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1 #!/bin/bash
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2
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3 usage(){
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4 echo "
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5 Written by Brian Bushnell and Shijie Yao
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6 Last modified Jan 7, 2020
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7
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8 Description: Starts a server that translates NCBI taxonomy.
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9
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10 Usage: taxserver.sh tree=<taxtree file> table=<gitable file> port=<number>
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11
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12 Usage examples:
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13 taxserver.sh tree=tree.taxtree.gz table=gitable.int1d.gz port=1234
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14
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15 On Genepool:
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16 taxserver.sh tree=auto table=auto port=1234
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17
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18 For accession number support, add accession=<something> E.g.:
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19
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20 External:
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21 taxserver.sh -Xmx45g tree=tree.taxtree.gz table=gitable.int1d.gz accession=prot.accession2taxid.gz,nucl_wgs.accession2taxid.gz port=1234
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22
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23 On Genepool:
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24 taxserver.sh tree=auto table=auto accession=auto port=1234
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25
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26 If all expected files are in some specific location, you can also do this:
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27 taxserver.sh -Xmx45g tree=auto table=auto accession=auto port=1234 taxpath=/path/to/files
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28
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29 To kill remotely, launch with the flag kill=password, then access /kill/password
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30
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31 Parameters:
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32
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33 tree=auto taxtree path. Always necessary.
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34 table=auto gitable path. Necessary for gi number support.
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35 accession=null Comma-delimited paths of accession files.
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36 Necessary for accession support.
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37 img=null IMG dump file.
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38 pattern=null Pattern file, for storing accessions more efficiently.
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39 port=3068 Port number.
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40 domain= Domain to be displayed in the help message.
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41 Default is taxonomy.jgi-psf.org.
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42 dbname= Set the name of the database in the help message.
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43 sketchcomparethreads=16 Limit compare threads per connection.
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44 sketchloadthreads=4 Limit load threads (for local queries of fastq).
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45 sketchonly=f Don't hash taxa names.
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46 k=31 Kmer length, 1-32. To maximize sensitivity and
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47 specificity, dual kmer lengths may be used: k=31,24
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48 prealloc=f Preallocate some data structures for faster loading.
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49
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50 Security parameters:
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51
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52 killcode= Set a password to allow remote killing.
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53 oldcode= Set the password of a prior instance.
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54 oldaddress= Attempt to kill a prior instance after initialization,
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55 by sending the old code to this address. For example,
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56 taxonomy.jgi-psf.org/kill/
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57 allowremotefileaccess=f Allow non-internal queries to use internal files
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58 for sketching in local mode.
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59 allowlocalhost=f Consider a query internal if it originates from localhost
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60 without being proxied.
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61 addressprefix=128. Queries originating from this IP address prefix will be
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62 considered internal.
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63
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64
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65 Unrecognized parameters with no = symbol will be treated as sketch files.
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66 Other sketch parameters such as index and k are also allowed.
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67 Please consult bbmap/docs/guides/TaxonomyGuide.txt and BBSketchGuide.txt for more information.
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68
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69 Java Parameters:
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70 -Xmx This will set Java's memory usage, overriding autodetection.
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71 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
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72 The max is typically 85% of physical memory.
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73 -eoom This flag will cause the process to exit if an
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74 out-of-memory exception occurs. Requires Java 8u92+.
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75 -da Disable assertions.
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76
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77 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
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78 "
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79 }
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80
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81 #This block allows symlinked shellscripts to correctly set classpath.
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82 pushd . > /dev/null
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83 DIR="${BASH_SOURCE[0]}"
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84 while [ -h "$DIR" ]; do
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85 cd "$(dirname "$DIR")"
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86 DIR="$(readlink "$(basename "$DIR")")"
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87 done
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88 cd "$(dirname "$DIR")"
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89 DIR="$(pwd)/"
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90 popd > /dev/null
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91
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92 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
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93 CP="$DIR""current/"
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94
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95 z="-Xmx45g"
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96 z2="-Xms45g"
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97 set=0
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98
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99 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
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100 usage
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101 exit
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102 fi
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103
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104 calcXmx () {
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105 source "$DIR""/calcmem.sh"
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106 setEnvironment
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107 parseXmx "$@"
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108 }
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109 calcXmx "$@"
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110
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111 taxserver() {
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112 local CMD="java $EA $EOOM $z $z2 -cp $CP tax.TaxServer $@"
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113 echo $CMD >&2
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114 eval $CMD
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115 }
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116
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117 taxserver "$@"
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