Mercurial > repos > petr-novak > dante_ltr

comparison tests.sh @ 7:c33d6583e548 draft

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"planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
author petr-novak
date Fri, 24 Jun 2022 14:19:48 +0000
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children ff01d4263391
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6:b91ca438a1cb 7:c33d6583e548
1 #!/bin/bash
2 # set to stop in case of error
3 set -e
4 # first argument is cpu number
5 NCPU_TO_USE=$1
6 eval "$(conda shell.bash hook)"
7 conda activate dante_ltr
8 echo "Running tests 1, detection of LTRs"
9 ./extract_putative_ltr.R -s test_data/sample_genome.fasta \
10 -g test_data/sample_DANTE.gff3 -o tmp/test_output1 -c $NCPU_TO_USE
11
12
13 cat tmp/test_output1_statistics.csv
14
15 echo "Running tests 2, filtering gff"
16 ./clean_ltr.R -g tmp/test_output1.gff3 -s test_data/sample_genome.fasta \
17 -o tmp/test_output2 -c $NCPU_TO_USE
18
19 echo "Running tests 3, detection of LTRs, allow missing domains"
20 ./extract_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
22
23
24 cat tmp/test_output3_statistics.csv
25
26 echo "Running tests 4, filtering gff"
27 ./clean_ltr.R -g tmp/test_output3.gff3 -s test_data/sample_genome.fasta \
28 -o tmp/test_output4 -c $NCPU_TO_USE
29
30