|
jpayne@69
|
1 #!/bin/bash
|
|
jpayne@69
|
2
|
|
jpayne@69
|
3 usage(){
|
|
jpayne@69
|
4 echo "
|
|
jpayne@69
|
5 Written by Brian Bushnell
|
|
jpayne@69
|
6 Last modified October 3, 2017
|
|
jpayne@69
|
7
|
|
jpayne@69
|
8 Description: Creates polymer sequences.
|
|
jpayne@69
|
9 Can be used in conjunction with mutate.sh to generate low-complexity sequence.
|
|
jpayne@69
|
10
|
|
jpayne@69
|
11 Usage: makepolymers.sh out=<output file> k=<repeat length> minlen=<sequence length>
|
|
jpayne@69
|
12
|
|
jpayne@69
|
13 I/O parameters:
|
|
jpayne@69
|
14 out=<file> Output genome.
|
|
jpayne@69
|
15 overwrite=f (ow) Set to false to force the program to abort rather than
|
|
jpayne@69
|
16 overwrite an existing file.
|
|
jpayne@69
|
17
|
|
jpayne@69
|
18 Processing parameters:
|
|
jpayne@69
|
19 k=1 Length of repeating polymeric units.
|
|
jpayne@69
|
20 To generate a sweep of multiple values of k,
|
|
jpayne@69
|
21 specify both mink and maxk.
|
|
jpayne@69
|
22 minlen=31 Ensure sequences are at least this long.
|
|
jpayne@69
|
23 Specifically, minlen=X will ensure sequences are long enough
|
|
jpayne@69
|
24 that all possible kmers of length X are present.
|
|
jpayne@69
|
25
|
|
jpayne@69
|
26 Java Parameters:
|
|
jpayne@69
|
27 -Xmx This will set Java's memory usage, overriding autodetection.
|
|
jpayne@69
|
28 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will
|
|
jpayne@69
|
29 specify 200 megs. The max is typically 85% of physical memory.
|
|
jpayne@69
|
30 -eoom This flag will cause the process to exit if an out-of-memory
|
|
jpayne@69
|
31 exception occurs. Requires Java 8u92+.
|
|
jpayne@69
|
32 -da Disable assertions.
|
|
jpayne@69
|
33
|
|
jpayne@69
|
34 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
|
|
jpayne@69
|
35 "
|
|
jpayne@69
|
36 }
|
|
jpayne@69
|
37
|
|
jpayne@69
|
38 #This block allows symlinked shellscripts to correctly set classpath.
|
|
jpayne@69
|
39 pushd . > /dev/null
|
|
jpayne@69
|
40 DIR="${BASH_SOURCE[0]}"
|
|
jpayne@69
|
41 while [ -h "$DIR" ]; do
|
|
jpayne@69
|
42 cd "$(dirname "$DIR")"
|
|
jpayne@69
|
43 DIR="$(readlink "$(basename "$DIR")")"
|
|
jpayne@69
|
44 done
|
|
jpayne@69
|
45 cd "$(dirname "$DIR")"
|
|
jpayne@69
|
46 DIR="$(pwd)/"
|
|
jpayne@69
|
47 popd > /dev/null
|
|
jpayne@69
|
48
|
|
jpayne@69
|
49 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
|
|
jpayne@69
|
50 CP="$DIR""current/"
|
|
jpayne@69
|
51
|
|
jpayne@69
|
52 z="-Xmx4g"
|
|
jpayne@69
|
53 z2="-Xms4g"
|
|
jpayne@69
|
54 set=0
|
|
jpayne@69
|
55
|
|
jpayne@69
|
56 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
|
|
jpayne@69
|
57 usage
|
|
jpayne@69
|
58 exit
|
|
jpayne@69
|
59 fi
|
|
jpayne@69
|
60
|
|
jpayne@69
|
61 calcXmx () {
|
|
jpayne@69
|
62 source "$DIR""/calcmem.sh"
|
|
jpayne@69
|
63 setEnvironment
|
|
jpayne@69
|
64 parseXmx "$@"
|
|
jpayne@69
|
65 if [[ $set == 1 ]]; then
|
|
jpayne@69
|
66 return
|
|
jpayne@69
|
67 fi
|
|
jpayne@69
|
68 freeRam 4000m 84
|
|
jpayne@69
|
69 z="-Xmx${RAM}m"
|
|
jpayne@69
|
70 z2="-Xms${RAM}m"
|
|
jpayne@69
|
71 }
|
|
jpayne@69
|
72 calcXmx "$@"
|
|
jpayne@69
|
73
|
|
jpayne@69
|
74 makepolymers() {
|
|
jpayne@69
|
75 local CMD="java $EA $EOOM $z $z2 -cp $CP jgi.MakePolymers $@"
|
|
jpayne@69
|
76 echo $CMD >&2
|
|
jpayne@69
|
77 eval $CMD
|
|
jpayne@69
|
78 }
|
|
jpayne@69
|
79
|
|
jpayne@69
|
80 makepolymers "$@"
|
