iqbal-lab-org/Mykrobe_tb_workflow:tb
$ singularity pull shub://iqbal-lab-org/Mykrobe_tb_workflow:tb
Singularity Recipe
Bootstrap: debootstrap
OSVersion: bionic
MirrorURL: http://us.archive.ubuntu.com/ubuntu/
%help
A container to hold all the tools required for running Mykrobe predict.
Run `singularity exec tb.simg` followed by any of the following:
- pistis
- porechop
- mykrobe
- minimap2
- samtools
- NanoStat
%environment
PATH=/usr/local/bin:$PATH
%post
apt update
apt install -y software-properties-common
apt-add-repository universe
apt update
apt install -y python3-pip git wget libncurses5-dev libbz2-dev liblzma-dev zlib1g-dev
export LC_ALL=C.UTF-8
export LANG=C.UTF-8
echo 'export LC_ALL=C.UTF-8' >> $SINGULARITY_ENVIRONMENT
echo 'export LANG=C.UTF-8' >> $SINGULARITY_ENVIRONMENT
# ========================
# INSTALL Mykrobe
# ========================
COMMIT=8f7fd05b9b94fa3cc40df2845187fa35393b9c2a
git clone https://github.com/Mykrobe-tools/mykrobe-atlas-cli.git mykrobe
cd mykrobe
git checkout "$COMMIT"
wget https://goo.gl/DXb9hN -O - | tar -vxzf -
rm -fr src/mykrobe/data
mv mykrobe-data src/mykrobe/data
pip3 install .
# ================================
# INSTALL pistis
# ================================
pip3 install pistis==0.3.3
# ================================
# INSTALL porechop
# ================================
PORECHOP_VERSION=0.2.4
PORECHOP_URL=https://github.com/rrwick/Porechop/archive/v${PORECHOP_VERSION}.tar.gz
wget "$PORECHOP_URL"
tar xzf v${PORECHOP_VERSION}.tar.gz
rm v${PORECHOP_VERSION}.tar.gz
cd Porechop-${PORECHOP_VERSION}
python3 setup.py install
cd ~
# ================================
# INSTALL minimap2
# ================================
MM2_VERSION=2.10
MM2_URL=https://github.com/lh3/minimap2/releases/download/v${MM2_VERSION}/minimap2-${MM2_VERSION}_x64-linux.tar.bz2
wget "$MM2_URL" -O - | tar -jxvf -
cp ./minimap2-${MM2_VERSION}_x64-linux/minimap2 /usr/local/bin
# ================================
# INSTALL samtools
# ================================
SAMTOOLS_VERSION=1.7
SAMTOOLS_URL=https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2
wget "$SAMTOOLS_URL" -O - | tar -jxvf -
cd samtools-${SAMTOOLS_VERSION}
./configure
make
make install
cd ~
# ================================
# INSTALL nanostats
# ================================
pip3 install nanostat==1.1.2
Collection
- Name: iqbal-lab-org/Mykrobe_tb_workflow
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/iqbal-lab-org-Mykrobe_tb_workflow-tb |
collection name | iqbal-lab-org/Mykrobe_tb_workflow |
branch | master |
tag | tb |
commit | aa75d26ca06332aa85125b9c9010faf12d4910f7 |
version (container hash) | 8426a58819db4f0ce3de5f999c3843da |
build date | 2019-10-21T08:55:43.194Z |
size (MB) | 1228 |
size (bytes) | 486961183 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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