Add changes

_recipes/BenGSt/repo_for_reizel_lab/containers/2024/methylKitAvgMethylOverRegions/Singularity

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+Bootstrap: docker
+From: bioconductor/bioconductor_docker:RELEASE_3_19
+
+%post
+    R -e 'install.packages(c("rtracklayer", "data.table", "dplyr", "parallel", "argparser", "IRanges"))'
+    R -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")'
+    R -e 'BiocManager::install(c("GenomeInfoDb", "GenomicRanges", "methylKit"))'

_recipes/BenGSt/repo_for_reizel_lab/containers/2024/methylKitDMRs/Singularity

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+Bootstrap: docker
+From: bioconductor/bioconductor_docker:RELEASE_3_19
+
+%post
+    R -e 'install.packages(c("argparser", "dplyr", "stringr"))'
+    R -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")'
+    R -e 'BiocManager::install("methylKit")'

_recipes/HuffordLab-Containers/necat/Singularity

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+Bootstrap: docker
+From: ubuntu:16.04
+
+%environment
+   export PATH=$PATH:/opt/NECAT/Linux-amd64/bin
+
+%labels
+   Author Arun Seetharam
+   Version v1
+   Maintainer arnstrm@iastate.edu
+
+%help
+   This is a container for the NECAT
+
+%test
+   which necat.pl
+   which pigz
+   which ctgcns
+
+%post
+   apt-get update
+   apt-get install -y build-essential wget curl git autoconf
+   apt-get install -y gcc g++ make
+   apt-get install -y zlib1g-dev libgomp1 libgomp1 libpam-systemd-
+   apt-get install -y libcurl4-gnutls-dev libxml2-dev libssl-dev libbz2-dev
+   apt-get install -y gfortran
+   apt-get install -y perl python3 python3-pip 
+# instll necat
+   cd opt/
+   git clone https://github.com/xiaochuanle/NECAT.git
+   cd NECAT/src
+   make
+   cd ../Linux-amd64/bin
+
+
+

_recipes/J-Andy/eQTL-analysis/Singularity

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+Bootstrap: docker
+From: rocker/r-ver:4.3.0
+
+%post
+    # Install system utilities and dependencies for R packages
+    apt-get update && apt-get install -y \
+        libcurl4-openssl-dev \
+        libssl-dev \
+        libxml2-dev \
+        wget \
+        vim \
+        less \
+        && apt-get clean \
+        && rm -rf /var/lib/apt/lists/*
+
+    # Ensure output directory is created and has proper permissions
+    mkdir -p /usr/src/app/output
+    # chmod 777 /usr/src/app/output  # Make the output directory writable by any user
+
+    # Install R packages from CRAN
+    R -e "install.packages(c('dplyr', 'ggplot2', 'ggrepel', 'testthat'), repos='http://cran.rstudio.com/')"
+
+    # Install qvalue from Bioconductor
+    R -e "if (!requireNamespace('BiocManager', quietly = TRUE)) install.packages('BiocManager')"
+    R -e "BiocManager::install('qvalue')"
+
+    # Create working directory
+    mkdir -p /usr/src/app
+
+    # Download R scripts and data
+    wget https://raw.githubusercontent.com/J-Andy/eQTL-analysis/main/main.R -O /usr/src/app/main.R
+    wget https://raw.githubusercontent.com/J-Andy/eQTL-analysis/main/unit_tests.R -O /usr/src/app/unit_tests.R
+    wget https://raw.githubusercontent.com/J-Andy/eQTL-analysis/main/Gene_KOs.tsv -O /usr/src/app/Gene_KOs.tsv
+    wget https://raw.githubusercontent.com/J-Andy/eQTL-analysis/main/Mutations.tsv -O /usr/src/app/Mutations.tsv
+
+%environment
+    # Set the working directory and environment variables inside the container
+    export R_LIBS_USER=/usr/local/lib/R/site-library
+    export WORKDIR=/usr/src/app
+
+%runscript
+    # Command to run the R script when the container starts
+    cd /usr/src/app
+    exec Rscript main.R

_recipes/ReproNim/containers/images/bids/Singularity.bids-nibabies--24.1.0

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+#
+# Automagically prepared for ReproNim/containers distribution.
+# See http://github.com/ReproNim/containers for more info
+#
+Bootstrap: docker
+From: nipreps/nibabies:24.1.0
+
+%post
+
+# Create commonly present root directories to avoid need in overlays not supported
+# on older systems
+mkdir -p /ihome /data /data2 /zfs /isi /dartfs /dartfs-hpc
+
+%environment
+export LANG="C.UTF-8"
+export LC_ALL="C.UTF-8"
+
+# TODO: Take advantage of the fact that it is a bids-app somehow?

_recipes/ReproNim/containers/images/bids/Singularity.bids-qsirecon--0.23.1

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+#
+# Automagically prepared for ReproNim/containers distribution.
+# See http://github.com/ReproNim/containers for more info
+#
+Bootstrap: docker
+From: pennlinc/qsirecon:0.23.1
+
+%post
+
+# Create commonly present root directories to avoid need in overlays not supported
+# on older systems
+mkdir -p /ihome /data /data2 /zfs /isi /dartfs /dartfs-hpc
+
+%environment
+export LANG="C.UTF-8"
+export LC_ALL="C.UTF-8"
+
+# TODO: Take advantage of the fact that it is a bids-app somehow?

_recipes/UPPMAX/ticket_297240/Singularity

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+Bootstrap: docker
+From: mcr.microsoft.com/devcontainers/anaconda
+# From: pnnlmiscscripts/anaconda:latest
+
+
+%post
+    # From https://github.com/brucemoran/Singularity/blob/8eb44591284ffb29056d234c47bf8b1473637805/shub/bases/recipe.CentOs7-R_3.5.2#L21
+    echo 'export LANG=en_US.UTF-8 LANGUAGE=C LC_ALL=C LC_CTYPE=C LC_COLLATE=C  LC_TIME=C LC_MONETARY=C LC_PAPER=C LC_MEASUREMENT=C' >> $SINGULARITY_ENVIRONMENT
+
+    conda install hcc::cellranger
+
+
+%runscript
+python "$@"

_recipes/UPPMAX/ticket_297240/Singularity_approach_3

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+Bootstrap: docker
+From: continuumio/anaconda3
+
+%post
+    # From https://github.com/brucemoran/Singularity/blob/8eb44591284ffb29056d234c47bf8b1473637805/shub/bases/recipe.CentOs7-R_3.5.2#L21
+    echo 'export LANG=en_US.UTF-8 LANGUAGE=C LC_ALL=C LC_CTYPE=C LC_COLLATE=C  LC_TIME=C LC_MONETARY=C LC_PAPER=C LC_MEASUREMENT=C' >> $SINGULARITY_ENVIRONMENT
+
+    # conda install --channel "conda-forge" pyopenssl=17.0.0.*
+    # conda install --channel "timl" pyopenssl=17.0.0
+    conda install --channel "free" pyopenssl=17.0.0
+
+    conda install --channel "bioconda" bcftools
+    conda install --channel "HCC" cellranger
+
+
+%runscript
+python "$@"

_recipes/UPPMAX/ticket_297240/Singularity_approach_4

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+Bootstrap: docker
+From: mcr.microsoft.com/devcontainers/anaconda
+# From: pnnlmiscscripts/anaconda:latest
+
+
+%post
+    # From https://github.com/brucemoran/Singularity/blob/8eb44591284ffb29056d234c47bf8b1473637805/shub/bases/recipe.CentOs7-R_3.5.2#L21
+    echo 'export LANG=en_US.UTF-8 LANGUAGE=C LC_ALL=C LC_CTYPE=C LC_COLLATE=C  LC_TIME=C LC_MONETARY=C LC_PAPER=C LC_MEASUREMENT=C' >> $SINGULARITY_ENVIRONMENT
+
+    conda install hcc::cellranger
+
+
+%runscript
+python "$@"

_recipes/UPPMAX/ticket_297240/Singularity_approach_5

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+Bootstrap: docker
+From: chainguard/bazel:latest
+
+%post
+    # From https://github.com/brucemoran/Singularity/blob/8eb44591284ffb29056d234c47bf8b1473637805/shub/bases/recipe.CentOs7-R_3.5.2#L21
+    echo 'export LANG=en_US.UTF-8 LANGUAGE=C LC_ALL=C LC_CTYPE=C LC_COLLATE=C  LC_TIME=C LC_MONETARY=C LC_PAPER=C LC_MEASUREMENT=C' >> $SINGULARITY_ENVIRONMENT
+
+    cd /opt
+    git clone https://github.com/10XGenomics/cellranger
+    cd cellranger
+
+    # Tip from https://stackoverflow.com/q/61869719
+    touch WORKSPACE
+
+    # Tip from https://raw.githubusercontent.com/10XGenomics/cellranger/main/conda_spec.bzl
+    echo 'load(":conda_spec.bzl", "anaconda_workspace")' > WORKSPACE
+    echo 'anaconda_workspace()' >> WORKSPACE
+
+    # Tip from error message
+    touch BUILD
+
+    bazel build conda_spec.bzl
+
+%runscript
+python "$@"

_recipes/WarwickRSE/basics-of-linux-scrtp-git/pong_game/singularity/team_server/Singularity.def

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+Bootstrap: ubuntu
+From: ubuntu:latest
+
+%post
+    # Update and install SSH server
+    apt-get update && apt-get install -y openssh-server
+
+    # Allow root login via SSH
+    sed -i 's/PermitRootLogin prohibit-password/PermitRootLogin yes/' /etc/ssh/sshd_config
+
+    # Set the working directory
+    mkdir -p /pong_game
+    cd /pong_game
+
+    # Copy create_users.sh and run it
+    cp /path/to/create_users.sh /pong_game/create_users.sh
+    bash /pong_game/create_users.sh
+
+    # Clean up the script after execution
+    rm /pong_game/create_users.sh
+
+    # Setup SSH keys for umpire
+    mkdir -p /home/umpire/.ssh
+    cp /path/to/keys.pub /home/umpire/.ssh/authorized_keys
+    chmod 700 /home/umpire/.ssh
+    chmod 600 /home/umpire/.ssh/authorized_keys
+    chown -R umpire:umpire /home/umpire/.ssh
+
+%files
+    # Include the necessary scripts and key files
+    create_users.sh /pong_game/create_users.sh
+    keys.pub /home/umpire/.ssh/authorized_keys
+
+%runscript
+    # Start the SSH service and then launch a bash shell
+    service ssh start
+    exec /bin/bash

_recipes/WarwickRSE/basics-of-linux-scrtp-git/pong_game/singularity/umpire/Singularity.def

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+Bootstrap: ubuntu
+From: ubuntu:latest
+
+%post
+    # Set working directory
+    mkdir -p /pong_game
+    cd /pong_game
+
+    # Update the package list and install OpenSSH server
+    apt-get update && apt-get install -y openssh-server
+
+    # Modify SSH configuration to allow root login
+    sed -i 's/PermitRootLogin prohibit-password/PermitRootLogin yes/' /etc/ssh/sshd_config
+
+    # Add umpire user and set the password
+    useradd -ms /bin/bash umpire
+    echo 'umpire:qwerty2000' | chpasswd
+
+    # Change ownership of the /pong_game directory to the umpire user
+    chown -R umpire:umpire /pong_game
+
+    # Install Python3 and pip
+    apt-get update && apt-get install -y python3-full python3-pip
+
+    # Install python-lorem via pip
+    pip3 install python-lorem --break-system-packages
+
+    # Set up SSH keys for the umpire user
+    mkdir -p /home/umpire/.ssh
+    cp /path/to/keys /home/umpire/.ssh/
+    chown -R umpire:umpire /home/umpire/.ssh
+
+%files
+    # Copy the necessary scripts to the container
+    make_points.sh /pong_game/make_points.sh
+    make_points.py /pong_game/make_points.py
+    calculate_points.py /pong_game/calculate_points.py
+    keys /home/umpire/.ssh/
+
+%runscript
+    # Start the SSH service and execute the make_points.sh script
+    service ssh start
+    exec /bin/bash /pong_game/make_points.sh

_recipes/aswinnarayanan/ci-dev/Singularity

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+Bootstrap: docker
+From: busybox:latest
+
+%runscript
+echo "Hello World!"

_recipes/cokelaer/damona/damona/software/adapterremoval/Singularity.adapterremoval_2.3.3

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+Bootstrap: docker
+From: python:3.11-slim
+
+%labels
+    Author thomas cokelaer
+
+%post
+
+    VERSION="2.3.3"
+
+     apt-get update --fix-missing \
+    && apt-get install -y wget make g++ zlib1g-dev libbz2-dev \
+    && cd /usr/local/ \
+    && wget -O adapterremoval-${VERSION}.tar.gz https://github.com/MikkelSchubert/adapterremoval/archive/v${VERSION}.tar.gz \
+    && tar xvzf adapterremoval-${VERSION}.tar.gz \
+    && rm -f adapterremoval-${VERSION}.tar.gz \
+    && cd /usr/local/adapterremoval-${VERSION} \
+    && make && make install \
+    && apt-get remove -y wget make g++ zlib1g-dev libbz2-dev \
+    && apt-get autoremove -y \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/* \
+
+
+%runscript
+    exec AdapterRemoval "$@"
+

_recipes/cokelaer/damona/damona/software/bbmap/Singularity.bbmap_39.1.0

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+Bootstrap: docker
+From: python:3.11-slim
+
+%labels
+    Author thomas cokelaer
+
+%post
+
+    VERSION="39.01"
+
+    apt-get update --fix-missing\
+        && apt-get install -y wget default-jre\
+        && cd /usr/local/ \
+        && wget -O BBMap_${VERSION}.tar.gz https://sourceforge.net/projects/bbmap/files/BBMap_${VERSION}.tar.gz/download \
+        && tar -xzvf BBMap_${VERSION}.tar.gz \
+        && rm -rf  BBMap_${VERSION}.tar.gz \
+        && mv bbmap/* /usr/local/bin/ \
+        && rm -rf bbmap \
+        && apt-get remove -y wget gcc \
+        && apt-get autoremove -y \
+        && apt-get clean \
+        && rm -rf /var/lib/apt/lists/* 
+
+
+%runscript
+    exec bbmap.sh "$@"
+

_recipes/cokelaer/damona/damona/software/dsrc/Singularity.dsrc_2.0.2

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+Bootstrap: docker
+From: alpine:3.20
+
+%post
+
+    VERSION="2.0.2"
+    # update and install python/bach
+    apk update \
+        && apk add --no-cache bash python3 py3-pip \
+        && apk add --no-cache g++ make boost boost-dev boost-system boost-thread boost-static pigz \
+        && wget https://github.com/refresh-bio/DSRC/archive/v${VERSION}.tar.gz \
+        && tar -xzvf v${VERSION}.tar.gz \
+        && rm -rf v${VERSION}.tar.gz \
+        && cd DSRC-${VERSION} \
+        && make bin \
+        && mv bin/dsrc /usr/local/bin/ \
+        && cd /usr/local \
+        && rm -rf /usr/local/DSRC-${VERSION} \
+        && apk del wget g++ make \
+        && rm -rf /var/cache/apk*
+
+
+%environment
+    export LC_ALL=C
+
+%runscript
+    exec dsrc "$@"
+