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update singularity support #113

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a6757dd
add an admonition about out-of-date containers
owlang Mar 19, 2026
632de08
create singularity.def
owlang Mar 23, 2026
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7 changes: 0 additions & 7 deletions Singularity
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9 changes: 6 additions & 3 deletions docs/html/usage/installation.html
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Expand Up @@ -224,8 +224,12 @@ <h2>Option 1: Install from source in GitHub<a class="headerlink" href="#option-1
</div></blockquote>
</section>
<section id="option-2-running-fithichip-with-docker-or-singularity">
<h2>Option 2: Running FitHiChIP with Docker or Singularity<a class="headerlink" href="#option-2-running-fithichip-with-docker-or-singularity" title="Permalink to this heading"></a></h2>
<p>To not deal with any dependencies and be sure that program will execute correctly, we have prepared images for you to run your analysis in.</p>
<h2>Option 2: Running FitHiChIP with Docker or Singularity<a class="headerlink" href="#option-2-running-fithichip-with-docker-or-singularity" title="Permalink to this heading"></a></h2>
<div class="admonition note">
<p class="admonition-title caution">Warning</p>
<p>These container instructions are out of date!</p>
</div>
<p>To not deal with any dependencies and be sure that program will execute correctly, we have prepared images for you to run your analysis in.</p>
<p><strong>Choose a container system:</strong></p>
<blockquote>
<div><ul class="simple">
Expand Down Expand Up @@ -282,7 +286,6 @@ <h2>Option 2: Running FitHiChIP with Docker or Singularity<a class="headerlink"
</section>
</section>


</div>
</div>
<footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
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241 changes: 241 additions & 0 deletions singularity.def
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Bootstrap: docker
From: continuumio/miniconda3:23.5.2-0

%labels
Author "Olivia Lang"
Version "FitHiChIP-11.0_HiCPro-3.1.0"
Description "FitHiChIP + HiC-Pro via continuumio/miniconda3:23.5.2-0"

%help
Singularity container for FitHiChIP, built on the official Miniconda3 base image.

Tool install locations:
conda env : /opt/conda
HiC-Pro : /usr/local/bin/HiC-Pro_3.1.0
FitHiChIP : /opt/FitHiChIP

Run FitHiChIP:
FitHiChIP_HiCPro.sh uses relative paths to call its R scripts,
so it MUST be run from /opt/FitHiChIP as the working directory:

singularity run fithichip.sif /absolute/path/to/config.txt

%environment
export PATH="/usr/local/bin:/opt/conda/bin:/usr/local/bin/HiC-Pro_3.1.0/bin:/usr/local/bin/HiC-Pro_3.1.0/scripts:/opt/FitHiChIP:$PATH"
export R_LIBS_SITE="/opt/R_libs"
export LC_ALL=C
export LANG=C

%post
export DEBIAN_FRONTEND=noninteractive
export LC_ALL=C
export LANG=C
export PATH="/opt/conda/bin:$PATH"

# -----------------------------------------------------------------------
# 1. System packages — only what conda cannot provide
# git for cloning, build-essential + make for HiC-Pro compilation
# -----------------------------------------------------------------------
apt-get update -y
apt-get install -y --no-install-recommends \
bc \
build-essential \
git \
make \
unzip
apt-get clean
rm -rf /var/lib/apt/lists/*

# -----------------------------------------------------------------------
# 2. Configure conda channels
# flexible priority avoids unsolvable environments when mixing
# bioconda and conda-forge packages
# -----------------------------------------------------------------------
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority flexible

# -----------------------------------------------------------------------
# 3. All tools and Python libraries in a single conda solve
# python=3.11 required; all HiC-Pro Python deps installed here:
# bx-python, scipy, pysam, iced (checked by check_pythonlib.py)
# hic-straw is the bioconda package name for hicstraw
# -----------------------------------------------------------------------
conda install --yes \
python=3.11 \
bedtools \
bowtie2 \
bx-python \
cooler \
hic-straw \
iced \
macs2 \
networkx \
pysam \
r-base \
r-plyr \
samtools \
scipy \
ucsc-bedtobigbed
conda clean --all --yes

# -----------------------------------------------------------------------
# 4. R packages
# -----------------------------------------------------------------------
mkdir -p /opt/R_libs
export R_LIBS_SITE=/opt/R_libs

# CRAN packages required by FitHiChIP
Rscript -e '
options(repos = c(CRAN = "https://cloud.r-project.org"))
install.packages(
c("optparse", "ggplot2", "data.table", "splines",
"fdrtool", "plyr", "dplyr"),
lib = "/opt/R_libs",
Ncpus = parallel::detectCores()
)
'

# Bioconductor packages for differential loop analysis
Rscript -e '
options(repos = c(CRAN = "https://cloud.r-project.org"))
install.packages("BiocManager", lib = "/opt/R_libs")
library(BiocManager, lib.loc = "/opt/R_libs")
BiocManager::install(
c("GenomicRanges", "edgeR"),
lib = "/opt/R_libs",
ask = FALSE,
update = FALSE
)
'

# -----------------------------------------------------------------------
# 5. Fix conda which function
# conda init defines a shell function named 'which' that shadows the
# system binary. Unset it in /etc/bash.bashrc so it is removed for all
# bash shells at both build time and runtime.
# -----------------------------------------------------------------------
echo "unset -f which 2>/dev/null || true" >> /etc/bash.bashrc

# -----------------------------------------------------------------------
# 6. HiC-Pro
# The continuumio base image provides conda at /opt/conda — no symlink needed.
# HiC-Pro default install prefix produces the tree at /usr/local/bin/HiC-Pro_3.1.0/
# -----------------------------------------------------------------------
# Clone into a separate source dir; make install copies built files to
# the default PREFIX (/usr/local/bin/HiC-Pro_3.1.0).
git clone --branch v3.1.0 --depth 1 https://github.com/nservant/HiC-Pro.git /opt/src/HiC-Pro
cd /opt/src/HiC-Pro

CONDA_BIN=/opt/conda/bin
sed -i "s|BOWTIE2_PATH =.*|BOWTIE2_PATH = ${CONDA_BIN}|" config-install.txt
sed -i "s|SAMTOOLS_PATH =.*|SAMTOOLS_PATH = ${CONDA_BIN}|" config-install.txt
sed -i "s|PYTHON_PATH =.*|PYTHON_PATH = ${CONDA_BIN}|" config-install.txt
sed -i "s|R_PATH =.*|R_PATH = ${CONDA_BIN}|" config-install.txt
make configure
make CONFIG_SYS=config-install.txt install

# FitHiChIP locates HiC-Pro via: HiCProBasedir=$(dirname $(dirname $(which HiC-Pro)))
# /usr/local/bin/HiC-Pro_3.1.0/bin is on PATH so which returns the full path,
# and dirname/dirname correctly resolves to /usr/local/bin/HiC-Pro_3.1.0
# where scripts/build_matrix lives.

# Remove the source tree now that the install is complete
rm -rf /opt/src/HiC-Pro

# -----------------------------------------------------------------------
# 7. FitHiChIP
# -----------------------------------------------------------------------
cd /opt
git clone --branch 11.0 --depth 1 https://github.com/ay-lab/FitHiChIP.git
chmod -R +x /opt/FitHiChIP/*.sh 2>/dev/null || true

# Pre-download interact.as from UCSC to /opt/FitHiChIP
# DiffAnalysisHiChIP.r checks for this file relative to getwd();
# FitHiChIP should be run from /opt/FitHiChIP so it is found here.
wget -q https://genome.ucsc.edu/goldenPath/help/examples/interact/interact.as \
-O /opt/FitHiChIP/interact.as

# Ensure R_LIBS_SITE is set for interactive bash shells (e.g. singularity shell)
echo "export R_LIBS_SITE=/opt/R_libs" >> /etc/bash.bashrc

echo ""
echo "=== FitHiChIP build complete ==="

%runscript
if [ $# -eq 0 ]; then
echo "FitHiChIP Singularity container"
echo ""
echo "Usage:"
echo " singularity run fithichip.sif <absolute_path_to_config>"
echo ""
echo " The config file must use absolute paths for all inputs/outputs."
echo " FitHiChIP is run from /opt/FitHiChIP as the working directory."
exit 1
fi
cd /opt/FitHiChIP
exec bash FitHiChIP_HiCPro.sh -C "$1"

%test
export PATH="/usr/local/bin:/opt/conda/bin:/usr/local/bin/HiC-Pro_3.1.0/bin:/usr/local/bin/HiC-Pro_3.1.0/scripts:/opt/FitHiChIP:$PATH"
export R_LIBS_SITE="/opt/R_libs"

echo "=== which ==="
unset -f which 2>/dev/null || true
type which
type HiC-Pro

echo ""
echo "=== Tool versions ==="
python3 --version
bedtools --version | head -1
bowtie2 --version | head -1
bgzip --version | head -1
tabix --version | head -1
macs2 --version
samtools --version | head -1
R --version | head -1
HiC-Pro --version

echo ""
echo "=== HiC-Pro internals ==="
test -f /usr/local/bin/HiC-Pro_3.1.0/scripts/build_matrix \
&& echo " build_matrix found" \
|| { echo " ERROR: build_matrix not found"; exit 1; }
test -f /usr/local/bin/HiC-Pro_3.1.0/scripts/cutsite_trimming \
&& echo " cutsite_trimming found" \
|| { echo " ERROR: cutsite_trimming not found"; exit 1; }

echo ""
echo "=== Python libraries ==="
python3 -c "import bx; print('bx-python ', bx.__version__)"
python3 -c "import cooler; print('cooler ', cooler.__version__)"
python3 -c "import hicstraw; print('hicstraw ', hicstraw.__version__)"
python3 -c "import iced; print('iced ', iced.__version__)"
python3 -c "import networkx; print('networkx ', networkx.__version__)"
python3 -c "import numpy; print('numpy ', numpy.__version__)"
python3 -c "import pysam; print('pysam ', pysam.__version__)"
python3 -c "import scipy; print('scipy ', scipy.__version__)"

echo ""
echo "=== R packages ==="
Rscript -e '
.libPaths(c("/opt/R_libs", .libPaths()))
pkgs <- c("optparse","ggplot2","data.table","splines",
"fdrtool","plyr","dplyr","GenomicRanges","edgeR")
for (pkg in pkgs) {
if (!requireNamespace(pkg, quietly = TRUE))
stop(paste("MISSING R package:", pkg))
cat(sprintf(" %-20s OK\n", pkg))
}
'

echo ""
echo "=== FitHiChIP scripts ==="
test -f /opt/FitHiChIP/FitHiChIP_HiCPro.sh \
&& echo " FitHiChIP_HiCPro.sh found" \
|| { echo " ERROR: FitHiChIP_HiCPro.sh not found"; exit 1; }

echo ""
echo "=== All checks passed ==="