Mercurial > repos > rliterman > csp2
comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/fetchproks.sh @ 69:33d812a61356
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 17:55:14 -0400 |
| parents | |
| children |
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| 67:0e9998148a16 | 69:33d812a61356 |
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| 1 #!/bin/bash | |
| 2 | |
| 3 usage(){ | |
| 4 echo " | |
| 5 Written by Brian Bushnell | |
| 6 Last modified December 19, 2019 | |
| 7 | |
| 8 Description: Writes a shell script to download one genome assembly | |
| 9 and gff per genus or species, from ncbi. Attempts to select the best assembly | |
| 10 on the basis of contiguity. | |
| 11 | |
| 12 Usage: fetchproks.sh <url> <outfile> <max species per genus: int> <use best: t/f> | |
| 13 | |
| 14 Examples: | |
| 15 fetchproks.sh ftp://ftp.ncbi.nih.gov/genomes/refseq/bacteria/ bacteria.sh 2 true | |
| 16 fetchproks.sh ftp://ftp.ncbi.nih.gov/genomes/refseq/archaea/ archaea.sh 0 true | |
| 17 fetchproks.sh ftp://ftp.ncbi.nih.gov/genomes/refseq/viral/ viral.sh 0 true | |
| 18 fetchproks.sh ftp://ftp.ncbi.nih.gov/genomes/refseq/protozoa/ protozoa.sh 0 true | |
| 19 fetchproks.sh ftp://ftp.ncbi.nih.gov/genomes/refseq/invertebrate/ invertebrate.sh 0 true | |
| 20 fetchproks.sh ftp://ftp.ncbi.nih.gov/genomes/refseq/fungi/ fungi.sh 0 true | |
| 21 fetchproks.sh ftp://ftp.ncbi.nih.gov/genomes/refseq/plant/ plant.sh 0 true | |
| 22 fetchproks.sh ftp://ftp.ncbi.nih.gov/genomes/refseq/vertebrate_mammalian/ vertebrate_mammalian.sh 0 true | |
| 23 fetchproks.sh ftp://ftp.ncbi.nih.gov/genomes/refseq/vertebrate_other/ vertebrate_other.sh 0 true | |
| 24 | |
| 25 Mitochondrion, plasmid, and plastid are different and use gbff2gff. | |
| 26 | |
| 27 Processing parameters: | |
| 28 None yet! | |
| 29 | |
| 30 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. | |
| 31 " | |
| 32 } | |
| 33 | |
| 34 #This block allows symlinked shellscripts to correctly set classpath. | |
| 35 pushd . > /dev/null | |
| 36 DIR="${BASH_SOURCE[0]}" | |
| 37 while [ -h "$DIR" ]; do | |
| 38 cd "$(dirname "$DIR")" | |
| 39 DIR="$(readlink "$(basename "$DIR")")" | |
| 40 done | |
| 41 cd "$(dirname "$DIR")" | |
| 42 DIR="$(pwd)/" | |
| 43 popd > /dev/null | |
| 44 | |
| 45 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" | |
| 46 CP="$DIR""current/" | |
| 47 | |
| 48 z="-Xmx1g" | |
| 49 z2="-Xms1g" | |
| 50 set=0 | |
| 51 | |
| 52 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then | |
| 53 usage | |
| 54 exit | |
| 55 fi | |
| 56 | |
| 57 calcXmx () { | |
| 58 source "$DIR""/calcmem.sh" | |
| 59 setEnvironment | |
| 60 parseXmx "$@" | |
| 61 } | |
| 62 calcXmx "$@" | |
| 63 | |
| 64 fetchproks() { | |
| 65 local CMD="java $EA $EOOM $z -cp $CP prok.FetchProks $@" | |
| 66 echo $CMD >&2 | |
| 67 eval $CMD | |
| 68 } | |
| 69 | |
| 70 fetchproks "$@" |