annotate tests.sh @ 8:9de392f2fc02 draft

"planemo upload commit d6433b48c9bae079edb06364147f19500501c986"
author petr-novak
date Tue, 28 Jun 2022 12:33:22 +0000
parents c33d6583e548
children ff01d4263391
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
7
c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
diff changeset
1 #!/bin/bash
c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
diff changeset
2 # set to stop in case of error
c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
diff changeset
3 set -e
c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
diff changeset
4 # first argument is cpu number
c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
diff changeset
5 NCPU_TO_USE=$1
c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
diff changeset
6 eval "$(conda shell.bash hook)"
c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
diff changeset
7 conda activate dante_ltr
c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
diff changeset
8 echo "Running tests 1, detection of LTRs"
c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
diff changeset
9 ./extract_putative_ltr.R -s test_data/sample_genome.fasta \
c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
diff changeset
10 -g test_data/sample_DANTE.gff3 -o tmp/test_output1 -c $NCPU_TO_USE
c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
diff changeset
11
c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
diff changeset
12
c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
diff changeset
13 cat tmp/test_output1_statistics.csv
c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
diff changeset
14
c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
diff changeset
15 echo "Running tests 2, filtering gff"
c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
diff changeset
16 ./clean_ltr.R -g tmp/test_output1.gff3 -s test_data/sample_genome.fasta \
c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
diff changeset
17 -o tmp/test_output2 -c $NCPU_TO_USE
c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
diff changeset
18
c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
diff changeset
19 echo "Running tests 3, detection of LTRs, allow missing domains"
c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
diff changeset
20 ./extract_putative_ltr.R -s test_data/sample_genome.fasta \
c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
diff changeset
21 -g test_data/sample_DANTE.gff3 -o tmp/test_output3 -c $NCPU_TO_USE -M 2
c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
diff changeset
22
c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
diff changeset
23
c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
diff changeset
24 cat tmp/test_output3_statistics.csv
c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
diff changeset
25
c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
diff changeset
26 echo "Running tests 4, filtering gff"
c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
diff changeset
27 ./clean_ltr.R -g tmp/test_output3.gff3 -s test_data/sample_genome.fasta \
c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
diff changeset
28 -o tmp/test_output4 -c $NCPU_TO_USE
c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
diff changeset
29
c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
diff changeset
30