|
0
|
1 #!/bin/bash
|
|
|
2
|
|
|
3 source $(dirname $0)/util.sh
|
|
|
4 source $1
|
|
|
5
|
|
|
6 PLACED_SEQS=$(extify jplace ${PLACED_SEQS})
|
|
|
7 NBC_SEQS=$(extify fasta ${NBC_SEQS})
|
|
|
8
|
|
|
9 guppy redup \
|
|
|
10 -m \
|
|
|
11 -d ${DEDUP_INFO} \
|
|
|
12 -o ${REDUPED_SEQS} \
|
|
|
13 ${PLACED_SEQS}
|
|
|
14
|
|
|
15 REDUPED_SEQS=$(extify jplace ${REDUPED_SEQS})
|
|
|
16
|
|
|
17 rppr prep_db \
|
|
|
18 -c ${REFPKG} \
|
|
|
19 --sqlite ${CLASS_DB}
|
|
|
20
|
|
|
21 guppy classify \
|
|
|
22 -c ${REFPKG} \
|
|
|
23 -j ${GALAXY_SLOTS:-4} \
|
|
|
24 --pp \
|
|
|
25 --sqlite ${CLASS_DB} \
|
|
|
26 --classifier hybrid2 \
|
|
|
27 --nbc-sequences ${NBC_SEQS} \
|
|
4
|
28 ${PLACED_SEQS}
|
|
0
|
29
|
|
|
30 multiclass_concat.py --dedup-info ${DEDUP_INFO} ${CLASS_DB}
|
