Mercurial > repos > iuc > mitos2
view gen.sh @ 8:73b018c57e96 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit a3f57ea5cedcf7ceb70ea815e965325fab6cc90c
author | iuc |
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date | Sat, 23 Mar 2024 14:08:35 +0000 |
parents | dd589aa77943 |
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## Activate MITOS(1) conda env conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name mitos2 mitos=1.0.5 zip conda activate mitos1 tmp=$(mktemp -d) 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 for i in bed faa fas geneorder gff seq do cp $tmp/result.$i test-data/NC_012920.$i done cp $tmp/result test-data/NC_012920.mito cp $tmp/plots/trnA-*.svg test-data/NC_012920_trnA.svg cp $tmp/plots/prot.pdf test-data/NC_012920_prot.pdf cp $tmp/plots/rna.pdf test-data/NC_012920_ncrna.pdf rm -rf $tmp conda deactivate ## Activate MITOS2 conda env conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name mitos2 mitos=2.0.6 zip conda activate mitos2 # data for 1st test tmp=$(mktemp -d) 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 cp $tmp/result.bed test-data/mitos2_NC_012920.bed rm -rf $tmp # data for 3rd test tmp=$(mktemp -d) 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 for i in faa fas geneorder gff mitos seq do cp $tmp/result.$i test-data/mitos2_NC_012920.$i done cp $tmp/plots/prot.pdf test-data/mitos2_NC_012920_prot.pdf cp $tmp/plots/rna.pdf test-data/mitos2_NC_012920_ncrna.pdf rm -rf $tmp conda deactivate