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jlopez
RPACIB
Commits
405098af
Commit
405098af
authored
Jun 19, 2018
by
jlopez
Browse files
Add nextflow tools
parent
e3c8ea74
Changes
1
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container.yaml
View file @
405098af
...
...
@@ -40,6 +40,7 @@ containers: [
,{
name
:
"
msgfp"
,
version
:
"
9949"
,
description
:
"
MS/MS
database
search
tool"
,
documentation
:
"
http://proteomics.ucsd.edu/Software/MSGFPlus/"
,
install
:
[]
}
,{
name
:
"
minimap2"
,
version
:
"
2.1.0"
,
description
:
"
a
versatile
sequence
alignment
program
that
aligns
DNA
or
mRNA
sequences
against
a
large
reference
database"
,
documentation
:
"
https://github.com/lh3/minimap2"
,
install
:
[
"
cd
/opt/biotools/bin/;curl
-L
https://github.com/lh3/minimap2/releases/download/v2.10/minimap2-2.10_x64-linux.tar.bz2
|
tar
-jxvf
-
"
],
env
:
"
export
PATH:'$PATH':/opt/biotools/bin/minimap2-2.10_x64-linux/"
}
,{
name
:
"
nanopolish"
,
version
:
"
latest"
,
description
:
"
signal-level
analysis
of
Oxford
Nanopore
sequencing
data."
,
documentation
:
"
https://github.com/jts/nanopolish"
,
install
:
[
"
cd
/opt/biotools/bin;git
clone
--recursive
https://github.com/jts/nanopolish.git;cd
nanopolish;make;"
],
env
:
"
export
PATH='$PATH':/opt/biotools/bin/nanopolish"
}
,{
name
:
"
nextflow"
,
version
:
"
0.30.1"
,
description
:
"
Data-driven
computational
pipelines"
,
documentation
:
"
https://www.nextflow.io/"
,
install
:
[
"
conda
install
-c
bioconda
nextflow=0.30.1"
]}
,{
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
"
]
}
,{
name
:
"
openms"
,
version
:
"
2.2.0"
,
description
:
"
C++
libraries
ans
tools
for
MS/MS
data
analysis"
,
documentation
:
"
http://ftp.mi.fu-berlin.de/pub/OpenMS/release2.2.0-documentation/html/index.html"
,
install
:
[]
}
,{
name
:
"
pepnovo"
,
version
:
"
20101117"
,
description
:
"
de
novo
sequencing
of
low
precision
MS/MS
data"
,
documentation
:
"
http://proteomics.ucsd.edu/Software/PepNovo/"
,
install
:
[
"
conda
install
pepnovo=20101117"
]
}
...
...
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