Mercurial > repos > petr-novak > dante_ltr

annotate tests.sh @ 8:9de392f2fc02 draft

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"planemo upload commit d6433b48c9bae079edb06364147f19500501c986"
author petr-novak
date Tue, 28 Jun 2022 12:33:22 +0000
parents c33d6583e548
children ff01d4263391
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c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
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1 #!/bin/bash
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2 # set to stop in case of error
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3 set -e
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4 # first argument is cpu number
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5 NCPU_TO_USE=$1
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6 eval "$(conda shell.bash hook)"
c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
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7 conda activate dante_ltr
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8 echo "Running tests 1, detection of LTRs"
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9 ./extract_putative_ltr.R -s test_data/sample_genome.fasta \
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10 -g test_data/sample_DANTE.gff3 -o tmp/test_output1 -c $NCPU_TO_USE
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13 cat tmp/test_output1_statistics.csv
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15 echo "Running tests 2, filtering gff"
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16 ./clean_ltr.R -g tmp/test_output1.gff3 -s test_data/sample_genome.fasta \
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17 -o tmp/test_output2 -c $NCPU_TO_USE
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19 echo "Running tests 3, detection of LTRs, allow missing domains"
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20 ./extract_putative_ltr.R -s test_data/sample_genome.fasta \
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21 -g test_data/sample_DANTE.gff3 -o tmp/test_output3 -c $NCPU_TO_USE -M 2
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24 cat tmp/test_output3_statistics.csv
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26 echo "Running tests 4, filtering gff"
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27 ./clean_ltr.R -g tmp/test_output3.gff3 -s test_data/sample_genome.fasta \
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28 -o tmp/test_output4 -c $NCPU_TO_USE
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