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jlopez
RPACIB
Commits
285af65d
Commit
285af65d
authored
Jun 06, 2018
by
khalid
Browse files
sra-toolkit
parents
bc0f1161
4958295a
Changes
2
Hide whitespace changes
Inline
Side-by-side
container.yaml
100644 → 100755
View file @
285af65d
...
...
@@ -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
:
"
"
,
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;
export
PATH=
\
$PATH:
\
$PWD/"
]
}
,{
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;
export
PATH=
\
$PATH:
\
$PWD/"
]
}
,{
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
:
[]
}
...
...
server/opt_home.R
View file @
285af65d
...
...
@@ -147,7 +147,7 @@ createLibPrePost <- function(result) {
result
<-
paste
(
result
,
"\tapt-get install -y wget libblas3 libblas-dev liblapack-dev liblapack3 curl"
,
sep
=
"\n"
)
result
<-
paste
(
result
,
"\tapt-get install -y gcc fort77 aptitude"
,
sep
=
"\n"
)
result
<-
paste
(
result
,
"\taptitude install -y g++ xorg-dev libreadline-dev gfortran"
,
sep
=
"\n"
)
result
<-
paste
(
result
,
"\tapt-get install -y libssl-dev libxml2-dev libpcre3-dev liblzma-dev libbz2-dev libcurl4-openssl-dev"
,
sep
=
"\n"
)
result
<-
paste
(
result
,
"\tapt-get install -y libssl-dev libxml2-dev libpcre3-dev liblzma-dev libbz2-dev libcurl4-openssl-dev
git
"
,
sep
=
"\n"
)
result
<-
paste
(
result
,
"\tapt-get update"
,
sep
=
"\n"
)
}
else
{
result
<-
paste
(
result
,
"RUN apt-get update"
,
sep
=
"\n"
)
...
...
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