Mercurial > repos > konradpaszkiewicz > oasesoptimiser
annotate oases_optimiser.sh @ 0:53e887dda799 default tip
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author | konradpaszkiewicz |
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date | Tue, 07 Jun 2011 17:41:37 -0400 |
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53e887dda799
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
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1 #!/bin/bash |
53e887dda799
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
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2 |
53e887dda799
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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3 min_k=$1 |
53e887dda799
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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4 max_k=$2 |
53e887dda799
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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5 input=$3 |
53e887dda799
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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6 args=$# |
53e887dda799
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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7 if [$args -gt 3]; then |
53e887dda799
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
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8 velvetoptions=$4 |
53e887dda799
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
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9 oasesoptions=$5 |
53e887dda799
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
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10 else |
53e887dda799
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
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11 velvetoptions='' |
53e887dda799
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
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12 oasesoptions='' |
53e887dda799
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
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13 fi |
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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
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14 |
53e887dda799
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
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15 for i in `seq $min_k 2 $max_k` |
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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
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16 do |
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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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17 velveth . $i $input |
53e887dda799
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
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18 velvetg . -read_trkg yes |
53e887dda799
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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19 oases . $oasesoptions |
53e887dda799
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
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20 mv transcripts.fa transcripts_$i.fa |
53e887dda799
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
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21 done |
53e887dda799
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
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22 |
53e887dda799
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
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23 velveth . $max_k -long transcripts_*.fa $input |
53e887dda799
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
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24 velvetg . -read_trkg yes $velvetoptions |
53e887dda799
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
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25 oases . -amos_file yes -unused_reads yes $oasesoptions |
53e887dda799
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
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26 |