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jlopez
RPACIB
Commits
4026ce02
Commit
4026ce02
authored
Nov 27, 2018
by
mmassaviol
Browse files
Add kallisto & salmon tools
parent
3848163c
Changes
1
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container.yaml
View file @
4026ce02
...
...
@@ -41,6 +41,7 @@ containers: [
,{
name
:
"
htslib"
,
version
:
"
1.8"
,
description
:
"
"
,
documentation
:
"
"
,
install
:
[
"
conda
install
htslib=1.8"
]
}
,{
name
:
"
jbrowse"
,
version
:
"
1.12.1"
,
description
:
"
"
,
documentation
:
"
"
,
install
:
[
"
conda
install
jbrowse=1.12.1"
]
}
,{
name
:
"
jellyfish"
,
version
:
"
2.2.6"
,
description
:
"
"
,
documentation
:
"
"
,
install
:
[
"
conda
install
jellyfish=2.2.6"
]
}
,{
name
:
"
kallisto"
,
version
:
"
0.44.0"
,
description
:
"
kallisto
is
a
program
for
quantifying
abundances
of
transcripts
from
RNA-Seq
data,
or
more
generally
of
target
sequences
using
high-throughput
sequencing
reads"
,
documentation
:
"
https://pachterlab.github.io/kallisto/manual"
,
install
:
[
"
conda
install
-c
bioconda
-c
conda-forge
kallisto=0.44.0"
]
}
,{
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
:
[]
}
...
...
@@ -66,6 +67,7 @@ containers: [
#,{ 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
:
"
salmon"
,
version
:
"
0.11.3"
,
description
:
"
Salmon
is
a
tool
for
quantifying
the
expression
of
transcripts
using
RNA-seq
data"
,
documentation
:
"
https://salmon.readthedocs.io/en/latest/"
,
install
:
"
conda
install
-c
bioconda
-c
conda-forge
salmon=0.11.3"
}
,{
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"
]
}
,{
name
:
"
samtools"
,
version
:
"
1.3.1"
,
description
:
"
Tools
for
manipulating
next-generation
sequencing
data"
,
documentation
:
"
https://github.com/samtools/samtools"
,
install
:
[
"
conda
install
samtools=1.3.1"
]
}
...
...
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