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1 #!/bin/sh
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2
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3 #
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4 # Arguments check and suage information
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5 #
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6 SRC="."
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7 DEST="$1"
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8 if [ -z "$DEST" ]; then
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9 cat<<EOF
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10
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11 FASTX-toolkit Galaxy Installation script.
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12
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13 This script copies the FASTX-Toolkit files into the specified Galaxy directory.
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14
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15 Usage: $0 [GALAXY-DIRECTORY]
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16
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17 GALAXY-DIRECTORY - root directory of the Galaxy server.
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18
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19 EOF
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20 exit
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21 fi
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22
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23
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24 echo
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25 echo "FASTX-toolkit Galaxy Installation script."
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26 echo
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27
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28 #
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29 # Sanity checks for the specified galaxy directory
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30 #
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31 echo -n "Checking Galaxy destination directory..."
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32 [ -d "$DEST" ] ||
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33 { echo "Error: directory '$DEST' does not exist!" ; exit 1 ; }
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34
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35 [ -r "$DEST/tool_conf.xml" ] ||
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36 { echo "Error: file '$DEST/tool_conf.xml' does not exist! (is '$DEST' the root of the Galaxy server?)" ; exit 1 ; }
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37
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38 for subdir in tools tool-data test-data static; do
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39 [ -d "$DEST/$subdir" ] ||
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40 { echo "Error: sub-directory '$DEST/$subdir' does not exist! (is '$DEST' the root of the Galaxy server?)" ; exit 1 ; }
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41 done
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42 echo "ok"
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43
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44 #
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45 # Sanity checks for the FASTX-toolkit files
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46 #
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47 echo -n "Checking FASTX-toolkit source directory..."
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48 [ -r "$SRC/galaxy/fastx_toolkit_conf.xml" ] ||
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49 { echo "Error: file '$SRC/galaxy/fastx_toolkit_conf.xml' does not exist! (is '$SRC' the root of FASTX-toolkit ?)" ; exit 1 ; }
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50
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51 for subdir in tools tools/fastx_toolkit tool-data test-data static static/fastx_icons; do
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52 [ -d "$SRC/galaxy/$subdir" ] ||
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53 { echo "Error: sub-directory '$SRC/galaxy/$subdir' does not exist! (is '$SRC' the root of FASTX-toolkit?)" ; exit 1 ; }
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54 done
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55 echo "ok"
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56
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57
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58 #
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59 # Copy FASTX-Toolkit files into Galaxy server
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60 #
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61 echo -n "Creating static/fastx_icons directory..."
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62 mkdir -p "$DEST/static/fastx_icons" || exit 1 ;
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63 echo "OK"
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64
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65 echo -n "Copying static/fastx_icons..."
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66 cp $SRC/galaxy/static/fastx_icons/*.png "$DEST/static/fastx_icons" || exit 1 ;
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67 echo "OK"
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68
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69 echo -n "Copying test-data files..."
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70 cp $SRC/galaxy/test-data/fast* "$DEST/test-data" || exit 1 ;
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71 echo "OK"
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72
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73 echo -n "Copying tool-data files..."
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74 cp $SRC/galaxy/tool-data/fastx_clipper_sequences.txt "$DEST/tool-data/" || exit 1;
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75 echo "OK"
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76
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77 echo -n "Creaing tools/fastx_toolkit directory..."
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78 mkdir -p "$DEST/tools/fastx_toolkit" || exit 1;
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79 echo "OK"
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80
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81 #
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82 # Be extra careful when copying the XML files -
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83 # Ask the user for confirmation if the XML files already exists
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84 # (so that if they were changed, they will not be blindly overwriten)
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85 echo "==="
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86 echo "=== NOTE:"
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87 echo "==="
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88 echo "If the FASTX-toolkit XML files already exist on your galaxy server,"
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89 echo "You will be prompted to confirm overwriting them."
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90 echo "If you have made any changes to the XML files, DO NOT overwrite your files."
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91 echo
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92 echo -n "Copying FASTX-toolkit XML tool configuration..."
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93 cp -i $SRC/galaxy/tools/fastx_toolkit/*.xml "$DEST/tools/fastx_toolkit"
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94 echo "ok"
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95
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96
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97
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98 #
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99 # Instruct the user what to do next
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100 #
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101 cat<<EOF
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102 FASTX-toolkit files copied to your galaxy server directory.
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103
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104 Additionally, you'll need to make the following manual configurations:
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105
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106 1. Add the content of
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107 $SRC/galaxy/fastx_toolkit_conf.xml
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108 to
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109 $DEST/tool_conf.xml
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110
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111 2. Update the adapters file:
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112
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113 $DEST/tool-data/fastx_clipper_sequences.txt
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114
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115 And add valid adapters/linkers.
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116
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117 3. Edit "fastx_barcode_splitter_galaxy_wrapper.sh", change
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118 The two variables BASEPATH and PUBLICURL to valid path/URL.
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119 See README for detailed explanation (under the
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120 "Special configuration for Barcode-Splitter" section).
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121
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122 EOF
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123
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