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m-unlock
docker
Commits
350a0b61
Commit
350a0b61
authored
3 years ago
by
Jasper Koehorst
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setup script removed, rsync added to docker engine
parent
5b3c30f8
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kubernetes/Dockerfile
+2
-2
2 additions, 2 deletions
kubernetes/Dockerfile
kubernetes/scripts/setup.sh
+0
-119
0 additions, 119 deletions
kubernetes/scripts/setup.sh
with
2 additions
and
121 deletions
kubernetes/Dockerfile
+
2
−
2
View file @
350a0b61
...
...
@@ -23,10 +23,10 @@ ENV DEBIAN_FRONTEND=noninteractive LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LANGUAGE=en_U
# Fix issue with scipy no lapack/blas resources found and other compilation problems
# Install ubuntu modules and the workflow application # --no-install-recommends
RUN
apt-get update
&&
apt-get
install
--yes
build-essential cpanminus curl git gnupg htop libfontconfig1 locales nano nodejs pigz python3-dev python3-distutils python3.8 raptor2-utils raptor2-utils sshpass unzip wget zip libblas-dev liblapack-dev zlib1g-dev pkg-config libhdf5-100 libhdf5-dev gfortran libblas-dev liblapack-dev zlib1g-dev pkg-config libhdf5-100 libhdf5-dev gfortran libbz2-dev python-setuptools libidn11
RUN
apt-get update
&&
apt-get
install
--yes
build-essential cpanminus curl git gnupg htop libfontconfig1 locales nano nodejs pigz python3-dev python3-distutils python3.8 raptor2-utils raptor2-utils sshpass unzip wget zip libblas-dev liblapack-dev zlib1g-dev pkg-config libhdf5-100 libhdf5-dev gfortran libblas-dev liblapack-dev zlib1g-dev pkg-config libhdf5-100 libhdf5-dev gfortran libbz2-dev python-setuptools libidn11
rsync
RUN
curl https://bootstrap.pypa.io/get-pip.py
-o
get-pip.py
&&
python3.8 get-pip.py
&&
\
python3.8
-m
pip
install
cwltool
==
3.1.202
11004060744
&&
\
python3.8
-m
pip
install
cwltool
==
3.1.202
20224085855
&&
\
cwltool
--version
&&
python3.8
-m
pip
install
html5lib
# Enable icommands
...
...
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kubernetes/scripts/setup.sh
deleted
100644 → 0
+
0
−
119
View file @
5b3c30f8
# Installs packages on the computational nodes
R_location
=
/unlock/infrastructure/R/library
conda_location
=
/unlock/infrastructure/conda
python_location
=
/unlock/infrastructure/python_venv
# Ensures that R can use the library folder
mkdir
--parents
$R_location
################################################################
# Conda environments
################################################################
# Update conda
source
/root/miniconda/bin/activate
conda update
-y
-n
base
-c
defaults conda
# New attempt for picrust
if
[[
!
-d
"
$conda_location
/picrust2_v2.4.2"
]]
then
mamba create
--yes
--prefix
$conda_location
/picrust2_v2.4.2
-c
bioconda
-c
conda-forge
picrust2
=
2.4.2
fi
# Krona and install taxonomy
if
[[
!
-d
"
$conda_location
/krona_v2.8.1"
]]
then
mamba create
--yes
--prefix
$conda_location
/krona_v2.8.1
-c
bioconda krona
krona
=
2.8.1
conda activate
$conda_location
/krona_v2.8.1
ktUpdateTaxonomy.sh
fi
# Medaka
if
[[
!
-d
"
$conda_location
/medaka_v1.5.0"
]]
then
mamba create
--yes
--prefix
$conda_location
/medaka_v1.5.0
-c
bioconda
-c
conda-forge
medaka
=
1.5.0
fi
# pycoQC
if
[[
!
-d
"
$conda_location
/pycoqc_v2.5.2"
]]
then
mamba create
--yes
--prefix
$conda_location
/pycoqc_v2.5.2
-c
conda-forge
-c
bioconda
pycoqc
=
2.5.2
fi
# LongQC
# ?
# NanoQC
if
[[
!
-d
"
$conda_location
/nanoqc_v0.9.4"
]]
then
mamba create
--yes
--prefix
$conda_location
/nanoqc_v0.9.4
-c
conda-forge
-c
bioconda
nanoqc
=
0.9.4
fi
# Busco
if
[[
!
-d
"
$conda_location
/busco_v5.2.2"
]]
then
mamba create
--yes
--prefix
$conda_location
/busco_v5.2.2
-c
conda-forge
-c
bioconda
busco
=
5.2.2
fi
# GTDB-Tk
if
[[
!
-d
"
$conda_location
/gtdbtk_v1.7.0"
]]
then
mamba create
--yes
--prefix
$conda_location
/gtdbtk_v1.7.0
-c
conda-forge
-c
bioconda
gtdbtk
=
1.7.0
echo
"export GTDBTK_DATA_PATH=/unlock/references/databases/GTDBTK/release202/"
>
$conda_location
/gtdbtk_v1.7.0/etc/conda/activate.d/gtdbtk.sh
fi
# CheckM
if
[[
!
-d
"
$conda_location
/checkm_v1.1.3"
]]
then
mamba create
--yes
--prefix
$conda_location
/checkm_v1.1.3
-c
conda-forge
-c
bioconda checkm-genome
=
1.1.3
conda activate
$conda_location
/checkm_v1.1.3
checkm data setRoot /unlock/references/databases/CheckM/
conda deactivate
fi
# HUMAnN 3
if
[[
!
-d
"
$conda_location
/humann_v3.0.1"
]]
then
mamba create
--yes
--prefix
$conda_location
/humann_v3.0.1
-c
biobakery
-c
bioconda
-c
conda-forge
humann
=
3.0.1
conda activate /unlock/infrastructure/conda/humann_v3.0.1
humann_config
--update
database_folders nucleotide /unlock/references/databases/HUMAnN/chocophlan
humann_config
--update
database_folders utility_mapping /unlock/references/databases/HUMAnN/utility_mapping
humann_config
--update
database_folders protein /unlock/references/databases/HUMAnN/uniref
conda deactivate
fi
# KEGG - kofamscan
if
[[
!
-d
"
$conda_location
/kofamscan_v1.3.0"
]]
then
mamba create
--yes
--prefix
$conda_location
/kofamscan_v1.3.0
-c
conda-forge
-c
bioconda
kofamscan
=
1.3.0
fi
################################################################
# Pip environments
################################################################
# Python virtual environment
python3
-m
venv /unlock/infrastructure/venv
# Activate venv
source
/unlock/infrastructure/venv/bin/activate
# Upgrade because we can
/unlock/infrastructure/venv/bin/python3
-m
pip
install
--upgrade
pip
## Pip dependencies
python3
-m
pip
install
wheel biom-format pysam numpy matplotlib checkm-genome gtdbtk rdflib python-irodsclient html5lib
python3
-m
pip
install
cwltool
==
3.1.20211004060744
cwltool
--version
&&
python3
-m
pip
install
html5lib
## Pip quast rc1 for 3.9 support
wget https://github.com/ablab/quast/releases/download/quast_5.1.0rc1/quast-5.1.0rc1.tar.gz
pip
install
quast-5.1.0rc1.tar.gz
deactivate
################################################################
# R Packages
################################################################
R
-e
"install.packages('docopt',dependencies=TRUE, repos='https://packagemanager.rstudio.com/all/__linux__/bionic/latest')"
Rscript /scripts/install2.R
-n
10
-s
-l
$R_location
-r
https://packagemanager.rstudio.com/all/__linux__/bionic/latest data.table futile.logger ggplot2 optparse plyr readr reshape2 scales viridis yaml parallel castor
\ No newline at end of file
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