Mercurial > repos > dereeper > pangenome_explorer
diff singularity/panexplorer.def @ 3:e42d30da7a74 draft
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author | dereeper |
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date | Thu, 30 May 2024 11:52:25 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/singularity/panexplorer.def Thu May 30 11:52:25 2024 +0000 @@ -0,0 +1,221 @@ +Bootstrap: docker +From: debian:latest + +%labels + software=pggb + about.home=https://github.com/pangenome/pggb + +%runscript + echo "This is what happens when you run the container..." + +%post + echo "Hello from inside the container" + apt-get update + apt-get install -y bash wget r-base-core r-cran-svglite r-cran-upsetr r-cran-optparse r-cran-dendextend r-cran-gplots r-bioc-ctc ncbi-blast+ ncbi-blast+-legacy roary prokka snakemake python3 cd-hit mafft mcl phylip python3-pip libstatistics-linefit-perl bioperl libstatistics-distributions-perl pdf2svg python3-biopython r-cran-heatmaply python3-pandas python3-numpy python3-seaborn python3-xarray python3-plotly pipx autoconf libgsl-dev fastani python3-virtualenv cmake samtools curl make g++-11 pybind11-dev libbz2-dev bc libatomic-ops-dev autoconf libgsl-dev zlib1g-dev libzstd-dev libjemalloc-dev libhts-dev build-essential pkg-config time pigz bcftools libcairo2-dev unzip parallel circos multiqc + + wget https://repo.anaconda.com/miniconda/Miniconda3-py38_4.8.3-Linux-x86_64.sh + chmod +x Miniconda3-py38_4.8.3-Linux-x86_64.sh + ./Miniconda3-py38_4.8.3-Linux-x86_64.sh -b -p /opt/miniconda3 + ln -s /opt/miniconda3/bin/conda /usr/bin/conda + + + +############################# +# singularity +############################# +# apt-get install -y build-essential libssl-dev uuid-dev libgpgme11-dev squashfs-tools libseccomp-dev pkg-config +# export VERSION=1.11 OS=linux ARCH=amd64 && \ +# wget https://go.dev/dl/go1.21.4.linux-amd64.tar.gz +# tar -C /usr/local -xzvf go1.21.4.linux-amd64.tar.gz && \ +# rm go1.21.4.linux-amd64.tar.gz +# echo 'export GOPATH=${HOME}/go' >> ~/.bashrc && \ +# echo 'export PATH=/usr/local/go/bin:${PATH}:${GOPATH}/bin' >> ~/.bashrc && \ +# . ~/.bashrc +# go get -d github.com/sylabs/singularity +# export VERSION=v3.0.3 # or another tag or branch if you like && \ +# cd $GOPATH/src/github.com/sylabs/singularity && \ +# git fetch && \ +# git checkout $VERSION # omit this command to install the latest bleeding edge code from master +# export VERSION=3.0.3 && # adjust this as necessary \ +# mkdir -p $GOPATH/src/github.com/sylabs && \ +# cd $GOPATH/src/github.com/sylabs && \ +# wget https://github.com/sylabs/singularity/releases/download/v4.0.1/singularity-ce-4.0.1.tar.gz && \ +# tar -xzf singularity-ce-4.0.1.tar.gz && \ +# cd ./singularity && \ +# ./mconfig + +################################ +# pggb +################################ + + git clone --recursive https://github.com/ekg/wfmash.git && cd wfmash && cmake -H. -Bbuild && cmake --build build -- -j 3 && cp build/bin/wfmash /usr/local/bin/wfmash && cp build/lib/libwfa2cpp.so.0 /usr/local/lib/ && cp build/lib/libwfa2cpp.so /usr/local/lib/ && cp build/lib/libwfa2.so.0 /usr/local/lib/ && cp build/lib/libwfa2.so /usr/local/lib/ && cd ../ && rm -rf wfmash # buildkit + + git clone --recursive https://github.com/ekg/seqwish && cd seqwish && git pull && git checkout f44b402f0c2e02988d431d9b2e5eba9727cf93a9 && git submodule update --init --recursive && cmake -H. -Bbuild && cmake --build build -- -j $(nproc) && cp bin/seqwish /usr/local/bin/seqwish && cd ../ && rm -rf seqwish # buildkit + + git clone --recursive https://github.com/pangenome/smoothxg && cd smoothxg && git pull && git checkout aaa0b283e13ca57c4e6e4e67a03451925f5342f1 && git submodule update --init --recursive && cmake -H. -Bbuild && cmake --build build -- -j $(nproc) && cp bin/smoothxg /usr/local/bin/smoothxg && cp deps/odgi/bin/odgi /usr/local/bin/odgi && cd ../ && rm -rf odgi # buildkit + + /bin/sh -c curl https://sh.rustup.rs -sSf | sh -s -- -y # buildkit + + git clone https://github.com/marschall-lab/GFAffix.git && cd GFAffix && git pull && git checkout d630eb7d9827340f5f292e57cb3cb5e31e6f86f0 && cargo install --force --path . && mv /root/.cargo/bin/gfaffix /usr/local/bin/gfaffix && cd ../ && rm -rf GFAffix # buildkit + +# pipx install multiqc==1.16 # buildkit +# cp -rf /root/.local/bin/multiqc /usr/local/bin +# chmod 777 /usr/local/bin/multiqc + + wget https://github.com/vgteam/vg/releases/download/v1.52.0/vg && chmod +x vg && mv vg /usr/local/bin/vg # buildkit + + git clone https://github.com/pangenome/vcfbub && cd vcfbub && git pull && git checkout 26a1f0cb216a423f8547c4ad0e0ce38cb9d324b9 && cargo install --force --path . && mv /root/.cargo/bin/vcfbub /usr/local/bin/vcfbub && cd ../ && rm -rf vcfbub + + git clone --recursive https://github.com/vcflib/vcflib.git && cd vcflib && git checkout 7c1a31a430d339adcb9a0c2fd3fd02d3b30e3549 && mkdir -p build && cd build && cmake -DZIG=OFF -DCMAKE_BUILD_TYPE=Debug .. && cmake --build . -- -j $(nproc) && mv vcfwave /usr/local/bin/vcfwave && mv vcfuniq /usr/local/bin/vcfuniq && cd ../ && rm -rf vcflib # buildkit + +: pipx install igraph==0.10.4 # buildkit + + #pipx install pycairo==1.23.0 # buildkit + + #git clone https://github.com/ekg/fastix.git && cd fastix && git pull && git checkout 331c1159ea16625ee79d1a82522e800c99206834 && cargo install --force --path . && mv /root/.cargo/bin/fastix /usr/local/bin/fastix && cd ../ && rm -rf fastix # buildkit + + #git clone https://github.com/ekg/pafplot.git && cd pafplot && git pull && git checkout 7dda24c0aeba8556b600d53d748ae3103ec85501 && cargo install --force --path . && mv /root/.cargo/bin/pafplot /usr/local/bin/ && cd ../ && rm -rf pafplot # buildkit + + git clone https://github.com/pangenome/pggb.git + sed -i "s/which time/\/usr\/bin\/which time/g" pggb/pggb + cp pggb/pggb /usr/local/bin/pggb # buildkit + chmod 777 /usr/local/bin/pggb # buildkit + cp pggb/partition-before-pggb /usr/local/bin/partition-before-pggb # buildkit + chmod a+rx /usr/local/bin/partition-before-pggb # buildkit + + wget -qO- https://get.nextflow.io | bash + chmod 777 nextflow + cp nextflow /usr/local/bin/nextflow +################################### + + git clone https://github.com/aleimba/bac-genomics-scripts.git + cp -rf bac-genomics-scripts /usr/local/bin + + R --quiet --slave -e 'install.packages("micropan", version = "1.3.0", repos="https://cloud.r-project.org/")' + + R --quiet --slave -e 'devtools::install_github("KlausVigo/phangorn")' + + + #pip3 install git+https://github.com/gtonkinhill/panaroo + + wget http://downloads.sourceforge.net/project/pgap/PGAP-1.2.1/PGAP-1.2.1.tar.gz + tar -xzvf PGAP-1.2.1.tar.gz + cp -rf PGAP-1.2.1 /usr/local/bin + sed -i "s/\/home\/zhaoyb\/work\/PGAP\/PGAP\/Programs\/ExtraBin\/mcl/\/usr\/bin\/mcl/g" /usr/local/bin/PGAP-1.2.1/PGAP.pl + sed -i "s/\/home\/zhaoyb\/work\/PGAP\/PGAP\/Programs\/ExtraBin\//\/usr\/bin\//g" /usr/local/bin/PGAP-1.2.1/PGAP.pl + sed -i "s/\/share\/ibm-1\/bin\//\/usr\/bin\//g" /usr/local/bin/PGAP-1.2.1/PGAP.pl + + wget https://github.com/davidemms/OrthoFinder/releases/latest/download/OrthoFinder.tar.gz + tar -xzvf OrthoFinder.tar.gz + cp -rf OrthoFinder /usr/bin/ + + git clone https://github.com/gpertea/gffread + cd gffread + make release + cp -rf gffread /usr/bin/ + + curl -o datasets 'https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v1/linux-amd64/datasets' + chmod +x datasets + cp -rf datasets /usr/bin/ + + wget http://github.com/bbuchfink/diamond/releases/download/v2.1.8/diamond-linux64.tar.gz + tar xzf diamond-linux64.tar.gz + cp -rf ./diamond /usr/bin/OrthoFinder/bin/ + + git clone https://github.com/SouthGreenPlatform/PanExplorer_workflow.git + + export PANEX_PATH=/usr/local/bin/PanExplorer_workflow + cp -rf PanExplorer_workflow /usr/local/bin + wget https://ftp.ncbi.nlm.nih.gov/pub/mmdb/cdd/little_endian/Cog_LE.tar.gz + tar -xzvf Cog_LE.tar.gz + cp -rf Cog.* $PANEX_PATH/COG + + echo "#!/bin/bash" >/usr/bin/consense + echo "phylip consense $*" >>/usr/bin/consense + chmod 755 /usr/bin/consense + echo "#!/bin/bash" >/usr/bin/neighbor + echo "phylip neighbor $*" >>/usr/bin/neighbor + chmod 755 /usr/bin/neighbor + echo "#!/bin/bash" >/usr/bin/seqboot + echo "phylip seqboot $*" >>/usr/bin/seqboot + chmod 755 /usr/bin/seqboot + echo "#!/bin/bash" >/usr/bin/dnadist + echo "phylip dnadist $*" >>/usr/bin/dnadist + chmod 755 /usr/bin/dnadist + echo "#!/bin/bash" >/usr/bin/dnapars + echo "phylip dnapars $*" >>/usr/bin/dnapars + chmod 755 /usr/bin/dnapars + echo "#!/bin/bash" >/usr/bin/dnaml + echo "phylip dnaml $*" >>/usr/bin/dnaml + chmod 755 /usr/bin/dnaml + + wget https://mmseqs.com/latest/mmseqs-linux-sse41.tar.gz --no-check-certificate + tar xvfz mmseqs-linux-sse41.tar.gz + cp -rf mmseqs/bin/mmseqs /usr/bin/ + + export PIPX_HOME=/opt/pipx + export PIPX_BIN_DIR=/usr/local/bin + pipx install panacota + + git clone https://github.com/lh3/gfatools + cd gfatools && make + cp -rf gfatools /usr/bin/ + + conda install -y -c bioconda minimap2 + + + #conda install -y -c bioconda liftoff + + #git clone https://github.com/agshumate/Liftoff liftoff + #cd liftoff + #python setup.py install + #pipx install Liftoff + + #wget https://github.com/ComparativeGenomicsToolkit/cactus/releases/download/v2.6.9/cactus-bin-v2.6.9.tar.gz + wget https://github.com/ComparativeGenomicsToolkit/cactus/releases/download/v2.6.9/cactus-bin-legacy-v2.6.9.tar.gz + tar -xzf cactus-bin-legacy-v2.6.9.tar.gz + chown -R root cactus-bin-v2.6.9 + cd cactus-bin-v2.6.9 + virtualenv -p python3 venv-cactus-v2.6.9 + printf "export PATH=$(pwd)/bin:\$PATH\nexport PYTHONPATH=$(pwd)/lib:\$PYTHONPATH\n" >> venv-cactus-v2.6.9/bin/activate + . venv-cactus-v2.6.9/bin/activate + python3 -m pip install -U setuptools pip + python3 -m pip install -U . + python3 -m pip install -U -r ./toil-requirement.txt + mkdir /usr/bin/cactus + cd .. + cp -rf cactus-bin-v2.6.9 /usr/bin/ + chmod -R 777 /usr/bin/cactus-bin-v2.6.9 + + git clone https://github.com/vigsterkr/circos.git + cd circos + ./install-unix + cd .. + cp -rf circos /usr/local/bin/ + + #wget https://github.com/ParBLiSS/FastANI/archive/master.zip + #unzip master.zip + #cd FastANI-master/ + #autoconf + #./configure --with-gsl=/usr/ + #make + +# apt-get -y install build-essential bzip2 ca-certificates libglib2.0-0 libxext6 libsm6 libxrender1 +# rm -rf /var/lib/apt/lists/* +# #Installing Anaconda 2 and Conda 4.5.11 +# wget -c https://repo.continuum.io/archive/Anaconda2-5.3.0-Linux-x86_64.sh +# /bin/bash Anaconda2-5.3.0-Linux-x86_64.sh -bfp /usr/local +# #Conda configuration of channels from .condarc file +# conda config --file /.condarc --add channels defaults +# conda config --file /.condarc --add channels conda-forge +# conda config --file /.condarc --add channels bioconda +# conda update conda +# #List installed environments +# conda list + +# conda install -c bioconda orthofinder + +%environment + export PATH=$PATH:/usr/games:/usr/bin/OrthoFinder:/usr/bin/OrthoFinder/bin:/usr/bin/cactus-bin-v2.6.9/bin:/usr/bin/cactus-bin-v2.6.9/venv-cactus-v2.6.9/bin:/usr/local/bin/circos/bin + export PYTHONPATH=$PYTHONPATH:/usr/bin/cactus-bin-v2.6.9/lib + export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/