# HG changeset patch
# User galaxytrakr
# Date 1773436936 0
# Node ID 8e7a84e62b43035d8f80a8753f0fccbb0b0c8632
planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd
diff -r 000000000000 -r 8e7a84e62b43 Dockerfile
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/Dockerfile Fri Mar 13 21:22:16 2026 +0000
@@ -0,0 +1,175 @@
+# =========================
+# CSP2 for Galaxy/AWS Batch (offline Nextflow)
+# =========================
+
+# ---------- Build stage ----------
+FROM ubuntu:focal AS build
+
+ARG DEBIAN_FRONTEND=noninteractive
+ARG CSP2_VER="0.9.0"
+ARG BEDTOOLS_VER="2.31.1"
+ARG MUMMER_VER="4.0.0"
+ARG SKESA_VER="2.4.0"
+ARG MASH_VER="2.3"
+ARG BBMAP_VER="38.90"
+ARG PYTHON_VER="3.8"
+ARG SOURCEFORGE_MIRROR="psychz"
+ARG IQTREE_VER="2.0.6"
+
+# Use a stable working directory
+WORKDIR /workspace
+
+# Base build deps (include Java to verify/prewarm Nextflow here)
+RUN apt-get update && apt-get install -y --no-install-recommends \
+ tzdata gpg-agent software-properties-common build-essential \
+ zlib1g-dev libghc-bzlib-dev liblzma-dev wget ca-certificates \
+ cmake curl git xz-utils openjdk-17-jre-headless \
+ && rm -rf /var/lib/apt/lists/*
+
+# Python venv for runtime tools
+RUN add-apt-repository 'ppa:deadsnakes/ppa' && apt-get update && \
+ apt-get install -y --no-install-recommends \
+ python${PYTHON_VER} python${PYTHON_VER}-dev python${PYTHON_VER}-venv \
+ && python${PYTHON_VER} -m venv --copies /opt/venv \
+ && rm -rf /var/lib/apt/lists/*
+
+ENV PATH="/opt/venv/bin:${PATH}"
+
+# Core Python packages
+RUN pip install --no-cache-dir -U \
+ pandas~=1.2.0 pybedtools refchooser scikit-learn
+
+# ---- Fetch sources/artifacts ----
+
+# bedtools
+ADD https://github.com/arq5x/bedtools2/archive/refs/tags/v${BEDTOOLS_VER}.tar.gz .
+# mummer
+ADD https://github.com/mummer4/mummer/releases/download/v${MUMMER_VER}rc1/mummer-${MUMMER_VER}rc1.tar.gz .
+# skesa prebuilt bins
+ADD https://github.com/ncbi/SKESA/releases/download/${SKESA_VER}/skesa.centos.7.7 .
+ADD https://github.com/ncbi/SKESA/releases/download/${SKESA_VER}/gfa_connector.centos7.7 .
+ADD https://github.com/ncbi/SKESA/releases/download/${SKESA_VER}/kmercounter.centos7.7 .
+# mash
+ADD https://github.com/marbl/Mash/releases/download/v${MASH_VER}/mash-Linux64-v${MASH_VER}.tar .
+# iqtree2
+ADD https://github.com/Cibiv/IQ-TREE/releases/download/v${IQTREE_VER}/iqtree-${IQTREE_VER}-Linux.tar.gz .
+
+# ---- Build/install tools into /usr/local ----
+# bedtools
+RUN tar -xzf v${BEDTOOLS_VER}.tar.gz && rm v${BEDTOOLS_VER}.tar.gz && \
+ cd bedtools2-${BEDTOOLS_VER} && make -j && make install
+
+# Install MUMmer and copy Perl modules where dnadiff expects them
+RUN tar -xvf mummer-${MUMMER_VER}rc1.tar.gz && rm mummer-${MUMMER_VER}rc1.tar.gz && \
+ cd mummer-${MUMMER_VER}rc1 && \
+ ./configure --prefix=/usr/local && make -j && make install && ldconfig && \
+ mkdir -p /usr/local/lib/mummer && cp -a scripts/*.pm /usr/local/lib/mummer/
+
+# skesa tools (rename and install)
+RUN install -m 0755 skesa.centos.7.7 /usr/local/bin/skesa && \
+ install -m 0755 gfa_connector.centos7.7 /usr/local/bin/gfa_connector && \
+ install -m 0755 kmercounter.centos7.7 /usr/local/bin/kmercounter
+
+# mash
+RUN tar -xvf mash-Linux64-v${MASH_VER}.tar && \
+ install -m 0755 mash-Linux64-v${MASH_VER}/mash /usr/local/bin/mash
+
+# bbmap (grab all scripts/binaries)
+RUN wget -O BBMap_${BBMAP_VER}.tar.gz \
+ "https://sourceforge.net/projects/bbmap/files/BBMap_${BBMAP_VER}.tar.gz/download?use_mirror=${SOURCEFORGE_MIRROR}" && \
+ tar -xvf BBMap_${BBMAP_VER}.tar.gz && \
+ cp -a bbmap/* /usr/local/bin/ && \
+ rm -rf bbmap BBMap_${BBMAP_VER}.tar.gz
+
+# iqtree2
+RUN tar -xzf iqtree-${IQTREE_VER}-Linux.tar.gz && \
+ install -m 0755 iqtree-${IQTREE_VER}-Linux/bin/iqtree2 /usr/local/bin/iqtree && \
+ rm -rf iqtree-${IQTREE_VER}-Linux iqtree-${IQTREE_VER}-Linux.tar.gz
+
+# choose a version
+ARG NXF_VER="25.04.7"
+
+# install that exact launcher & prewarm framework into /opt/nextflow
+RUN curl -fsSL -o /usr/local/bin/nextflow \
+ "https://github.com/nextflow-io/nextflow/releases/download/v${NXF_VER}/nextflow" \
+ && chmod 0755 /usr/local/bin/nextflow \
+ && mkdir -p /opt/nextflow \
+ && chmod -R a+rwX /opt/nextflow \
+ && NXF_HOME=/opt/nextflow NXF_OFFLINE=false NXF_VER=${NXF_VER} /usr/local/bin/nextflow -version \
+ && ls -l /usr/local/bin/nextflow
+
+# ---------- Runtime stage ----------
+FROM ubuntu:focal AS runtime
+
+ARG DEBIAN_FRONTEND=noninteractive
+ARG CSP2_VER="0.9.0"
+
+# Python venv for runtime tools
+# Lean runtime libs + Python3.8 + Perl (no PPAs)
+RUN apt-get update && apt-get install -y --no-install-recommends \
+ ca-certificates openjdk-17-jre-headless bash tzdata perl perl-modules-5.30 \
+ libgomp1 liblzma5 zlib1g libbz2-1.0 coreutils make curl gawk \
+ python3.8 python3.8-venv python3.8-distutils \
+ && rm -rf /var/lib/apt/lists/*
+
+# Bring over tools and Python venv
+COPY --from=build /usr/local/bin/ /usr/local/bin/
+COPY --from=build /usr/local/libexec/mummer /usr/local/libexec/mummer
+COPY --from=build /usr/local/share/ /usr/local/share/
+COPY --from=build /opt/venv /opt/venv
+
+# Bring over Nextflow launcher and baked framework cache
+COPY --from=build /usr/local/bin/nextflow /usr/local/bin/nextflow
+COPY --from=build /opt/nextflow /opt/nextflow
+
+# Ensure any UID (Galaxy user) can execute nextflow and write minimal state into the cache
+RUN chmod 0755 /usr/local/bin/nextflow \
+ && chmod -R a+rwX /opt/nextflow
+
+# Bring the modules into the runtime image (if not already)
+COPY --from=build /usr/local/lib/mummer /usr/local/lib/mummer
+
+# Bring MUMmer shared libs into the runtime image
+COPY --from=build /usr/local/lib /usr/local/lib
+
+# Make sure dynamic linker can find them
+RUN ldconfig || true
+
+# Belt-and-suspenders for minimal images
+ENV LD_LIBRARY_PATH="/usr/local/lib:${LD_LIBRARY_PATH}"
+
+# Permissions: allow any UID to read/execute the libs
+RUN chmod -R a+rX /usr/local/lib
+
+# Make modules readable by any UID; create compatibility symlink if needed
+RUN chmod -R a+rX /usr/local/lib/mummer /usr/local/libexec/mummer && \
+ test -d /usr/local/lib/mummer || ln -s /usr/local/libexec/mummer /usr/local/lib/mummer
+
+# Ensure the common mummer executables are executable by all
+RUN chmod 0755 /usr/local/bin/dnadiff /usr/local/bin/nucmer /usr/local/bin/promer /usr/local/bin/show-snps || true
+
+# Help Perl find modules regardless of layout
+ENV PERL5LIB="/usr/local/lib/mummer:/usr/local/libexec/mummer:/usr/local/share/mummer:${PERL5LIB}"
+
+# Runtime environment
+ENV PATH="/opt/venv/bin:/usr/local/bin:${PATH}" \
+ LC_ALL=C \
+ NXF_HOME=/opt/nextflow \
+ NXF_OFFLINE=true \
+ CSP2_VER=${CSP2_VER}
+
+# Install the CSP2 pipeline under /opt/csp2 (avoid /app which Galaxy mounts)
+WORKDIR /opt/csp2
+
+# Copy your pipeline (these paths must exist in the build context)
+COPY bin ./bin
+COPY conf ./conf
+COPY subworkflows ./subworkflows
+COPY CSP2.nf ./CSP2.nf
+COPY nextflow.config ./nextflow.config
+
+# permissions for arbitrary UID
+RUN chmod -R a+rX /opt/csp2 && chmod -R a+rX /opt/nextflow
+
+# IMPORTANT: No ENTRYPOINT for Galaxy/AWS Batch. Neutral CMD.
+CMD ["/bin/bash"]
diff -r 000000000000 -r 8e7a84e62b43 cfsan2snp-screen.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cfsan2snp-screen.xml Fri Mar 13 21:22:16 2026 +0000
@@ -0,0 +1,170 @@
+
+ Screen query assemblies against reference assemblies
+
+ quay.io/galaxytrakr/csp2:0.9.7.7-galaxy_0.1
+
+ nextflow -version
+ nextflow_gal25.config
+
+ #set readext=""
+ #for $reads in $coll
+ && ln -sf '${reads}' 'queries/${reads.element_identifier.replace(": ", ".").replace(" ", "_")}.fasta'
+ #end for
+ #for $ref in $source.reference
+ #set renamedref=$ref.element_identifier.replace(": ", ".").replace(" ", "_").replace("(","").replace(")","")
+ && ln -sf '$ref' 'references/${renamedref}.fasta'
+ #end for
+ && echo "*** Files in queries directory: ***"
+ && ls -lah queries/
+ && nextflow run /opt/csp2/CSP2.nf -c nextflow_gal25.config
+ --runmode screen
+ --fasta queries
+ --ref_fasta 'references'
+ --min_cov $opt.min_cov
+ --min_iden $opt.min_iden
+ --min_len $opt.min_len
+ --ref_edge $opt.ref_edge
+ --query_edge $opt.query_edge
+ --dwin $opt.dwin
+ --wsnps $opt.wsnps
+ --out CSP2_Screen_Output
+ --quiet
+ && echo "*** Files in output directory: ***"
+ && ls -lahR CSP2_Screen_Output
+ && tail -n +2 CSP2_Screen_Output/Isolate_Data.tsv > ${isolate_data}
+ && tail -n +2 CSP2_Screen_Output/Raw_MUMmer_Summary.tsv > ${raw_mummer}
+ && tail -n +2 CSP2_Screen_Output/Screening_Results.tsv > ${screening_results}
+ && echo "*** Nextflow log follows: ***"
+ && cat .nextflow.log
+]]>
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+ This tool takes query assemblies and reference assemblies and calculates the pairwise distance between each query/reference combination. If no reference is provided, all queries are compared to all other queries.
+
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+ 10.XXXX/placeholder.doi
+ @article{example2024,title={CFSAN SNP Pipeline 2 (CSP2): a pipeline for fast and accurate SNP distance estimation from bacterial genome assemblies.},author={Doe, John and Smith, Jane},journal={Submitted},year={2024}}
+
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diff -r 000000000000 -r 8e7a84e62b43 cfsan2snp-snp.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cfsan2snp-snp.xml Fri Mar 13 21:22:16 2026 +0000
@@ -0,0 +1,183 @@
+
+ Run SNP Pipeline analysis on isolates using one or more references.
+
+ quay.io/galaxytrakr/csp2:0.9.7.7-galaxy_0.1
+
+ nextflow -version
+ nextflow_gal25.config
+
+ #set readext=""
+ #for $reads in $coll
+ && ln -sf '${reads}' 'queries/${reads.element_identifier.replace(": ", ".").replace(" ", "_")}.fasta'
+ #end for
+ #for $ref in $source.reference
+ #set renamedref=$ref.element_identifier.replace(": ", ".").replace(" ", "_").replace("(","").replace(")","")
+ && ln -sf '$ref' 'references/${renamedref}.fasta'
+ #end for
+
+ && echo "*** Files in queries directory: ***"
+ && ls -lah queries/
+ && nextflow run /opt/csp2/CSP2.nf -c nextflow_gal25.config
+ --runmode snp
+ --fasta queries
+ --ref_fasta 'references'
+ --min_cov $opt.min_cov
+ --min_iden $opt.min_iden
+ --min_len $opt.min_len
+ --ref_edge $opt.ref_edge
+ --query_edge $opt.query_edge
+ --dwin $opt.dwin
+ --wsnps $opt.wsnps
+ --out CSP2_SNP_Output
+ --quiet
+ && echo "*** Files in output directory: ***"
+ && ls -lahR CSP2_SNP_Output
+ && tail -n +2 CSP2_SNP_Output/Isolate_Data.tsv > ${isolate_data}
+ && tail -n +2 CSP2_SNP_Output/Raw_MUMmer_Summary.tsv > ${raw_mummer}
+ && tail -n +2 CSP2_SNP_Output/SNP_Analysis/${renamedref}/snp_distance_pairwise_preserved.tsv > ${snp_pairwise}
+ && cat CSP2_SNP_Output/SNP_Analysis/${renamedref}/snplist_preserved.txt > ${snp_list}
+ && cat CSP2_SNP_Output/SNP_Analysis/${renamedref}/snpma_preserved.fasta > ${snp_matrix}
+ && echo "*** Nextflow log follows: ***"
+ && cat .nextflow.log
+ ]]>
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+ This tool takes query assemblies and reference assemblies and calculates the pairwise distance between each query/reference combination. If no reference is provided, all queries are compared to all other queries.
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+ 10.XXXX/placeholder.doi
+ @article{example2024,title={CFSAN SNP Pipeline 2 (CSP2): a pipeline for fast and accurate SNP distance estimation from bacterial genome assemblies.},author={Doe, John and Smith, Jane},journal={Submitted},year={2024}}
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diff -r 000000000000 -r 8e7a84e62b43 nextflow.tmpl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/nextflow.tmpl Fri Mar 13 21:22:16 2026 +0000
@@ -0,0 +1,128 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ CSP2 Nextflow config file (for Dev25)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+profiles {
+ standard {
+ process.executor = 'local'
+ params.cores = @CORES@
+ params.python_module = ""
+ params.mummer_module = ""
+ params.skesa_module = ""
+ params.bedtools_module= ""
+ params.mash_module = ""
+ params.bbtools_module = ""
+ }
+}
+
+process {
+ cpus = @CORES@
+
+ withLabel: 'mummerMem' {
+ label = 'mummerMem'
+ cpus = 1
+ memory = '4 GB'
+ }
+ withLabel: 'skesaMem' {
+ label = 'skesaMem'
+ memory = '12 GB'
+ }
+}
+
+
+// Global default params
+params {
+
+ // Setting output directory
+
+ // Set name for output folder/file prefixes
+ out = "CSP2_${new java.util.Date().getTime()}"
+
+ // Set output parent directory [Default: CWD; Set this to have all output go to the same parent folder, with unique IDs set by --out]
+ outroot = ""
+
+ // CSP2 can run in the following run-modes:
+
+ // assemble: Assemble read data (--reads/--ref_reads) into FASTA via SKESA (ignores --fasta/--ref_fasta/--snpdiffs)
+ // align: Given query data (--reads/--fasta) and reference data (--ref_reads/--ref_fasta), run MUMmer alignment analysis for each query/ref combination (ignores --snpdiffs)
+ // screen: Given query data (--reads/--fasta) and reference data (--ref_reads/--ref_fasta) and/or MUMmer output (.snpdiffs), create a report for raw SNP distances between each query and reference assembly
+ // snp: Given query data (--reads/--fasta) and reference data (--ref_reads/--ref_fasta) and/or MUMmer output (.snpdiffs), generate alignments and pairwise distances for all queries based on each reference dataset
+
+ runmode = ""
+
+ // Location for isolate sequence data
+ reads = ""
+ fasta = ""
+
+ // Location for reference sequence data
+ ref_reads = ""
+ ref_fasta = ""
+
+ // IDs for reference sequences (Comma-separated list)
+ ref_id = ""
+
+ // Location for snpdiffs files
+ snpdiffs = ""
+
+ // Read read_info
+ readext = "fastq.gz"
+ forward = "_1.fastq.gz"
+ reverse = "_2.fastq.gz"
+
+ ref_readext = "fastq.gz"
+ ref_forward = "_1.fastq.gz"
+ ref_reverse = "_2.fastq.gz"
+
+ // Analytical variables
+
+ // Only consider queries if the reference genome is covered by at least % [Default: 85]
+ min_cov = 85
+
+ // Only consider SNPs from contig alignments longer than bp [Default: 500]
+ min_len = 500
+
+ // Only consider SNPs from contig alignments with % identity [Default: 99]
+ min_iden = 99
+
+ // Remove SNPs that occur within bp from the end of the reference contig [Default: 150]
+ ref_edge = 150
+
+ // Remove SNPs that occur within bp from the end of the query contig [Default: 150]
+ query_edge = 150
+
+ // SNP density filters: Given density windows provided by dwin, purge windows where more than the allowable window SNPs (wsnps) are found
+ // Default: 3 max per 1000bp, 2 max per 125bp, 1 max per 15bp, filtered from biggest window to smallest
+ // Set --dwin 0 to disable density filtering
+ dwin = "1000,125,15"
+ wsnps = "3,2,1"
+
+ // If running refchooser in snp mode, compare queries to the top X references [Default: 1]
+ n_ref = 1
+
+ // If the assembly file contains the string , remove it from the sample name (e.g. '_contigs_skesa')
+ trim_name = '""'
+
+ // If running SNP pipeline, set the maximum percent of isolates with missing data allowed in the final alignment/distances [Default: 50]
+ max_missing = 50
+
+ // Alternate directory for pybedtools tmp files [Default: "" (system default)]
+ tmp_dir = ""
+
+ // Set IDs for isolates to exclude from analysis (Comma-separated list)
+ exclude = ""
+
+ // By default, do not perform edge-filtered SNP rescuing
+ rescue = "norescue"
+
+ // Help function
+ help = "nohelp"
+ h = "nohelp"
+
+ // Bootstrap settings for iqTree
+ notree = "none" // Dummy setting to skip tree-building
+ b = 0 // Nonparametric bootstrap replicates
+ bb = 1000 // Ultrafast bootstrap replicates
+ model = "MFP+MERGE+ASC" // iqTree model
+}
diff -r 000000000000 -r 8e7a84e62b43 tool-data/all_fasta.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/all_fasta.loc.sample Fri Mar 13 21:22:16 2026 +0000
@@ -0,0 +1,10 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#
+#
+#So, all_fasta.loc could look something like this:
+#test1 test1 Test-Genome ./test-data/test1.fa
\ No newline at end of file
diff -r 000000000000 -r 8e7a84e62b43 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Fri Mar 13 21:22:16 2026 +0000
@@ -0,0 +1,7 @@
+
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+ value, dbkey, name, path
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+