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jlopez
RPACIB
Commits
6faff451
Commit
6faff451
authored
Jun 13, 2018
by
khalid
Browse files
Add recipe for minimap2 and nanopolish
parent
e67ec0ef
Changes
1
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container.yaml
View file @
6faff451
...
...
@@ -38,6 +38,8 @@ containers: [
,{
name
:
"
magicblast"
,
version
:
"
1.3.0"
,
description
:
"
Magic-BLAST
is
a
new
tool
for
mapping
large
sets
of
next-generation
RNA
or
DNA
sequencing
runs
against
a
whole
genome
or
transcriptome"
,
documentation
:
"
https://ncbi.github.io/magicblast/"
,
install
:
[
"
wget
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/magicblast/1.3.0/ncbi-magicblast-1.3.0-x64-linux.tar.gz
-O
/tmp/ncbi-magicblast-1.3.0-x64-linux.tar.gz
\\
"
,
"
&&
tar
xzfv
/tmp/ncbi-magicblast-1.3.0-x64-linux.tar.gz
-C
/opt/biotools/bin/
\\
"
,
"
&&
cd
/opt/biotools/bin/ncbi-magicblast-1.3.0/
\\
"
,
"
&&
chmod
-R
755
/opt/biotools/bin/ncbi-magicblast-1.3.0
\\
"
,
"
&&
ln
-s
/opt/biotools/bin/ncbi-magicblast-1.3.0/bin/magicblast
/opt/biotools/bin/magicblast_1.3.0
\\
"
,
"
&&
ln
-s
/opt/biotools/bin/ncbi-magicblast-1.3.0/bin/makeblastdb
/opt/biotools/bin/makeblastdb_1.3.0
\\
"
,
"
&&
rm
-rf
/tmp/ncbi-magicblast-1.3.0-x64-linux.tar.gz"
]
}
,{
name
:
"
msamanda"
,
version
:
"
1.0.0.5242"
,
description
:
"
scoring
system
to
identify
peptides
out
of
tandem
mass
spectrometry"
,
documentation
:
"
http://ms.imp.ac.at/?goto=msamanda"
,
install
:
[]
}
,{
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
:
"
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
$@
\"
>
/opt/biotools/bin/novor_1b'
&&
\\
"
,
"
&&
chmod
+x
/opt/biotools/bin/novor_1b
\\
"
,
"
&&
rm
-rf
/tmp/novor_academic_latest.zip
"
]
}
,{
name
:
"
openms"
,
version
:
"
2.2.0"
,
description
:
"
C++
libraries
ans
tools
for
MS/MS
data
analysis"
,
documentation
:
"
http://ftp.mi.fu-berlin.de/pub/OpenMS/release2.2.0-documentation/html/index.html"
,
install
:
[]
}
,{
name
:
"
pepnovo"
,
version
:
"
20101117"
,
description
:
"
de
novo
sequencing
of
low
precision
MS/MS
data"
,
documentation
:
"
http://proteomics.ucsd.edu/Software/PepNovo/"
,
install
:
[
"
conda
install
pepnovo=20101117"
]
}
...
...
@@ -63,7 +65,7 @@ containers: [
,{
name
:
"
soapec"
,
version
:
"
2.03"
,
description
:
"
A
correction
tool
for
SOAPdenovo"
,
documentation
:
"
http://soap.genomics.org.cn/soapdenovo.html"
,
install
:
[
"
conda
install
soapec=2.03"
]
}
,{
name
:
"
spades"
,
version
:
"
3.11.1"
,
description
:
"
Tools
(written
in
C
using
htslib)
for
manipulating
next-generation
sequencing
data"
,
documentation
:
"
http://bioinf.spbau.ru/spades"
,
install
:
[
"
conda
install
spades=3.11.1"
]
}
,{
name
:
"
spectra-cluster-cli"
,
version
:
"
1.0.1"
,
description
:
"
PRIDE
Cluster
algorithm
to
cluster
heterogeneous
mass
spectra"
,
documentation
:
"
https://github.com/spectra-cluster/spectra-cluster-cli"
,
install
:
[
"
conda
install
spectra-cluster-cli=1.0.1"
]
}
,{
name
:
"
sra-tools"
,
version
:
"
latest"
,
description
:
"
"
,
documentation
:
"
"
,
installation
:
[
"
cd
/opt/biotools;
wget
--output-document
sratoolkit.tar.gz
http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-ubuntu64.tar.gz;
tar
-vxzf
sratoolkit.tar.gz;
rm
sratoolkit.tar.gz;
mv
sratoolkit.*-ubuntu64
sratoolkit"
],
env
:
"
export
PATH=$PATH:
$PWD
/sratoolkit/bin"
}
,{
name
:
"
sra-tools"
,
version
:
"
latest"
,
description
:
"
"
,
documentation
:
"
"
,
installation
:
[
"
cd
/opt/biotools;
wget
--output-document
sratoolkit.tar.gz
http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-ubuntu64.tar.gz;
tar
-vxzf
sratoolkit.tar.gz;
rm
sratoolkit.tar.gz;
mv
sratoolkit.*-ubuntu64
sratoolkit"
],
env
:
"
export
PATH=$PATH:
/opt/biotools
/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
:
[]
}
...
...
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