Mercurial > repos > dereeper > pangenome_explorer

comparison singularity/panexplorer.def @ 3:e42d30da7a74 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author dereeper
date Thu, 30 May 2024 11:52:25 +0000
parents
children
comparison
equal deleted inserted replaced
2:97e4e3e818b6 3:e42d30da7a74
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/