-
Notifications
You must be signed in to change notification settings - Fork 46
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
finally I have a new singularity build
- Loading branch information
Showing
1 changed file
with
102 additions
and
75 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,78 +1,105 @@ | ||
| Bootstrap: docker | ||
|
|
||
| From: conda/miniconda3 | ||
| BootStrap: library | ||
| From: ubuntu:18.04 | ||
|
|
||
| %environment | ||
| PATH=/opt/bedtools2/bin:/usr/local/envs/py36/bin:/opt/souporcell:/opt/souporcell/troublet/target/release:/usr/local/condabin:/opt/minimap2-2.7:/root/.cargo/bin:/opt/vartrix-v1.1.3-x86_64-linux/:/opt:$PATH | ||
| # set up all essential environment variables | ||
| export LC_ALL=C | ||
| export PATH=/miniconda3/bin:/opt/minimap2-2.26_x64-linux:/opt/bedtools-2:/opt/freebayes/build:/opt/hisat2-2.2.1:/opt/bedtools2/bin:/opt/souporcell:/opt/souporcell/troublet/target/release:/usr/local/condabin:/opt/minimap2-2.26_x64-linux:/root/.cargo/bin:/opt:$PATH | ||
| export PYTHONPATH=/miniconda3/lib/python3.9/:$PYTHONPATH | ||
|
|
||
| # activate conda environment | ||
| source activate base; | ||
| conda activate; | ||
|
|
||
| %post | ||
| # update and install essential dependencies | ||
| apt-get -y update | ||
| apt-get update && apt-get install -y automake build-essential bzip2 wget git default-jre unzip | ||
| apt-get -y install wget | ||
| apt-get -y install curl | ||
|
|
||
| # download, install, and update miniconda3 | ||
| wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh | ||
| bash Miniconda3-latest-Linux-x86_64.sh -b -f -p /miniconda3/ | ||
| rm Miniconda3-latest-Linux-x86_64.sh | ||
|
|
||
| # install dependencies via conda | ||
| export PATH="/miniconda3/bin:$PATH" | ||
| conda install -y -c conda-forge pip numpy # general dependencies | ||
| conda update --all | ||
|
|
||
| apt-get -y install libncurses5-dev | ||
| apt-get -y install zlib1g-dev | ||
| apt-get -y install libbz2-dev | ||
| apt-get -y install liblzma-dev | ||
| apt-get -y install zip unzip | ||
| apt-get -y install pkg-config | ||
| cd /opt | ||
| wget https://cloud.biohpc.swmed.edu/index.php/s/oTtGWbWjaxsQ2Ho/download | ||
| mv download hisat2.zip | ||
| unzip hisat2.zip | ||
| wget https://github.com/lh3/minimap2/releases/download/v2.26/minimap2-2.26_x64-linux.tar.bz2 | ||
| tar -xf minimap2-2.26_x64-linux.tar.bz2 | ||
| cd .. | ||
| wget https://github.com/arq5x/bedtools2/releases/download/v2.28.0/bedtools-2.28.0.tar.gz | ||
| tar -xf bedtools-2.28.0.tar.gz | ||
| cd bedtools2 | ||
| make | ||
| cd .. | ||
| CARGO_HOME=/opt/.cargo RUSTUP_HOME=/opt/.cargo bash -c 'curl https://sh.rustup.rs -sSf | sh -s -- -y' | ||
| . /opt/.cargo/env | ||
| which cargo | ||
| rustup default stable | ||
| apt-get -y install git | ||
| cd /opt | ||
| git clone --recursive https://github.com/wheaton5/souporcell.git | ||
| cd souporcell/troublet | ||
| cargo build --release | ||
| cd /opt/souporcell/souporcell | ||
| cargo build --release | ||
| cd /opt | ||
| pip install pysam | ||
| pip install git+https://github.com/stan-dev/pystan2.git@master | ||
| pip install pyfaidx | ||
| pip install "setuptools<58" --upgrade | ||
| pip install pyvcf | ||
| pip install scipy | ||
| cd /opt | ||
| wget https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2 | ||
| tar xvfj htslib-1.9.tar.bz2 | ||
| cd htslib-1.9 | ||
| ./configure | ||
| make | ||
| make install | ||
| cd .. | ||
| wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2 | ||
| tar xvfj samtools-1.9.tar.bz2 | ||
| rm samtools-1.9.tar.bz2 | ||
| cd samtools-1.9 | ||
| ./configure | ||
| make | ||
| make install | ||
| cd .. | ||
| wget https://github.com/samtools/bcftools/releases/download/1.9/bcftools-1.9.tar.bz2 | ||
| tar xvfj bcftools-1.9.tar.bz2 | ||
| rm bcftools-1.9.tar.bz2 | ||
| cd bcftools-1.9 | ||
| ./configure | ||
| make | ||
| make install | ||
| cd /opt | ||
| wget https://github.com/freebayes/freebayes/releases/download/v1.3.6/freebayes-1.3.6-linux-amd64-static.gz | ||
| gunzip freebayes-1.3.6-linux-amd64-static.gz | ||
| mv freebayes-1.3.6-linux-amd64-static freebayes | ||
| chmod 777 freebayes | ||
| wget https://github.com/10XGenomics/vartrix/releases/download/v1.1.22/vartrix_linux | ||
| mv vartrix_linux vartrix | ||
| chmod 777 vartrix | ||
| cd .. | ||
|
|
||
|
|
||
| %labels | ||
| Author whheaton | ||
| Version v2.1 | ||
| MyLabel souporcell | ||
|
|
||
| %post -c /bin/bash | ||
| apt update | ||
| yes | apt-get install wget | ||
| yes | apt-get install build-essential | ||
| yes | apt-get install curl | ||
| echo blah | ||
| yes | /usr/local/bin/conda create -n py36 python=3.6 | ||
| . /opt/conda/bin/activate py36 | ||
| yes | apt-get install libncurses5-dev | ||
| yes | apt-get install zlib1g-dev | ||
| yes | apt-get install libbz2-dev | ||
| yes | apt-get install liblzma-dev | ||
| cd /opt | ||
| wget https://github.com/lh3/minimap2/archive/v2.7.tar.gz | ||
| tar -xzvf v2.7.tar.gz | ||
| cd minimap2-2.7 | ||
| make | ||
| cd .. | ||
| wget https://github.com/arq5x/bedtools2/releases/download/v2.28.0/bedtools-2.28.0.tar.gz | ||
| tar -zxvf bedtools-2.28.0.tar.gz | ||
| cd bedtools2 | ||
| make | ||
| cd .. | ||
| CARGO_HOME=/opt/.cargo RUSTUP_HOME=/opt/.cargo bash -c 'curl https://sh.rustup.rs -sSf | sh -s -- -y' | ||
| source /opt/.cargo/env | ||
| which cargo | ||
| rustup default stable | ||
| yes | apt-get install git | ||
| cd /opt | ||
| git clone https://github.com/wheaton5/souporcell.git | ||
| cd souporcell/troublet | ||
| cargo build --release | ||
| cd /opt/souporcell/souporcell | ||
| cargo build --release | ||
| cd /opt | ||
| yes | /usr/local/envs/py36/bin/pip install pysam | ||
| /usr/local/envs/py36/bin/pip install pyvcf | ||
| /usr/local/envs/py36/bin/pip install numpy | ||
| /usr/local/envs/py36/bin/pip install scipy | ||
| /usr/local/envs/py36/bin/pip install pystan==2.17.1.0 | ||
| /usr/local/envs/py36/bin/pip install pyfaidx | ||
| cd /opt | ||
| wget https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2 | ||
| tar xvfj htslib-1.9.tar.bz2 | ||
| cd htslib-1.9 | ||
| ./configure | ||
| make | ||
| make install | ||
| cd .. | ||
| wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2 | ||
| tar xvfj samtools-1.9.tar.bz2 | ||
| rm samtools-1.9.tar.bz2 | ||
| cd samtools-1.9 | ||
| ./configure | ||
| make | ||
| make install | ||
| cd .. | ||
| wget https://github.com/samtools/bcftools/releases/download/1.9/bcftools-1.9.tar.bz2 | ||
| tar xvfj bcftools-1.9.tar.bz2 | ||
| rm bcftools-1.9.tar.bz2 | ||
| cd bcftools-1.9 | ||
| ./configure | ||
| make | ||
| make install | ||
| cd /opt | ||
| wget https://github.com/ekg/freebayes/releases/download/v1.3.1/freebayes-v1.3.1 | ||
| mv freebayes-v1.3.1 freebayes | ||
| chmod 777 freebayes | ||
| wget https://github.com/10XGenomics/vartrix/releases/download/v1.1.16/vartrix_linux | ||
| mv vartrix_linux vartrix | ||
| chmod 777 vartrix |