Mercurial > repos > dereeper > pangenome_explorer
comparison 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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2:97e4e3e818b6 | 3:e42d30da7a74 |
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1 Bootstrap: docker | |
2 From: debian:latest | |
3 | |
4 %labels | |
5 software=pggb | |
6 about.home=https://github.com/pangenome/pggb | |
7 | |
8 %runscript | |
9 echo "This is what happens when you run the container..." | |
10 | |
11 %post | |
12 echo "Hello from inside the container" | |
13 apt-get update | |
14 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 | |
15 | |
16 wget https://repo.anaconda.com/miniconda/Miniconda3-py38_4.8.3-Linux-x86_64.sh | |
17 chmod +x Miniconda3-py38_4.8.3-Linux-x86_64.sh | |
18 ./Miniconda3-py38_4.8.3-Linux-x86_64.sh -b -p /opt/miniconda3 | |
19 ln -s /opt/miniconda3/bin/conda /usr/bin/conda | |
20 | |
21 | |
22 | |
23 ############################# | |
24 # singularity | |
25 ############################# | |
26 # apt-get install -y build-essential libssl-dev uuid-dev libgpgme11-dev squashfs-tools libseccomp-dev pkg-config | |
27 # export VERSION=1.11 OS=linux ARCH=amd64 && \ | |
28 # wget https://go.dev/dl/go1.21.4.linux-amd64.tar.gz | |
29 # tar -C /usr/local -xzvf go1.21.4.linux-amd64.tar.gz && \ | |
30 # rm go1.21.4.linux-amd64.tar.gz | |
31 # echo 'export GOPATH=${HOME}/go' >> ~/.bashrc && \ | |
32 # echo 'export PATH=/usr/local/go/bin:${PATH}:${GOPATH}/bin' >> ~/.bashrc && \ | |
33 # . ~/.bashrc | |
34 # go get -d github.com/sylabs/singularity | |
35 # export VERSION=v3.0.3 # or another tag or branch if you like && \ | |
36 # cd $GOPATH/src/github.com/sylabs/singularity && \ | |
37 # git fetch && \ | |
38 # git checkout $VERSION # omit this command to install the latest bleeding edge code from master | |
39 # export VERSION=3.0.3 && # adjust this as necessary \ | |
40 # mkdir -p $GOPATH/src/github.com/sylabs && \ | |
41 # cd $GOPATH/src/github.com/sylabs && \ | |
42 # wget https://github.com/sylabs/singularity/releases/download/v4.0.1/singularity-ce-4.0.1.tar.gz && \ | |
43 # tar -xzf singularity-ce-4.0.1.tar.gz && \ | |
44 # cd ./singularity && \ | |
45 # ./mconfig | |
46 | |
47 ################################ | |
48 # pggb | |
49 ################################ | |
50 | |
51 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 | |
52 | |
53 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 | |
54 | |
55 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 | |
56 | |
57 /bin/sh -c curl https://sh.rustup.rs -sSf | sh -s -- -y # buildkit | |
58 | |
59 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 | |
60 | |
61 # pipx install multiqc==1.16 # buildkit | |
62 # cp -rf /root/.local/bin/multiqc /usr/local/bin | |
63 # chmod 777 /usr/local/bin/multiqc | |
64 | |
65 wget https://github.com/vgteam/vg/releases/download/v1.52.0/vg && chmod +x vg && mv vg /usr/local/bin/vg # buildkit | |
66 | |
67 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 | |
68 | |
69 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 | |
70 | |
71 : pipx install igraph==0.10.4 # buildkit | |
72 | |
73 #pipx install pycairo==1.23.0 # buildkit | |
74 | |
75 #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 | |
76 | |
77 #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 | |
78 | |
79 git clone https://github.com/pangenome/pggb.git | |
80 sed -i "s/which time/\/usr\/bin\/which time/g" pggb/pggb | |
81 cp pggb/pggb /usr/local/bin/pggb # buildkit | |
82 chmod 777 /usr/local/bin/pggb # buildkit | |
83 cp pggb/partition-before-pggb /usr/local/bin/partition-before-pggb # buildkit | |
84 chmod a+rx /usr/local/bin/partition-before-pggb # buildkit | |
85 | |
86 wget -qO- https://get.nextflow.io | bash | |
87 chmod 777 nextflow | |
88 cp nextflow /usr/local/bin/nextflow | |
89 ################################### | |
90 | |
91 git clone https://github.com/aleimba/bac-genomics-scripts.git | |
92 cp -rf bac-genomics-scripts /usr/local/bin | |
93 | |
94 R --quiet --slave -e 'install.packages("micropan", version = "1.3.0", repos="https://cloud.r-project.org/")' | |
95 | |
96 R --quiet --slave -e 'devtools::install_github("KlausVigo/phangorn")' | |
97 | |
98 | |
99 #pip3 install git+https://github.com/gtonkinhill/panaroo | |
100 | |
101 wget http://downloads.sourceforge.net/project/pgap/PGAP-1.2.1/PGAP-1.2.1.tar.gz | |
102 tar -xzvf PGAP-1.2.1.tar.gz | |
103 cp -rf PGAP-1.2.1 /usr/local/bin | |
104 sed -i "s/\/home\/zhaoyb\/work\/PGAP\/PGAP\/Programs\/ExtraBin\/mcl/\/usr\/bin\/mcl/g" /usr/local/bin/PGAP-1.2.1/PGAP.pl | |
105 sed -i "s/\/home\/zhaoyb\/work\/PGAP\/PGAP\/Programs\/ExtraBin\//\/usr\/bin\//g" /usr/local/bin/PGAP-1.2.1/PGAP.pl | |
106 sed -i "s/\/share\/ibm-1\/bin\//\/usr\/bin\//g" /usr/local/bin/PGAP-1.2.1/PGAP.pl | |
107 | |
108 wget https://github.com/davidemms/OrthoFinder/releases/latest/download/OrthoFinder.tar.gz | |
109 tar -xzvf OrthoFinder.tar.gz | |
110 cp -rf OrthoFinder /usr/bin/ | |
111 | |
112 git clone https://github.com/gpertea/gffread | |
113 cd gffread | |
114 make release | |
115 cp -rf gffread /usr/bin/ | |
116 | |
117 curl -o datasets 'https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v1/linux-amd64/datasets' | |
118 chmod +x datasets | |
119 cp -rf datasets /usr/bin/ | |
120 | |
121 wget http://github.com/bbuchfink/diamond/releases/download/v2.1.8/diamond-linux64.tar.gz | |
122 tar xzf diamond-linux64.tar.gz | |
123 cp -rf ./diamond /usr/bin/OrthoFinder/bin/ | |
124 | |
125 git clone https://github.com/SouthGreenPlatform/PanExplorer_workflow.git | |
126 | |
127 export PANEX_PATH=/usr/local/bin/PanExplorer_workflow | |
128 cp -rf PanExplorer_workflow /usr/local/bin | |
129 wget https://ftp.ncbi.nlm.nih.gov/pub/mmdb/cdd/little_endian/Cog_LE.tar.gz | |
130 tar -xzvf Cog_LE.tar.gz | |
131 cp -rf Cog.* $PANEX_PATH/COG | |
132 | |
133 echo "#!/bin/bash" >/usr/bin/consense | |
134 echo "phylip consense $*" >>/usr/bin/consense | |
135 chmod 755 /usr/bin/consense | |
136 echo "#!/bin/bash" >/usr/bin/neighbor | |
137 echo "phylip neighbor $*" >>/usr/bin/neighbor | |
138 chmod 755 /usr/bin/neighbor | |
139 echo "#!/bin/bash" >/usr/bin/seqboot | |
140 echo "phylip seqboot $*" >>/usr/bin/seqboot | |
141 chmod 755 /usr/bin/seqboot | |
142 echo "#!/bin/bash" >/usr/bin/dnadist | |
143 echo "phylip dnadist $*" >>/usr/bin/dnadist | |
144 chmod 755 /usr/bin/dnadist | |
145 echo "#!/bin/bash" >/usr/bin/dnapars | |
146 echo "phylip dnapars $*" >>/usr/bin/dnapars | |
147 chmod 755 /usr/bin/dnapars | |
148 echo "#!/bin/bash" >/usr/bin/dnaml | |
149 echo "phylip dnaml $*" >>/usr/bin/dnaml | |
150 chmod 755 /usr/bin/dnaml | |
151 | |
152 wget https://mmseqs.com/latest/mmseqs-linux-sse41.tar.gz --no-check-certificate | |
153 tar xvfz mmseqs-linux-sse41.tar.gz | |
154 cp -rf mmseqs/bin/mmseqs /usr/bin/ | |
155 | |
156 export PIPX_HOME=/opt/pipx | |
157 export PIPX_BIN_DIR=/usr/local/bin | |
158 pipx install panacota | |
159 | |
160 git clone https://github.com/lh3/gfatools | |
161 cd gfatools && make | |
162 cp -rf gfatools /usr/bin/ | |
163 | |
164 conda install -y -c bioconda minimap2 | |
165 | |
166 | |
167 #conda install -y -c bioconda liftoff | |
168 | |
169 #git clone https://github.com/agshumate/Liftoff liftoff | |
170 #cd liftoff | |
171 #python setup.py install | |
172 #pipx install Liftoff | |
173 | |
174 #wget https://github.com/ComparativeGenomicsToolkit/cactus/releases/download/v2.6.9/cactus-bin-v2.6.9.tar.gz | |
175 wget https://github.com/ComparativeGenomicsToolkit/cactus/releases/download/v2.6.9/cactus-bin-legacy-v2.6.9.tar.gz | |
176 tar -xzf cactus-bin-legacy-v2.6.9.tar.gz | |
177 chown -R root cactus-bin-v2.6.9 | |
178 cd cactus-bin-v2.6.9 | |
179 virtualenv -p python3 venv-cactus-v2.6.9 | |
180 printf "export PATH=$(pwd)/bin:\$PATH\nexport PYTHONPATH=$(pwd)/lib:\$PYTHONPATH\n" >> venv-cactus-v2.6.9/bin/activate | |
181 . venv-cactus-v2.6.9/bin/activate | |
182 python3 -m pip install -U setuptools pip | |
183 python3 -m pip install -U . | |
184 python3 -m pip install -U -r ./toil-requirement.txt | |
185 mkdir /usr/bin/cactus | |
186 cd .. | |
187 cp -rf cactus-bin-v2.6.9 /usr/bin/ | |
188 chmod -R 777 /usr/bin/cactus-bin-v2.6.9 | |
189 | |
190 git clone https://github.com/vigsterkr/circos.git | |
191 cd circos | |
192 ./install-unix | |
193 cd .. | |
194 cp -rf circos /usr/local/bin/ | |
195 | |
196 #wget https://github.com/ParBLiSS/FastANI/archive/master.zip | |
197 #unzip master.zip | |
198 #cd FastANI-master/ | |
199 #autoconf | |
200 #./configure --with-gsl=/usr/ | |
201 #make | |
202 | |
203 # apt-get -y install build-essential bzip2 ca-certificates libglib2.0-0 libxext6 libsm6 libxrender1 | |
204 # rm -rf /var/lib/apt/lists/* | |
205 # #Installing Anaconda 2 and Conda 4.5.11 | |
206 # wget -c https://repo.continuum.io/archive/Anaconda2-5.3.0-Linux-x86_64.sh | |
207 # /bin/bash Anaconda2-5.3.0-Linux-x86_64.sh -bfp /usr/local | |
208 # #Conda configuration of channels from .condarc file | |
209 # conda config --file /.condarc --add channels defaults | |
210 # conda config --file /.condarc --add channels conda-forge | |
211 # conda config --file /.condarc --add channels bioconda | |
212 # conda update conda | |
213 # #List installed environments | |
214 # conda list | |
215 | |
216 # conda install -c bioconda orthofinder | |
217 | |
218 %environment | |
219 export PATH=$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 | |
220 export PYTHONPATH=$PYTHONPATH:/usr/bin/cactus-bin-v2.6.9/lib | |
221 export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/ |