Mercurial > repos > pjbriggs > amplicon_analysis_pipeline
diff install_amplicon_analysis-1.3.6.sh @ 4:86a12d75ebe4 draft default tip
planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8
| author | pjbriggs |
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| date | Fri, 20 Dec 2019 06:59:49 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/install_amplicon_analysis-1.3.6.sh Fri Dec 20 06:59:49 2019 -0500 @@ -0,0 +1,399 @@ +#!/bin/sh -e +# +# Prototype script to setup a conda environment with the +# dependencies needed for the Amplicon_analysis_pipeline +# script +# +# Handle command line +usage() +{ + echo "Usage: $(basename $0) [DIR]" + echo "" + echo "Installs the Amplicon_analysis_pipeline package plus" + echo "dependencies in directory DIR (or current directory " + echo "if DIR not supplied)" +} +if [ ! -z "$1" ] ; then + # Check if help was requested + case "$1" in + --help|-h) + usage + exit 0 + ;; + esac + # Assume it's the installation directory + cd $1 +fi +# Versions +PIPELINE_VERSION=1.3.6 +CONDA_REQUIRED_VERSION=4.6.14 +RDP_CLASSIFIER_VERSION=2.2 +# Directories +TOP_DIR=$(pwd)/Amplicon_analysis-${PIPELINE_VERSION} +BIN_DIR=${TOP_DIR}/bin +CONDA_DIR=${TOP_DIR}/conda +CONDA_BIN=${CONDA_DIR}/bin +CONDA_LIB=${CONDA_DIR}/lib +CONDA=${CONDA_BIN}/conda +ENV_NAME="amplicon_analysis_pipeline@${PIPELINE_VERSION}" +ENV_DIR=${CONDA_DIR}/envs/$ENV_NAME +# +# Functions +# +# Report failure and terminate script +fail() +{ + echo "" + echo ERROR $@ >&2 + echo "" + echo "$(basename $0): installation failed" + exit 1 +} +# +# Rewrite the shebangs in the installed conda scripts +# to remove the full path to conda 'bin' directory +rewrite_conda_shebangs() +{ + pattern="s,^#!${CONDA_BIN}/,#!/usr/bin/env ,g" + find ${CONDA_BIN} -type f -exec sed -i "$pattern" {} \; +} +# +# Reset conda version if required +reset_conda_version() +{ + CONDA_VERSION="$(${CONDA_BIN}/conda -V 2>&1 | head -n 1 | cut -d' ' -f2)" + echo conda version: ${CONDA_VERSION} + if [ "${CONDA_VERSION}" != "${CONDA_REQUIRED_VERSION}" ] ; then + echo "Resetting conda to last known working version $CONDA_REQUIRED_VERSION" + ${CONDA_BIN}/conda config --set allow_conda_downgrades true + ${CONDA_BIN}/conda install -y conda=${CONDA_REQUIRED_VERSION} + else + echo "conda version ok" + fi +} +# +# Install conda +install_conda() +{ + echo "++++++++++++++++" + echo "Installing conda" + echo "++++++++++++++++" + if [ -e ${CONDA_DIR} ] ; then + echo "*** $CONDA_DIR already exists ***" >&2 + return + fi + local cwd=$(pwd) + local wd=$(mktemp -d) + cd $wd + wget -q https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh + bash ./Miniconda2-latest-Linux-x86_64.sh -b -p ${CONDA_DIR} + echo Installed conda in ${CONDA_DIR} + echo -n "Adding conda bin to PATH..." + export PATH=${CONDA_BIN}:$PATH + echo "ok" + # Reset the conda version to a known working version + # (to avoid problems observed with e.g. conda 4.7.10) + echo "" + reset_conda_version + # Update the installation files + # This is to avoid problems when the length the installation + # directory path exceeds the limit for the shebang statement + # in the conda files + echo "" + echo -n "Rewriting conda shebangs..." + rewrite_conda_shebangs + echo "ok" + cd $cwd + rm -rf $wd/* + rmdir $wd +} +# +# Create conda environment +install_conda_packages() +{ + echo "+++++++++++++++++++++++++" + echo "Installing conda packages" + echo "+++++++++++++++++++++++++" + local cwd=$(pwd) + local wd=$(mktemp -d) + cd $wd + cat >environment.yml <<EOF +name: ${ENV_NAME} +channels: + - defaults + - conda-forge + - bioconda +dependencies: + - python=2.7 + - cutadapt=1.8 + - sickle-trim=1.33 + - bioawk=1.0 + - pandaseq=2.8.1 + - spades=3.10.1 + - fastqc=0.11.3 + - qiime=1.9.1 + - blast-legacy=2.2.26 + - fasta-splitter=0.2.6 + - rdp_classifier=$RDP_CLASSIFIER_VERSION + - vsearch=2.10.4 + - r=3.5.1 + - r-tidyverse=1.2.1 + - bioconductor-dada2=1.8 + - bioconductor-biomformat=1.8.0 +EOF + ${CONDA} env create --name "${ENV_NAME}" -f environment.yml + if [ $? -ne 0 ] ; then + fail "Non-zero exit status from 'conda env create'" + elif [ ! -e "${ENV_DIR}" ] ; then + fail "Failed to create conda environment: ${ENV_DIR} not found" + fi + echo Created conda environment in ${ENV_DIR} + cd $cwd + rm -rf $wd/* + rmdir $wd + # + # Patch qiime 1.9.1 tools to switch deprecated 'axisbg' + # matplotlib property to 'facecolor': + # https://matplotlib.org/api/prev_api_changes/api_changes_2.0.0.html + echo "" + for exe in make_2d_plots.py plot_taxa_summary.py ; do + echo -n "Patching ${exe}..." + find ${CONDA_DIR} -type f -name "$exe" -exec sed -i 's/axisbg=/facecolor=/g' {} \; + echo "done" + done + # + # Patch qiime 1.9.1 tools to switch deprecated 'set_axis_bgcolor' + # method call to 'set_facecolor': + # https://matplotlib.org/api/_as_gen/matplotlib.axes.Axes.set_axis_bgcolor.html + for exe in make_rarefaction_plots.py ; do + echo -n "Patching ${exe}..." + find ${CONDA_DIR} -type f -name "$exe" -exec sed -i 's/set_axis_bgcolor/set_facecolor/g' {} \; + echo "done" + done +} +# +# Install all the non-conda dependencies in a single +# function (invokes separate functions for each package) +install_non_conda_packages() +{ + echo "+++++++++++++++++++++++++++++" + echo "Installing non-conda packages" + echo "+++++++++++++++++++++++++++++" + # Temporary working directory + local wd=$(mktemp -d) + local cwd=$(pwd) + local wd=$(mktemp -d) + cd $wd + # Amplicon analysis pipeline + echo -n "Installing Amplicon_analysis_pipeline..." + if [ -e ${BIN_DIR}/Amplicon_analysis_pipeline.sh ] ; then + echo "already installed" + else + install_amplicon_analysis_pipeline + echo "ok" + fi + # ChimeraSlayer + echo -n "Installing ChimeraSlayer..." + if [ -e ${BIN_DIR}/ChimeraSlayer.pl ] ; then + echo "already installed" + else + install_chimeraslayer + echo "ok" + fi + # Uclust + # This no longer seems to be available for download from + # drive5.com so don't download + echo "WARNING uclust not available: skipping installation" +} +# +# Amplicon analyis pipeline +install_amplicon_analysis_pipeline() +{ + local wd=$(mktemp -d) + local cwd=$(pwd) + local wd=$(mktemp -d) + cd $wd + wget -q https://github.com/MTutino/Amplicon_analysis/archive/${PIPELINE_VERSION}.tar.gz + tar zxf ${PIPELINE_VERSION}.tar.gz + cd Amplicon_analysis-${PIPELINE_VERSION} + INSTALL_DIR=${TOP_DIR}/share/amplicon_analysis_pipeline-${PIPELINE_VERSION} + mkdir -p $INSTALL_DIR + ln -s $INSTALL_DIR ${TOP_DIR}/share/amplicon_analysis_pipeline + for f in *.sh *.R ; do + /bin/cp $f $INSTALL_DIR + done + /bin/cp -r uc2otutab $INSTALL_DIR + mkdir -p ${BIN_DIR} + cat >${BIN_DIR}/Amplicon_analysis_pipeline.sh <<EOF +#!/usr/bin/env bash +# +# Point to Qiime config +export QIIME_CONFIG_FP=${TOP_DIR}/qiime/qiime_config +# Set up the RDP jar file +export RDP_JAR_PATH=${TOP_DIR}/share/rdp_classifier/rdp_classifier-${RDP_CLASSIFIER_VERSION}.jar +# Set the Matplotlib backend +export MPLBACKEND="agg" +# Put the scripts onto the PATH +export PATH=${BIN_DIR}:${INSTALL_DIR}:\$PATH +# Activate the conda environment +export PATH=${CONDA_BIN}:\$PATH +source ${CONDA_BIN}/activate ${ENV_NAME} +# Execute the driver script with the supplied arguments +$INSTALL_DIR/Amplicon_analysis_pipeline.sh \$@ +exit \$? +EOF + chmod 0755 ${BIN_DIR}/Amplicon_analysis_pipeline.sh + cat >${BIN_DIR}/install_reference_data.sh <<EOF +#!/usr/bin/env bash -e +# +function usage() { + echo "Usage: \$(basename \$0) DIR" +} +if [ -z "\$1" ] ; then + usage + exit 0 +elif [ "\$1" == "--help" ] || [ "\$1" == "-h" ] ; then + usage + echo "" + echo "Install reference data into DIR" + exit 0 +fi +echo "==========================================" +echo "Installing Amplicon analysis pipeline data" +echo "==========================================" +if [ ! -e "\$1" ] ; then + echo "Making directory \$1" + mkdir -p \$1 +fi +cd \$1 +DATA_DIR=\$(pwd) +echo "Installing reference data under \$DATA_DIR" +$INSTALL_DIR/References.sh +echo "" +echo "Use '-r \$DATA_DIR' when running Amplicon_analysis_pipeline.sh" +echo "to use the reference data from this directory" +echo "" +echo "\$(basename \$0): finished" +EOF + chmod 0755 ${BIN_DIR}/install_reference_data.sh + cd $cwd + rm -rf $wd/* + rmdir $wd +} +# +# ChimeraSlayer +install_chimeraslayer() +{ + local cwd=$(pwd) + local wd=$(mktemp -d) + cd $wd + wget -q https://sourceforge.net/projects/microbiomeutil/files/__OLD_VERSIONS/microbiomeutil_2010-04-29.tar.gz + tar zxf microbiomeutil_2010-04-29.tar.gz + cd microbiomeutil_2010-04-29 + INSTALL_DIR=${TOP_DIR}/share/microbiome_chimeraslayer-2010-04-29 + mkdir -p $INSTALL_DIR + ln -s $INSTALL_DIR ${TOP_DIR}/share/microbiome_chimeraslayer + /bin/cp -r ChimeraSlayer $INSTALL_DIR + cat >${BIN_DIR}/ChimeraSlayer.pl <<EOF +#!/usr/bin/env bash +export PATH=$INSTALL_DIR:\$PATH +$INSTALL_DIR/ChimeraSlayer/ChimeraSlayer.pl $@ +EOF + chmod 0755 ${INSTALL_DIR}/ChimeraSlayer/ChimeraSlayer.pl + chmod 0755 ${BIN_DIR}/ChimeraSlayer.pl + cd $cwd + rm -rf $wd/* + rmdir $wd +} +# +# uclust required for QIIME/pyNAST +# License only allows this version to be used with those two packages +# See: http://drive5.com/uclust/downloads1_2_22q.html +install_uclust() +{ + local cwd=$(pwd) + local wd=$(mktemp -d) + cd $wd + wget -q http://drive5.com/uclust/uclustq1.2.22_i86linux64 + INSTALL_DIR=${TOP_DIR}/share/uclust-1.2.22 + mkdir -p $INSTALL_DIR + ln -s $INSTALL_DIR ${TOP_DIR}/share/uclust + /bin/mv uclustq1.2.22_i86linux64 ${INSTALL_DIR}/uclust + chmod 0755 ${INSTALL_DIR}/uclust + ln -s ${INSTALL_DIR}/uclust ${BIN_DIR} + cd $cwd + rm -rf $wd/* + rmdir $wd +} +setup_pipeline_environment() +{ + echo "+++++++++++++++++++++++++++++++" + echo "Setting up pipeline environment" + echo "+++++++++++++++++++++++++++++++" + # fasta_splitter.pl + echo -n "Setting up fasta_splitter.pl..." + if [ -e ${BIN_DIR}/fasta-splitter.pl ] ; then + echo "already exists" + elif [ ! -e ${ENV_DIR}/share/fasta-splitter/fasta-splitter.pl ] ; then + echo "failed" + fail "fasta-splitter.pl not found" + else + ln -s ${ENV_DIR}/share/fasta-splitter/fasta-splitter.pl ${BIN_DIR}/fasta-splitter.pl + echo "ok" + fi + # rdp_classifier.jar + local rdp_classifier_jar=rdp_classifier-${RDP_CLASSIFIER_VERSION}.jar + echo -n "Setting up rdp_classifier.jar..." + if [ -e ${TOP_DIR}/share/rdp_classifier/${rdp_classifier_jar} ] ; then + echo "already exists" + elif [ ! -e ${ENV_DIR}/share/rdp_classifier/rdp_classifier.jar ] ; then + echo "failed" + fail "rdp_classifier.jar not found" + else + mkdir -p ${TOP_DIR}/share/rdp_classifier + ln -s ${ENV_DIR}/share/rdp_classifier/rdp_classifier.jar ${TOP_DIR}/share/rdp_classifier/${rdp_classifier_jar} + echo "ok" + fi + # qiime_config + echo -n "Setting up qiime_config..." + if [ -e ${TOP_DIR}/qiime/qiime_config ] ; then + echo "already exists" + else + mkdir -p ${TOP_DIR}/qiime + cat >${TOP_DIR}/qiime/qiime_config <<EOF-qiime-config +qiime_scripts_dir ${ENV_DIR}/bin +EOF-qiime-config + echo "ok" + fi +} +# +# Top level script does the installation +echo "=======================================" +echo "Amplicon_analysis_pipeline installation" +echo "=======================================" +echo "Installing into ${TOP_DIR}" +if [ -e ${TOP_DIR} ] ; then + fail "Directory already exists" +fi +mkdir -p ${TOP_DIR} +install_conda +install_conda_packages +install_non_conda_packages +setup_pipeline_environment +echo "====================================" +echo "Amplicon_analysis_pipeline installed" +echo "====================================" +echo "" +echo "Install reference data using:" +echo "" +echo "\$ ${BIN_DIR}/install_reference_data.sh DIR" +echo "" +echo "Run pipeline scripts using:" +echo "" +echo "\$ ${BIN_DIR}/Amplicon_analysis_pipeline.sh ..." +echo "" +echo "(or add ${BIN_DIR} to your PATH)" +echo "" +echo "$(basename $0): finished" +## +#