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jlopez
RPACIB
Commits
ac28a6ef
Commit
ac28a6ef
authored
Jun 13, 2018
by
khalid
Browse files
Add a new env field to change envirenment variables needed by tools
parent
175fc339
Changes
2
Hide whitespace changes
Inline
Side-by-side
container.yaml
View file @
ac28a6ef
...
...
@@ -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;
echo
export
PATH='
$PATH':$PWD/bin
>>
/.singularity.d/env/90-environment.sh"
]
}
,{
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
:
[]
}
...
...
@@ -30,6 +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
:
[
"
conda
install
gatk=3.8"
]
}
,{
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"
]
}
...
...
@@ -62,7 +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;
chemin=`ls
-1
-d
sra*ubuntu*`;
echo
export
PATH='$PATH':$PWD/$chemin/bin
>>
/.singularity.d/env/90-environment.sh
"
]
}
,{
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
:
[]
}
...
...
pages/pages_def_home.R
View file @
ac28a6ef
...
...
@@ -16,7 +16,7 @@ tabHome = fluidPage(align="left",
tags
$
b
(
"Github R Packages: "
),
p
(
"Select each tool by clicking on the corresponding field in the table. They appear in the field below."
),
p
(
"Use 'Generate' button to generate your recipe in the preview area then copy/paste the text or use dowload button to get your file."
),
tags
$
b
(
"To build the image from the recipes file named ubuntu6.10_stacks2.0.simg :"
),
tags
$
b
(
"
For Singularity containers:
To build the image from the recipes file named ubuntu6.10_stacks2.0.simg :"
),
p
(
"sudo singularity build ubuntu6.10_stacks2.0.simg ubuntu6.10_stacks2.0.recipes"
),
tags
$
b
(
"To run a program inside the image container :"
),
p
(
" singularity exec ubuntu6.10_stacks2.0.simg python --version "
),
...
...
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