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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.
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6 Last modified July 29, 2019
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7
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8 Description: Creates gitable.int1d from accession files:
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9 ftp://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/*.accession2taxid.gz
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10 This is for use of gi numbers, which are deprecated by NCBI, and areneither
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11 necessary nor recemmended if accession numbers are present.
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12 See TaxonomyGuide and fetchTaxonomy.sh for more information.
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13
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14 Usage: gitable.sh shrunk.dead_nucl.accession2taxid.gz,shrunk.dead_prot.accession2taxid.gz,shrunk.dead_wgs.accession2taxid.gz,shrunk.nucl_gb.accession2taxid.gz,shrunk.nucl_wgs.accession2taxid.gz,shrunk.pdb.accession2taxid.gz,shrunk.prot.accession2taxid.gz gitable.int1d.gz
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15
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16 Java Parameters:
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17 -Xmx This will set Java's memory usage, overriding autodetection.
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18 -Xmx20g will specify 20 gigs of RAM. The max is typically 85% of physical memory.
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19 -eoom This flag will cause the process to exit if an out-of-memory
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20 exception occurs. Requires Java 8u92+.
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21 -da Disable assertions.
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22
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23 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
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24 "
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25 }
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26
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27 #This block allows symlinked shellscripts to correctly set classpath.
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28 pushd . > /dev/null
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29 DIR="${BASH_SOURCE[0]}"
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30 while [ -h "$DIR" ]; do
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31 cd "$(dirname "$DIR")"
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32 DIR="$(readlink "$(basename "$DIR")")"
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33 done
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34 cd "$(dirname "$DIR")"
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35 DIR="$(pwd)/"
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36 popd > /dev/null
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37
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38 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
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39 CP="$DIR""current/"
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40 JNI="-Djava.library.path=""$DIR""jni/"
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41 JNI=""
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42
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43 z="-Xmx24g"
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44 z2="-Xms24g"
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45 set=0
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46
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47 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
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48 usage
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49 exit
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50 fi
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51
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52 calcXmx () {
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53 source "$DIR""/calcmem.sh"
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54 setEnvironment
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55 parseXmx "$@"
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56 if [[ $set == 1 ]]; then
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57 return
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58 fi
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59 freeRam 24000m 84
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60 z="-Xmx${RAM}m"
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61 z2="-Xms${RAM}m"
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62 }
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63 calcXmx "$@"
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64
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65
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66 gitable() {
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67 local CMD="java $EA $EOOM $z $z2 -cp $CP tax.GiToTaxid $@"
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68 echo $CMD >&2
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69 eval $CMD
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70 }
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71
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72 gitable "$@"
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