Mercurial > repos > pjbriggs > amplicon_analysis_pipeline

annotate install_amplicon_analysis-1.3.5.sh @ 42:098ad1dd7760 draft

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planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
author pjbriggs
date Thu, 05 Dec 2019 11:48:01 +0000
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42
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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1 #!/bin/sh -e
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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2 #
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pjbriggs
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3 # Prototype script to setup a conda environment with the
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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4 # dependencies needed for the Amplicon_analysis_pipeline
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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5 # script
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pjbriggs
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6 #
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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7 # Handle command line
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pjbriggs
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8 usage()
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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9 {
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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10 echo "Usage: $(basename $0) [DIR]"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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11 echo ""
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pjbriggs
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12 echo "Installs the Amplicon_analysis_pipeline package plus"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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13 echo "dependencies in directory DIR (or current directory "
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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14 echo "if DIR not supplied)"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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15 }
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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16 if [ ! -z "$1" ] ; then
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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17 # Check if help was requested
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18 case "$1" in
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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19 --help|-h)
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20 usage
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21 exit 0
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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22 ;;
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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23 esac
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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24 # Assume it's the installation directory
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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25 cd $1
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26 fi
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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27 # Versions
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28 PIPELINE_VERSION=1.3.5
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29 CONDA_REQUIRED_VERSION=4.6.14
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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30 RDP_CLASSIFIER_VERSION=2.2
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31 # Directories
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32 TOP_DIR=$(pwd)/Amplicon_analysis-${PIPELINE_VERSION}
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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33 BIN_DIR=${TOP_DIR}/bin
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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34 CONDA_DIR=${TOP_DIR}/conda
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pjbriggs
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35 CONDA_BIN=${CONDA_DIR}/bin
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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36 CONDA_LIB=${CONDA_DIR}/lib
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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37 CONDA=${CONDA_BIN}/conda
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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38 ENV_NAME="amplicon_analysis_pipeline@${PIPELINE_VERSION}"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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39 ENV_DIR=${CONDA_DIR}/envs/$ENV_NAME
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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40 #
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41 # Functions
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42 #
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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43 # Report failure and terminate script
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44 fail()
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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45 {
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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46 echo ""
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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47 echo ERROR $@ >&2
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48 echo ""
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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49 echo "$(basename $0): installation failed"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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50 exit 1
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51 }
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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52 #
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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53 # Rewrite the shebangs in the installed conda scripts
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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54 # to remove the full path to conda 'bin' directory
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55 rewrite_conda_shebangs()
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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56 {
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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57 pattern="s,^#!${CONDA_BIN}/,#!/usr/bin/env ,g"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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58 find ${CONDA_BIN} -type f -exec sed -i "$pattern" {} \;
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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59 }
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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60 #
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61 # Reset conda version if required
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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62 reset_conda_version()
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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63 {
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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64 CONDA_VERSION="$(${CONDA_BIN}/conda -V 2>&1 | head -n 1 | cut -d' ' -f2)"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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65 echo conda version: ${CONDA_VERSION}
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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66 if [ "${CONDA_VERSION}" != "${CONDA_REQUIRED_VERSION}" ] ; then
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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67 echo "Resetting conda to last known working version $CONDA_REQUIRED_VERSION"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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68 ${CONDA_BIN}/conda config --set allow_conda_downgrades true
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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69 ${CONDA_BIN}/conda install -y conda=${CONDA_REQUIRED_VERSION}
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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70 else
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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71 echo "conda version ok"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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72 fi
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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73 }
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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74 #
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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75 # Install conda
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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76 install_conda()
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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77 {
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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78 echo "++++++++++++++++"
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79 echo "Installing conda"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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80 echo "++++++++++++++++"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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81 if [ -e ${CONDA_DIR} ] ; then
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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82 echo "*** $CONDA_DIR already exists ***" >&2
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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83 return
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84 fi
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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85 local cwd=$(pwd)
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86 local wd=$(mktemp -d)
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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87 cd $wd
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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88 wget -q https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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89 bash ./Miniconda2-latest-Linux-x86_64.sh -b -p ${CONDA_DIR}
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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90 echo Installed conda in ${CONDA_DIR}
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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91 # Reset the conda version to a known working version
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92 # (to avoid problems observed with e.g. conda 4.7.10)
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93 echo ""
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94 reset_conda_version
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95 # Update the installation files
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96 # This is to avoid problems when the length the installation
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
97 # directory path exceeds the limit for the shebang statement
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
98 # in the conda files
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
99 echo ""
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
100 echo -n "Rewriting conda shebangs..."
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
101 rewrite_conda_shebangs
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
102 echo "ok"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
103 echo -n "Adding conda bin to PATH..."
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
104 PATH=${CONDA_BIN}:$PATH
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
105 echo "ok"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
106 cd $cwd
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
107 rm -rf $wd/*
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
108 rmdir $wd
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
109 }
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
110 #
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
111 # Create conda environment
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
112 install_conda_packages()
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
113 {
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
114 echo "+++++++++++++++++++++++++"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
115 echo "Installing conda packages"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
116 echo "+++++++++++++++++++++++++"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
117 local cwd=$(pwd)
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
118 local wd=$(mktemp -d)
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
119 cd $wd
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
120 cat >environment.yml <<EOF
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
121 name: ${ENV_NAME}
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
122 channels:
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
123 - defaults
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
124 - conda-forge
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
125 - bioconda
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
126 dependencies:
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
127 - python=2.7
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
128 - cutadapt=1.8
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
129 - sickle-trim=1.33
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
130 - bioawk=1.0
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
131 - pandaseq=2.8.1
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
132 - spades=3.10.1
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
133 - fastqc=0.11.3
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
134 - qiime=1.9.1
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
135 - blast-legacy=2.2.26
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
136 - fasta-splitter=0.2.6
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
137 - rdp_classifier=$RDP_CLASSIFIER_VERSION
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
138 - vsearch=2.10.4
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
139 - r=3.5.1
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
140 - r-tidyverse=1.2.1
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
141 - bioconductor-dada2=1.8
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
142 - bioconductor-biomformat=1.8.0
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
143 EOF
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
144 ${CONDA} env create --name "${ENV_NAME}" -f environment.yml
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
145 echo Created conda environment in ${ENV_DIR}
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
146 cd $cwd
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
147 rm -rf $wd/*
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
148 rmdir $wd
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
149 #
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
150 # Patch qiime 1.9.1 tools to switch deprecated 'axisbg'
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
151 # matplotlib property to 'facecolor':
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
152 # https://matplotlib.org/api/prev_api_changes/api_changes_2.0.0.html
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
153 echo ""
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
154 for exe in make_2d_plots.py plot_taxa_summary.py ; do
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
155 echo -n "Patching ${exe}..."
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
156 find ${CONDA_DIR} -type f -name "$exe" -exec sed -i 's/axisbg=/facecolor=/g' {} \;
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
157 echo "done"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
158 done
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
159 #
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
160 # Patch qiime 1.9.1 tools to switch deprecated 'set_axis_bgcolor'
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
161 # method call to 'set_facecolor':
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
162 # https://matplotlib.org/api/_as_gen/matplotlib.axes.Axes.set_axis_bgcolor.html
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
163 for exe in make_rarefaction_plots.py ; do
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
164 echo -n "Patching ${exe}..."
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
165 find ${CONDA_DIR} -type f -name "$exe" -exec sed -i 's/set_axis_bgcolor/set_facecolor/g' {} \;
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
166 echo "done"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
167 done
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
168 }
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
169 #
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
170 # Install all the non-conda dependencies in a single
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
171 # function (invokes separate functions for each package)
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
172 install_non_conda_packages()
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
173 {
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
174 echo "+++++++++++++++++++++++++++++"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
175 echo "Installing non-conda packages"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
176 echo "+++++++++++++++++++++++++++++"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
177 # Temporary working directory
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
178 local wd=$(mktemp -d)
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
179 local cwd=$(pwd)
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
180 local wd=$(mktemp -d)
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
181 cd $wd
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
182 # Amplicon analysis pipeline
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
183 echo -n "Installing Amplicon_analysis_pipeline..."
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
184 if [ -e ${BIN_DIR}/Amplicon_analysis_pipeline.sh ] ; then
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
185 echo "already installed"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
186 else
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
187 install_amplicon_analysis_pipeline
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
188 echo "ok"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
189 fi
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
190 # ChimeraSlayer
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
191 echo -n "Installing ChimeraSlayer..."
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
192 if [ -e ${BIN_DIR}/ChimeraSlayer.pl ] ; then
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
193 echo "already installed"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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diff changeset
194 else
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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195 install_chimeraslayer
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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196 echo "ok"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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197 fi
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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198 # Uclust
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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199 # This no longer seems to be available for download from
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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200 # drive5.com so don't download
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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201 echo "WARNING uclust not available: skipping installation"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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202 }
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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203 #
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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204 # Amplicon analyis pipeline
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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205 install_amplicon_analysis_pipeline()
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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206 {
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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207 local wd=$(mktemp -d)
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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208 local cwd=$(pwd)
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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209 local wd=$(mktemp -d)
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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210 cd $wd
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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211 wget -q https://github.com/MTutino/Amplicon_analysis/archive/${PIPELINE_VERSION}.tar.gz
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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212 tar zxf ${PIPELINE_VERSION}.tar.gz
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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213 cd Amplicon_analysis-${PIPELINE_VERSION}
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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214 INSTALL_DIR=${TOP_DIR}/share/amplicon_analysis_pipeline-${PIPELINE_VERSION}
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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215 mkdir -p $INSTALL_DIR
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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216 ln -s $INSTALL_DIR ${TOP_DIR}/share/amplicon_analysis_pipeline
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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217 for f in *.sh *.R ; do
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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218 /bin/cp $f $INSTALL_DIR
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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219 done
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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220 /bin/cp -r uc2otutab $INSTALL_DIR
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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221 mkdir -p ${BIN_DIR}
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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222 cat >${BIN_DIR}/Amplicon_analysis_pipeline.sh <<EOF
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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223 #!/usr/bin/env bash
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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224 #
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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225 # Point to Qiime config
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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226 export QIIME_CONFIG_FP=${TOP_DIR}/qiime/qiime_config
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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227 # Set up the RDP jar file
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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228 export RDP_JAR_PATH=${TOP_DIR}/share/rdp_classifier/rdp_classifier-${RDP_CLASSIFIER_VERSION}.jar
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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229 # Set the Matplotlib backend
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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230 export MPLBACKEND="agg"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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231 # Put the scripts onto the PATH
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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232 export PATH=${BIN_DIR}:${INSTALL_DIR}:\$PATH
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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233 # Activate the conda environment
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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234 export PATH=${CONDA_BIN}:\$PATH
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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235 source ${CONDA_BIN}/activate ${ENV_NAME}
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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236 # Execute the driver script with the supplied arguments
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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237 $INSTALL_DIR/Amplicon_analysis_pipeline.sh \$@
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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diff changeset
238 exit \$?
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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239 EOF
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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240 chmod 0755 ${BIN_DIR}/Amplicon_analysis_pipeline.sh
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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diff changeset
241 cat >${BIN_DIR}/install_reference_data.sh <<EOF
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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242 #!/usr/bin/env bash -e
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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243 #
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pjbriggs
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244 function usage() {
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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245 echo "Usage: \$(basename \$0) DIR"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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246 }
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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247 if [ -z "\$1" ] ; then
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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248 usage
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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249 exit 0
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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250 elif [ "\$1" == "--help" ] || [ "\$1" == "-h" ] ; then
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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251 usage
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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252 echo ""
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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253 echo "Install reference data into DIR"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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254 exit 0
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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255 fi
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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diff changeset
256 echo "=========================================="
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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257 echo "Installing Amplicon analysis pipeline data"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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258 echo "=========================================="
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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259 if [ ! -e "\$1" ] ; then
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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260 echo "Making directory \$1"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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diff changeset
261 mkdir -p \$1
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
262 fi
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
263 cd \$1
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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264 DATA_DIR=\$(pwd)
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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265 echo "Installing reference data under \$DATA_DIR"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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diff changeset
266 $INSTALL_DIR/References.sh
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
267 echo ""
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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268 echo "Use '-r \$DATA_DIR' when running Amplicon_analysis_pipeline.sh"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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269 echo "to use the reference data from this directory"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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diff changeset
270 echo ""
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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271 echo "\$(basename \$0): finished"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
272 EOF
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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273 chmod 0755 ${BIN_DIR}/install_reference_data.sh
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
274 cd $cwd
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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275 rm -rf $wd/*
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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276 rmdir $wd
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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277 }
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
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278 #
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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279 # ChimeraSlayer
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
280 install_chimeraslayer()
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
281 {
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
282 local cwd=$(pwd)
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
283 local wd=$(mktemp -d)
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
284 cd $wd
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
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285 wget -q https://sourceforge.net/projects/microbiomeutil/files/__OLD_VERSIONS/microbiomeutil_2010-04-29.tar.gz
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
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diff changeset
286 tar zxf microbiomeutil_2010-04-29.tar.gz
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
287 cd microbiomeutil_2010-04-29
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
288 INSTALL_DIR=${TOP_DIR}/share/microbiome_chimeraslayer-2010-04-29
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
289 mkdir -p $INSTALL_DIR
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
290 ln -s $INSTALL_DIR ${TOP_DIR}/share/microbiome_chimeraslayer
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
291 /bin/cp -r ChimeraSlayer $INSTALL_DIR
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
292 cat >${BIN_DIR}/ChimeraSlayer.pl <<EOF
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
293 #!/usr/bin/env bash
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
294 export PATH=$INSTALL_DIR:\$PATH
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
295 $INSTALL_DIR/ChimeraSlayer/ChimeraSlayer.pl $@
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
296 EOF
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
297 chmod 0755 ${INSTALL_DIR}/ChimeraSlayer/ChimeraSlayer.pl
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
298 chmod 0755 ${BIN_DIR}/ChimeraSlayer.pl
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
299 cd $cwd
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
300 rm -rf $wd/*
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
301 rmdir $wd
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
302 }
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
303 #
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
304 # uclust required for QIIME/pyNAST
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
305 # License only allows this version to be used with those two packages
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
306 # See: http://drive5.com/uclust/downloads1_2_22q.html
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
307 install_uclust()
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
308 {
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
309 local cwd=$(pwd)
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
310 local wd=$(mktemp -d)
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
311 cd $wd
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
312 wget -q http://drive5.com/uclust/uclustq1.2.22_i86linux64
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
313 INSTALL_DIR=${TOP_DIR}/share/uclust-1.2.22
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
314 mkdir -p $INSTALL_DIR
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
315 ln -s $INSTALL_DIR ${TOP_DIR}/share/uclust
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
316 /bin/mv uclustq1.2.22_i86linux64 ${INSTALL_DIR}/uclust
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
317 chmod 0755 ${INSTALL_DIR}/uclust
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
318 ln -s ${INSTALL_DIR}/uclust ${BIN_DIR}
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
319 cd $cwd
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
320 rm -rf $wd/*
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
321 rmdir $wd
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
322 }
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
323 setup_pipeline_environment()
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
324 {
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
325 echo "+++++++++++++++++++++++++++++++"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
326 echo "Setting up pipeline environment"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
327 echo "+++++++++++++++++++++++++++++++"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
328 # fasta_splitter.pl
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
329 echo -n "Setting up fasta_splitter.pl..."
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
330 if [ -e ${BIN_DIR}/fasta-splitter.pl ] ; then
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
331 echo "already exists"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
332 elif [ ! -e ${ENV_DIR}/share/fasta-splitter/fasta-splitter.pl ] ; then
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
333 echo "failed"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
334 fail "fasta-splitter.pl not found"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
335 else
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
336 ln -s ${ENV_DIR}/share/fasta-splitter/fasta-splitter.pl ${BIN_DIR}/fasta-splitter.pl
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
337 echo "ok"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
338 fi
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
339 # rdp_classifier.jar
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
340 local rdp_classifier_jar=rdp_classifier-${RDP_CLASSIFIER_VERSION}.jar
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
341 echo -n "Setting up rdp_classifier.jar..."
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
342 if [ -e ${TOP_DIR}/share/rdp_classifier/${rdp_classifier_jar} ] ; then
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
343 echo "already exists"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
344 elif [ ! -e ${ENV_DIR}/share/rdp_classifier/rdp_classifier.jar ] ; then
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
345 echo "failed"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
346 fail "rdp_classifier.jar not found"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
347 else
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
348 mkdir -p ${TOP_DIR}/share/rdp_classifier
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
349 ln -s ${ENV_DIR}/share/rdp_classifier/rdp_classifier.jar ${TOP_DIR}/share/rdp_classifier/${rdp_classifier_jar}
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
350 echo "ok"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
351 fi
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
352 # qiime_config
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
353 echo -n "Setting up qiime_config..."
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
354 if [ -e ${TOP_DIR}/qiime/qiime_config ] ; then
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
355 echo "already exists"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
356 else
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
357 mkdir -p ${TOP_DIR}/qiime
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
358 cat >${TOP_DIR}/qiime/qiime_config <<EOF-qiime-config
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
359 qiime_scripts_dir ${ENV_DIR}/bin
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
360 EOF-qiime-config
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
361 echo "ok"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
362 fi
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
363 }
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
364 #
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
365 # Top level script does the installation
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
366 echo "======================================="
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
367 echo "Amplicon_analysis_pipeline installation"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
368 echo "======================================="
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
369 echo "Installing into ${TOP_DIR}"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
370 if [ -e ${TOP_DIR} ] ; then
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
371 fail "Directory already exists"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
372 fi
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
373 mkdir -p ${TOP_DIR}
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
374 install_conda
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
375 install_conda_packages
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
376 install_non_conda_packages
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
377 setup_pipeline_environment
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
378 echo "===================================="
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
379 echo "Amplicon_analysis_pipeline installed"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
380 echo "===================================="
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
381 echo ""
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
382 echo "Install reference data using:"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
383 echo ""
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
384 echo "\$ ${BIN_DIR}/install_reference_data.sh DIR"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
385 echo ""
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
386 echo "Run pipeline scripts using:"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
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387 echo ""
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
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388 echo "\$ ${BIN_DIR}/Amplicon_analysis_pipeline.sh ..."
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
389 echo ""
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
390 echo "(or add ${BIN_DIR} to your PATH)"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
391 echo ""
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
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392 echo "$(basename $0): finished"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
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393 ##
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
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394 #