Mercurial > repos > rliterman > csp2
comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/gitable.sh @ 69:33d812a61356
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 17:55:14 -0400 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| 67:0e9998148a16 | 69:33d812a61356 |
|---|---|
| 1 #!/bin/bash | |
| 2 | |
| 3 usage(){ | |
| 4 echo " | |
| 5 Written by Brian Bushnell. | |
| 6 Last modified July 29, 2019 | |
| 7 | |
| 8 Description: Creates gitable.int1d from accession files: | |
| 9 ftp://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/*.accession2taxid.gz | |
| 10 This is for use of gi numbers, which are deprecated by NCBI, and areneither | |
| 11 necessary nor recemmended if accession numbers are present. | |
| 12 See TaxonomyGuide and fetchTaxonomy.sh for more information. | |
| 13 | |
| 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 | |
| 15 | |
| 16 Java Parameters: | |
| 17 -Xmx This will set Java's memory usage, overriding autodetection. | |
| 18 -Xmx20g will specify 20 gigs of RAM. The max is typically 85% of physical memory. | |
| 19 -eoom This flag will cause the process to exit if an out-of-memory | |
| 20 exception occurs. Requires Java 8u92+. | |
| 21 -da Disable assertions. | |
| 22 | |
| 23 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. | |
| 24 " | |
| 25 } | |
| 26 | |
| 27 #This block allows symlinked shellscripts to correctly set classpath. | |
| 28 pushd . > /dev/null | |
| 29 DIR="${BASH_SOURCE[0]}" | |
| 30 while [ -h "$DIR" ]; do | |
| 31 cd "$(dirname "$DIR")" | |
| 32 DIR="$(readlink "$(basename "$DIR")")" | |
| 33 done | |
| 34 cd "$(dirname "$DIR")" | |
| 35 DIR="$(pwd)/" | |
| 36 popd > /dev/null | |
| 37 | |
| 38 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" | |
| 39 CP="$DIR""current/" | |
| 40 JNI="-Djava.library.path=""$DIR""jni/" | |
| 41 JNI="" | |
| 42 | |
| 43 z="-Xmx24g" | |
| 44 z2="-Xms24g" | |
| 45 set=0 | |
| 46 | |
| 47 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then | |
| 48 usage | |
| 49 exit | |
| 50 fi | |
| 51 | |
| 52 calcXmx () { | |
| 53 source "$DIR""/calcmem.sh" | |
| 54 setEnvironment | |
| 55 parseXmx "$@" | |
| 56 if [[ $set == 1 ]]; then | |
| 57 return | |
| 58 fi | |
| 59 freeRam 24000m 84 | |
| 60 z="-Xmx${RAM}m" | |
| 61 z2="-Xms${RAM}m" | |
| 62 } | |
| 63 calcXmx "$@" | |
| 64 | |
| 65 | |
| 66 gitable() { | |
| 67 local CMD="java $EA $EOOM $z $z2 -cp $CP tax.GiToTaxid $@" | |
| 68 echo $CMD >&2 | |
| 69 eval $CMD | |
| 70 } | |
| 71 | |
| 72 gitable "$@" |