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jlopez
RPACIB
Commits
3848163c
Commit
3848163c
authored
Aug 20, 2018
by
jlopez
Browse files
fix tools
parent
711d5101
Changes
1
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container.yaml
View file @
3848163c
...
...
@@ -14,12 +14,14 @@ containers: [
,{
name
:
"
bwa"
,
version
:
"
0.7.13"
,
description
:
"
Burrow-Wheeler
Aligner
for
pairwise
alignment
between
DNA
sequences"
,
documentation
:
"
http://bio-bwa.sourceforge.net/"
,
install
:
[
"
conda
install
bwa=0.7.13"
]
}
,{
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
:
"
cd-hit"
,
version
:
"
4.6.8"
,
description
:
"
CD-HIT
is
a
very
widely
used
program
for
clustering
and
comparing
protein
or
nucleotide
sequences."
,
documentation
:
"
http://weizhongli-lab.org/cd-hit/"
,
install
:
[
"
conda
install
-c
bioconda
cd-hit=4.6.8"
]}
,{
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
:
"
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
:
"
crux"
,
version
:
"
2.1"
,
description
:
"
a
software
toolkit
for
tandem
mass
spectrometry
analysis"
,
documentation
:
"
http://cruxtoolkit.sourceforge.net/"
,
install
:
[]
}
,{
name
:
"
dDocent"
,
version
:
"
2.5.5"
,
description
:
"
dDocent
is
an
interactive
bash
wrapper
to
QC,
assemble,
map,
and
call
SNPs
from
all
types
of
RAD
data"
,
documentation
:
"
http://ddocent.com/"
,
install
:
[
"
conda
install
-c
bioconda
ddocent=2.5.5"
]}
,{
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
:
"
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"
]
}
...
...
@@ -30,6 +32,7 @@ containers: [
,{
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
:
"
freebayes"
,
version
:
"
1.2.0"
,
description
:
"
Bayesian
haplotype-based
genetic
polymorphism
discovery
and
genotyping."
,
documentation
:
"
https://github.com/ekg/freebayes"
,
install
:
[
"
conda
install
-c
bioconda
freebayes=1.2.0"
]}
,{
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"
]
}
...
...
@@ -57,9 +60,11 @@ containers: [
,{
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"
]
}
,{
name
:
"
rad_haplotyper"
,
version
:
"
1.1.9"
,
description
:
"
A
program
for
building
SNP
haplotypes
from
RAD
sequencing
data"
,
documentation
:
"
https://github.com/chollenbeck/rad_haplotyper"
,
install
:
[
"
git
clone
https://github.com/chollenbeck/rad_haplotyper.git
&&
\\
"
,
"
cp
./rad_haplotyper/rad_haplotyper.pl
/opt/biotools/bin/
&&
\\
"
,
"
apt-get
install
-y
vcftools
&&
\\
"
,
"
cpan
App::cpanminus
&&
\\
"
,
"
cpanm
Vcf
&&
\\
"
,
"
cpanm
Data::Dumper
&&
\\
"
,
"
cpanm
Getopt::Long
&&
\\
"
,
"
cpanm
Pod::Usage
&&
\\
"
,
"
cpanm
Bio::Cigar
&&
\\
"
,
"
cpanm
List::MoreUtils
&&
\\
"
,
"
cpanm
Term::ProgressBar
&&
\\
"
,
"
cpanm
Parallel::ForkManager"
]}
,{
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
:
"
sambamba"
,
version
:
"
0.6.6"
,
description
:
"
Tools
for
working
with
SAM/BAM
data"
,
documentation
:
"
http://lomereiter.github.io/sambamba/"
,
install
:
[
"
conda
install
-c
bioconda
sambamba=0.6.6"
]}
,{
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
:
"
1.3"
,
description
:
"
Tools
for
manipulating
next-generation
sequencing
data"
,
documentation
:
"
https://github.com/samtools/samtools"
,
install
:
[
"
conda
install
samtools=1.3"
]
}
...
...
@@ -84,5 +89,6 @@ containers: [
,{
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
:
"
0.1.15"
,
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
:
"
vcflib"
,
version
:
"
1.0.0_rc1"
,
description
:
"
a
simple
C++
library
for
parsing
and
manipulating
VCF
files,
+
many
command-line
utilities"
,
documentation
:
"
https://github.com/vcflib/vcflib"
,
install
:
[
"
conda
install
-c
bioconda
vcflib=1.0.0_rc1"
]}
,{
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"
]
}
]
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