=
1
)
{
result
<-
paste
(
result
,
'\tR --slave -e "source(\'https://bioconductor.org/biocLite.R\'); \\'
,
sep
=
"\n"
)
result
<-
paste
(
result
,
'\tbiocLite()"\n'
,
sep
=
"\n"
)
listRBIO
<-
'\tR --slave -e "source(\'https://bioconductor.org/biocLite.R\'); \\'
listRBIO
<-
paste0
(
listRBIO
,
"\n\tbiocLite("
)
for
(
pkg
in
1
:
sizeBIO
){
if
(
pkg
<
sizeBIO
)
{
listRBIO
<-
paste0
(
listRBIO
,
'\''
,
selectBIO
[
pkg
],
'\', '
)
}
else
{
listRBIO
<-
paste0
(
listRBIO
,
'\''
,
selectBIO
[
pkg
],
'\')"'
)
}
}
result
<-
paste
(
result
,
listRBIO
,
sep
=
"\n"
)
}
}
# }
}
result
<-
paste
(
result
,
"\n"
,
sep
=
"\n"
)
if
(
!
is.null
(
input
$
rgithubpackagelist
))
{
...
...
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