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jlopez
RPACIB
Commits
2750b110
Commit
2750b110
authored
Apr 05, 2018
by
jlopez
Browse files
Add Dockerfile generator
parent
cfcbf3b2
Changes
4
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Side-by-side
R/helper_functions.R
View file @
2750b110
...
...
@@ -61,7 +61,7 @@ getBioconductorPackage <- function() {
return
(
result
)
}
getInstallToolPackageBioContainer
<-
function
(
tool
)
{
getInstallToolPackageBioContainer
<-
function
(
tool
,
containerType
)
{
data
<-
allBIOCONTAINER
...
...
@@ -76,7 +76,7 @@ getInstallToolPackageBioContainer <- function(tool) {
if
(
tools
$
name
==
name
)
{
if
(
tools
$
version
==
version
)
{
res
<-
paste0
(
"\t"
,
tools
$
install
,
collapse
=
'\n'
)
res
<-
paste0
(
"\t"
,
tools
$
install
,
collapse
=
'\n'
)
return
(
res
)
}
}
...
...
container.yaml
View file @
2750b110
containers
:
[
{
name
:
"
abyss"
,
version
:
"
1.9.0"
,
description
:
"
ABySS
is
a
*de
novo*
sequence
assembler"
,
documentation
:
"
https://github.com/bcgsc/abyss#abyss"
,
install
:
[
"
conda
install
abyss=1.9.0"
]
}
{
name
:
"
abyss"
,
version
:
"
1.9.0"
,
description
:
"
ABySS
is
a
*de
novo*
sequence
assembler"
,
documentation
:
"
https://github.com/bcgsc/abyss#abyss"
,
install
:
[
"
conda
install
abyss=1.9.0"
]}
#,{ name: "aliscore", version: "2.0", description: "Aliscore is designed to filter alignment ambiguous or randomly similar sites in multiple sequence alignments (MSA).", documentation: "https://www.zfmk.de/dateien/atoms/files/aliscore_v.2.0_manual_0.pdf", install: ["wget http://software.zfmk.de/ALISCORE_v2.0.zip && unzip /tmp/ALISCORE_v2.0.zip -d ./ \\", "&& unzip /tmp/ALISCORE_v2.0/Aliscore_v.2.0.zip -d /opt/biotools/bin/Aliscore/ \\", "&& chmod -R 755 /opt/biotools/bin/Aliscore \\", "&& rm -rf /tmp/ALISCORE_v2.0" ] }
,{
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"
]
}
...
...
@@ -33,7 +33,7 @@ containers: [
,{
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"
]
}
,{
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
:
"
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
"
]
}
...
...
pages/pages_def_home.R
View file @
2750b110
...
...
@@ -10,7 +10,7 @@ tabHome = fluidPage(align="left",
textInput
(
"imageName"
,
"Image Name"
,
""
),
br
(),
radioButtons
(
"containerType"
,
"Container type:"
,
choices
=
list
(
"Singularity"
=
"singularity"
),
selected
=
"singularity"
),
radioButtons
(
"containerType"
,
"Container type:"
,
choices
=
list
(
"Singularity"
=
"singularity"
,
"Docker"
=
"docker"
),
selected
=
"singularity"
),
br
(),
#selectizeInput('rcranpackagelist', 'R CRAN:', choices = NULL, multiple=TRUE, options = list(maxItems = 30000)),
selectizeInput
(
'rtemplate'
,
'R origin:'
,
choices
=
c
(
`None`
=
'none'
,
`R from source`
=
'source'
,
`R from r-base`
=
'base'
,
`R from CRAN depo`
=
'cran'
),
selected
=
"source"
,
multiple
=
FALSE
),
...
...
server/opt_home.R
View file @
2750b110
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