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annotate gen.sh @ 2:1f4933f5a323 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 84c175ed516a3b0074ca06d6546b76f1cbc4fb68"
author iuc
date Wed, 02 Jun 2021 18:39:05 +0000
parents 39b6485e2d34
children
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39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
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1 ## Activate MITOS(1) conda env
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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2 conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name mitos2 mitos=1.0.5 zip
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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3
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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4 conda activate mitos1
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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6 tmp=$(mktemp -d)
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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7 runmitos.py --input test-data/NC_012920.fasta --code 2 --outdir $tmp --refdir '/home/maze/workspace/tools-iuc/tools/mitos/test-data/mitos1-refdata/' && zip -9 -y -r $tmp/result.zip $tmp
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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9 for i in bed faa fas geneorder gff seq
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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10 do
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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11 cp $tmp/result.$i test-data/NC_012920.$i
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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12 done
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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13 cp $tmp/result test-data/NC_012920.mito
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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14 cp $tmp/plots/trnA-*.svg test-data/NC_012920_trnA.svg
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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15 cp $tmp/plots/prot.pdf test-data/NC_012920_prot.pdf
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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16 cp $tmp/plots/rna.pdf test-data/NC_012920_ncrna.pdf
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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17 rm -rf $tmp
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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19 conda deactivate
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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21 ## Activate MITOS2 conda env
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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22 conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name mitos2 mitos=2.0.6 zip
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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23
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
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24 conda activate mitos2
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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25
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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26 # data for 1st test
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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27 tmp=$(mktemp -d)
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
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28 runmitos.py --input test-data/NC_012920.fasta --code 2 --outdir $tmp --refdir './test-data/' --refseqver 'refseq63m/' --intron 0 --oril 0 --orih 0 --finovl 50 --fragovl 0.2 --fragfac 10.0 --evalue 2.0 --cutoff 0.50 --clipfac 10.0 --ncev 0.01 --maxtrnaovl 50 --maxrrnaovl 50 --noplots
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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29 cp $tmp/result.bed test-data/mitos2_NC_012920.bed
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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30 rm -rf $tmp
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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32 # data for 3rd test
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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33 tmp=$(mktemp -d)
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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34 runmitos.py --input test-data/NC_012920.fasta --code 2 --outdir $tmp --refdir './test-data/' --refseqver 'refseq63m/' --intron 0 --oril 0 --orih 0 --evalue 3.0 --cutoff 0.49 --clipfac 9.0 --ncbicode --alarab --oldstst --ncev 0.1 --sensitive --maxtrnaovl 51 --maxrrnaovl 49 && zip -9 -y -r $tmp/result.zip $tmp
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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35 for i in faa fas geneorder gff mitos seq
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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36 do
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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37 cp $tmp/result.$i test-data/mitos2_NC_012920.$i
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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38 done
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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39 cp $tmp/plots/prot.pdf test-data/mitos2_NC_012920_prot.pdf
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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40 cp $tmp/plots/rna.pdf test-data/mitos2_NC_012920_ncrna.pdf
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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41 rm -rf $tmp
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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42
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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43 conda deactivate