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Merge pull request #886 from Kincekara/ksnp
adds ksnp 4.1
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| FROM ubuntu:jammy as app | ||
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| ARG KSNPVER=4.1 | ||
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| LABEL base.image="ubuntu:jammy" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="kSNP" | ||
| LABEL software.version="${KSNPVER}" | ||
| LABEL description="K-mer-based phylogenetic inference" | ||
| LABEL website="https://sourceforge.net/projects/ksnp/" | ||
| LABEL license="https://github.com/kissake/kSNP${KSNPVER}/blob/%40/THE%20BSD%20OPENSOURCE%20LICENSE.pdf" | ||
| LABEL maintainer="Jeremiah Nisbet" | ||
| LABEL maintainer.email="[email protected]" | ||
| LABEL maintainer2="Kutluhan Incekara" | ||
| LABEL maintainer2.email="[email protected]" | ||
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| RUN apt-get update && apt-get install --no-install-recommends -y \ | ||
| wget \ | ||
| ca-certificates \ | ||
| unzip \ | ||
| python3 \ | ||
| libgomp1 && \ | ||
| apt-get autoclean && rm -rf /var/lib/apt/lists/* | ||
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| RUN wget -O kSNP.zip https://sourceforge.net/projects/ksnp/files/kSNP${KSNPVER}%20Linux%20package.zip && \ | ||
| unzip -j kSNP.zip "kSNP${KSNPVER} Linux package/kSNP${KSNPVER}pkg/*" -d "/usr/local/bin/" &&\ | ||
| rm kSNP.zip | ||
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| ENV LC_ALL=C | ||
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| CMD [kSNP4] | ||
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| WORKDIR /data | ||
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| ## Test ## | ||
| FROM app as test | ||
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| COPY kSNP_test.sh RunExamples.sh ./ | ||
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| RUN bash ./kSNP_test.sh | ||
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| # kSNP4 container | ||
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| Main tool: kSNP4 https://sourceforge.net/projects/ksnp/files/ | ||
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| Additional tools: None | ||
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| Full documentation: https://sourceforge.net/projects/ksnp/files/kSNP4%20User%20Guide.pdf/download | ||
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| Summary: | ||
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| kSNP4 is a program that identifies the pan-genome SNPs in a set of genome sequences, and estimates | ||
| phylogenetic trees based upon those SNPs. Because there are many potential downstream applications of SNP | ||
| information, kSNP4 also provides output files that include a multiple alignment of all of the SNP positions and | ||
| files that provide information about the positions of each SNP in each genome and annotations. kSNP4 can | ||
| analyze both complete (finished) genomes and unfinished genomes in assembled contigs or raw, unassembled | ||
| reads. Finished and unfinished genomes can be analyzed together, and kSNP4 can automatically download | ||
| Genbank files of the finished genomes (and annotated genome assemblies) and incorporate the information in | ||
| those files into the SNP annotation. Core SNPs, those present in all of the genomes, can optionally be | ||
| analyzed separately to generate a multiple SNP alignment and trees based on only the core SNPs. kSNP4 also | ||
| can provide a separate analysis of those SNPS that occur in at least a user-determined fraction of the genomes. | ||
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| # Example Usage | ||
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| ```bash | ||
| kSNP4 -in Eco100.in -k 21 -outdir Run1 -annotate annotatedGenomes | ||
| ``` |
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| #!/bin/bash | ||
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| # For debugging, use below as first line. | ||
| #!/bin/bash -vx | ||
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| # Examples are default in Example/Example<#>/... | ||
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| # Since this script will be in the source, default to making sure that the | ||
| # binary dependencies (jellyfish, mummer, consense, etc.) are available: | ||
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| MISSINGEXAMPLES=0 | ||
| echo "Checking for required example files:" | ||
| [ -d Examples/ ] || MISSINGEXAMPLES=1 | ||
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| if [ ${MISSINGEXAMPLES} -gt 0 ] | ||
| then | ||
| echo "Missing critical files under Examples/; are you sure you have unpacked the Examples?" | ||
| exit 1 | ||
| else | ||
| echo "... Found examples." | ||
| fi | ||
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| # Typically the in_list file must be modified to run the examples. | ||
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| # The output directory and log output locations can be specified. There may | ||
| # be hidden path dependencies such that the output directory must be a sub- | ||
| # directory of the current. | ||
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| # Current working directory: | ||
| CURRENT=`pwd` | ||
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| # Create our test directory (temporary directory) | ||
| mkdir TestResults | ||
| TEMPDIR="TestResults" | ||
| INLIST1="${TEMPDIR}/in_list1" | ||
| ANNDGENOMES1="${CURRENT}/Examples/Example1/Results/annotatedGenomes" | ||
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| RUN11DIR="${TEMPDIR}/Run11" | ||
| RUN11LOG="${TEMPDIR}/Run11Log" | ||
| RUN11ERRORLOG="${TEMPDIR}/Run11ErrorLog" | ||
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| RUN12DIR="${TEMPDIR}/Run12" | ||
| RUN12LOG="${TEMPDIR}/Run12Log" | ||
| RUN12ERRORLOG="${TEMPDIR}/Run12ErrorLog" | ||
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| RUN13DIR="${TEMPDIR}/Run13" | ||
| RUN13LOG="${TEMPDIR}/Run13Log" | ||
| RUN13ERRORLOG="${TEMPDIR}/Run13ErrorLog" | ||
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| INLIST2="${TEMPDIR}/in_list2" | ||
| ANNDGENOMES2="${CURRENT}/Examples/Example2/Results/annotatedGenomes" | ||
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| RUN21DIR="${TEMPDIR}/Run21" | ||
| RUN21LOG="${TEMPDIR}/Run21Log" | ||
| RUN21ERRORLOG="${TEMPDIR}/Run21ErrorLog" | ||
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| RUN22DIR="${TEMPDIR}/Run22" | ||
| RUN22LOG="${TEMPDIR}/Run22Log" | ||
| RUN22ERRORLOG="${TEMPDIR}/Run22ErrorLog" | ||
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| # Copy first in_list into place | ||
| # sed -e "s/^.*\/Genomes/Genomes/" < Examples/Example1/ExampleRuns/in_list | while read LINE ; do echo "${CURRENT}/Examples/Example1/${LINE}" ; done > "${INLIST1}" | ||
| MakeKSNP4infile -indir Examples/Example1/Genomes/ -outfile "${INLIST1}" | ||
| echo "Generated in_list for Example1:" | ||
| cat "${INLIST1}" | ||
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| ### # Example 1 | ||
| ### Run1: | ||
| ### kSNP4 -in in_list -outdir Run1 -k 13 | tee Run1Log | ||
| ### | ||
| ### Run2: | ||
| ### kSNP4 -in in_list -outdir Run2 -k 13 -annotate annotated_genomes | tee Run2Log | ||
| ### | ||
| ### Run3: | ||
| ### kSNP4 -in in_list -outdir Run3 -k 13 -annotate annotated_genomes -ML -NJ -vcf -core -min_frac 0.75 | tee Run3Log | ||
| ### | ||
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| kSNP4 -in "${INLIST1}" -outdir "${RUN11DIR}" -k 13 2>&1 | tee "${RUN11LOG}" | ||
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| kSNP4 -in "${INLIST1}" -outdir "${RUN12DIR}" -k 13 -annotate "${ANNDGENOMES1}" 2>&1 | tee "${RUN12LOG}" | ||
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| kSNP4 -in "${INLIST1}" -outdir "${RUN13DIR}" -k 13 -annotate "${ANNDGENOMES1}" -ML -NJ -vcf -core -min_frac 0.75 2>&1 | tee "${RUN13LOG}" | ||
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| ### # Example2 | ||
| ### | ||
| ### Run1: | ||
| ### kSNP4 -in in_list -outdir Run1 -k 19 -annotate annotated_genomes | tee Run1Log | ||
| ### | ||
| ### Run2: Note: replace ### with the path to SNPs_all in the Run1 directory! If any directory names in the path contain spaces be sure to enclose those directory names in quotes (" "). | ||
| ### | ||
| ### kSNP4 -in in_list2 -outdir Run2 -k 19 -annotate annotated_genomes -SNPs_all ###Examples/Example2/ExampleRuns/Run1/SNPs_all### | tee Run2Log | ||
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| # Copy in_list into place | ||
| # sed -e "s/^.*\/Genomes/Genomes/" < Examples/Example2/in_list | while read LINE ; do echo "${CURRENT}/Examples/Example2/${LINE}" ; done > "${INLIST21}" | ||
| MakeKSNP4infile -indir Examples/Example2/Genomes/ -outfile "${INLIST2}" | ||
| echo "Generated in_list for example2, run 1:" | ||
| cat "${INLIST2}" | ||
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| # Copy in_list into place | ||
| # sed -e "s/^.*\/Genomes/Genomes/" < Examples/Example2/in_list2 | while read LINE ; do echo "${CURRENT}/Examples/Example2/${LINE}" ; done > "${INLIST22}" | ||
| # echo "Generated in_list for example2, run 2:" | ||
| # cat "${INLIST22}" | ||
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| { # The second has a dependency on the first. | ||
| kSNP4 -in "${INLIST2}" -outdir "${RUN21DIR}" -k 21 -annotate "${ANNDGENOMES2}" 2>&1 | tee "${RUN21LOG}" | ||
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| # kSNP4 -in "${INLIST22}" -outdir "${RUN22DIR}" -k 19 -annotate "${ANNDGENOMES2}" -SNPs_all "${RUN21DIR}/SNPs_all" 2>&1 | tee "${RUN22LOG}" | ||
| } | ||
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| echo "Waiting for all examples to complete." | ||
| wait | ||
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| echo "Exiting for review: ${TEMPDIR}" | ||
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| #!/bin/bash | ||
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| wget https://sourceforge.net/projects/ksnp/files/Examples.zip/download | ||
| mv download Examples.zip | ||
| unzip Examples.zip | ||
| ./RunExamples.sh | ||
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