Skip to content
GitLab
Menu
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
9a05c39c
Commit
9a05c39c
authored
Jun 06, 2018
by
khalid
Browse files
best installation of cross-species-scaffolding dependencies
parent
8c5cc686
Changes
1
Show whitespace changes
Inline
Side-by-side
container.yaml
View file @
9a05c39c
...
...
@@ -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
:
[
"
git
clone
https://github.com/thackl/cross-species-scaffolding.git;
apt-get
-y
install
samtools;
cd
cross-species-scaffolding;
make
dependencies;
echo
export
PATH=$PATH:$PWD/
>>
/
etc/profile.d/conda
.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
:
[
"
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;sed
-i
's/make/make
\
&
\
&
make
install/g'
Makefile;
make
dependencies;
echo
export
PATH=
'
$PATH
'
:$PWD/
>>
/
.singularity.d/env/90-environment
.sh"
]
}
,{
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
:
[]
}
...
...
@@ -62,7 +62,7 @@ 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
>>
/
etc/profile.d/conda
.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;
chemin=`ls
-1
-d
sra*ubuntu*`;
echo
export
PATH=
'
$PATH
'
:$PWD/$chemin/bin
>>
/
.singularity.d/env/90-environment
.sh"
]
}
,{
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
:
[]
}
...
...
Write
Preview
Supports
Markdown
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