Mercurial > repos > drosofff > msp_oases

annotate oases_optimiser.sh @ 0:eedbe32980bb draft

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planemo upload for repository https://bitbucket.org/drosofff/gedtools/
author drosofff
date Sun, 21 Jun 2015 14:38:06 -0400
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eedbe32980bb planemo upload for repository https://bitbucket.org/drosofff/gedtools/
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1 #!/bin/bash
eedbe32980bb planemo upload for repository https://bitbucket.org/drosofff/gedtools/
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2
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3 min_k=$1
eedbe32980bb planemo upload for repository https://bitbucket.org/drosofff/gedtools/
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4 max_k=$2
eedbe32980bb planemo upload for repository https://bitbucket.org/drosofff/gedtools/
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5 input=$3
eedbe32980bb planemo upload for repository https://bitbucket.org/drosofff/gedtools/
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6 job_dir=$4
eedbe32980bb planemo upload for repository https://bitbucket.org/drosofff/gedtools/
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7
eedbe32980bb planemo upload for repository https://bitbucket.org/drosofff/gedtools/
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8 for i in `seq $min_k 2 $max_k`
eedbe32980bb planemo upload for repository https://bitbucket.org/drosofff/gedtools/
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9 do
eedbe32980bb planemo upload for repository https://bitbucket.org/drosofff/gedtools/
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10 velveth $job_dir/outputFolder_$i $i $input
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11 velvetg $job_dir/outputFolder_$i -read_trkg yes
eedbe32980bb planemo upload for repository https://bitbucket.org/drosofff/gedtools/
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12 oases $job_dir/outputFolder_$i
eedbe32980bb planemo upload for repository https://bitbucket.org/drosofff/gedtools/
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13 done
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14
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15 velveth $job_dir/MergedAssemblyFolder 27 -long outputFolder_*/transcripts.fa
eedbe32980bb planemo upload for repository https://bitbucket.org/drosofff/gedtools/
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16 velvetg $job_dir/MergedAssemblyFolder -read_trkg yes -conserveLong yes
eedbe32980bb planemo upload for repository https://bitbucket.org/drosofff/gedtools/
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17 oases $job_dir/MergedAssemblyFolder -merge yes
eedbe32980bb planemo upload for repository https://bitbucket.org/drosofff/gedtools/
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