Mercurial > repos > petr-novak > dante_ltr

comparison tests.sh @ 12:ff01d4263391 draft

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"planemo upload commit 414119ad7c44562d2e956b765e97ca113bc35b2b-dirty"
author petr-novak
date Thu, 21 Jul 2022 08:23:15 +0000
parents c33d6583e548
children 559940c04c44
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11:54bd36973253 12:ff01d4263391
1 #!/bin/bash 1 #!/bin/bash
2 # set to stop in case of error 2 # set to stop in case of error
3 set -e 3 set -e
4 # first argument is cpu number 4 # first argument is cpu number
5 NCPU_TO_USE=$1 5 NCPU_TO_USE=$1
6
7 # test if NCPU_TO_USE is set:
8 if [ -z "${NCPU_TO_USE}" ]; then
9 echo "NCPU_TO_USE is not set, using 10"
10 NCPU_TO_USE=10
11 fi
12
6 eval "$(conda shell.bash hook)" 13 eval "$(conda shell.bash hook)"
7 conda activate dante_ltr 14 conda activate dante_ltr
8 echo "Running tests 1, detection of LTRs" 15 echo "Running tests 1, detection of LTRs"
9 ./extract_putative_ltr.R -s test_data/sample_genome.fasta \ 16 ./detect_putative_ltr.R -s test_data/sample_genome.fasta \
10 -g test_data/sample_DANTE.gff3 -o tmp/test_output1 -c $NCPU_TO_USE 17 -g test_data/sample_DANTE.gff3 -o tmp/test_output1 -c $NCPU_TO_USE
11 18
12 19
13 cat tmp/test_output1_statistics.csv 20 cat tmp/test_output1_statistics.csv
14 21
15 echo "Running tests 2, filtering gff" 22 echo "Running tests 2, filtering gff"
16 ./clean_ltr.R -g tmp/test_output1.gff3 -s test_data/sample_genome.fasta \ 23 ./clean_ltr.R -g tmp/test_output1.gff3 -s test_data/sample_genome.fasta \
17 -o tmp/test_output2 -c $NCPU_TO_USE 24 -o tmp/test_output2 -c $NCPU_TO_USE
18 25
19 echo "Running tests 3, detection of LTRs, allow missing domains" 26 echo "Running tests 3, detection of LTRs, allow missing domains"
20 ./extract_putative_ltr.R -s test_data/sample_genome.fasta \ 27 ./detect_putative_ltr.R -s test_data/sample_genome.fasta \
21 -g test_data/sample_DANTE.gff3 -o tmp/test_output3 -c $NCPU_TO_USE -M 2 28 -g test_data/sample_DANTE.gff3 -o tmp/test_output3 -c $NCPU_TO_USE -M 2
22 29
23 30
24 cat tmp/test_output3_statistics.csv 31 cat tmp/test_output3_statistics.csv
25 32
26 echo "Running tests 4, filtering gff" 33 echo "Running tests 4, filtering gff"
27 ./clean_ltr.R -g tmp/test_output3.gff3 -s test_data/sample_genome.fasta \ 34 ./clean_ltr.R -g tmp/test_output3.gff3 -s test_data/sample_genome.fasta \
28 -o tmp/test_output4 -c $NCPU_TO_USE 35 -o tmp/test_output4 -c $NCPU_TO_USE
29 36
30 37
38 echo "Running tests 5, detection of LTRs using python wrapper"
39 ./detect_putative_ltr_wrapper.py -s test_data/sample_genome.fasta \
40 -g test_data/sample_DANTE.gff3 -o tmp/test_output5 -c $NCPU_TO_USE \
41 -S 10000000
42 cat tmp/test_output5_statistics.csv
43
44 echo "Running tests 4, filtering gff"
45 ./clean_ltr.R -g tmp/test_output5.gff3 -s test_data/sample_genome.fasta \
46 -o tmp/test_output6 -c $NCPU_TO_USE