Mercurial > repos > drosofff > msp_oases

annotate oases_optimiser.sh @ 0:435711ba68e3 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
author drosofff
date Fri, 29 May 2015 12:41:13 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
435711ba68e3 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
1 #!/bin/bash
435711ba68e3 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
2
435711ba68e3 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
3 min_k=$1
435711ba68e3 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
4 max_k=$2
435711ba68e3 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
5 input=$3
435711ba68e3 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
6 job_dir=$4
435711ba68e3 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
7
435711ba68e3 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
8 for i in `seq $min_k 2 $max_k`
435711ba68e3 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
9 do
435711ba68e3 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
10 velveth $job_dir/outputFolder_$i $i $input
435711ba68e3 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
11 velvetg $job_dir/outputFolder_$i -read_trkg yes
435711ba68e3 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
12 oases $job_dir/outputFolder_$i
435711ba68e3 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
13 done
435711ba68e3 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
14
435711ba68e3 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
15 velveth $job_dir/MergedAssemblyFolder 27 -long outputFolder_*/transcripts.fa
435711ba68e3 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
16 velvetg $job_dir/MergedAssemblyFolder -read_trkg yes -conserveLong yes
435711ba68e3 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
17 oases $job_dir/MergedAssemblyFolder -merge yes
435711ba68e3 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
18