Mercurial > repos > iuc > bmtagger
comparison test-data/gen.sh @ 0:49a1cbbe5767 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bmtagger commit e3d492d96b0ffe79370ca090b3f749b0869e8b60
| author | iuc |
|---|---|
| date | Wed, 12 Nov 2025 12:03:46 +0000 |
| parents | |
| children |
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| -1:000000000000 | 0:49a1cbbe5767 |
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| 1 echo "> host" > host.fa | |
| 2 head -c 10000000 /dev/urandom | tr -dc 'ACGT' | head -c 100000 >> host.fa | |
| 3 echo "> contaminant" > contaminant.fa | |
| 4 head -c 10000000 /dev/urandom | tr -dc 'ACGT' | head -c 100000 >> contaminant.fa | |
| 5 | |
| 6 art_illumina -ss HS25 -i host.fa -p -l 75 -f 1 -m 200 -s 10 -o host.fq | |
| 7 art_illumina -ss HS25 -i contaminant.fa -p -l 75 -f 1 -m 200 -s 10 -o contaminant.fq | |
| 8 | |
| 9 cat host.fq1.fq contaminant.fq1.fq > host_and_contaminant.fq1.fq | |
| 10 cat host.fq2.fq contaminant.fq2.fq > host_and_contaminant.fq2.fq | |
| 11 | |
| 12 gzip -c host_and_contaminant.fq1.fq > host_and_contaminant.fq1.fq.gz | |
| 13 gzip -c host_and_contaminant.fq2.fq > host_and_contaminant.fq2.fq.gz | |
| 14 | |
| 15 # use 10-mers to reduce size | |
| 16 bmtool -d host.fa -o host.bitmask -w 10 | |
| 17 srprism mkindex -i host.fa -o host.srprism | |
| 18 makeblastdb -in host.fa -dbtype nucl |