Mercurial > repos > davidvanzessen > argalaxy_tools

annotate igblast/igblast.sh @ 14:dca3273a7291 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author davidvanzessen
date Fri, 07 Aug 2015 08:07:42 -0400
parents 010402c959aa
children 6e068ef43336
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
12
010402c959aa Uploaded
davidvanzessen
parents:
diff changeset
1 set -e
010402c959aa Uploaded
davidvanzessen
parents:
diff changeset
2
010402c959aa Uploaded
davidvanzessen
parents:
diff changeset
3 dir="$(cd "$(dirname "$0")" && pwd)"
010402c959aa Uploaded
davidvanzessen
parents:
diff changeset
4
010402c959aa Uploaded
davidvanzessen
parents:
diff changeset
5 input=$1
010402c959aa Uploaded
davidvanzessen
parents:
diff changeset
6 species=$2
010402c959aa Uploaded
davidvanzessen
parents:
diff changeset
7 locus=$3
010402c959aa Uploaded
davidvanzessen
parents:
diff changeset
8 output=$4
010402c959aa Uploaded
davidvanzessen
parents:
diff changeset
9
010402c959aa Uploaded
davidvanzessen
parents:
diff changeset
10
010402c959aa Uploaded
davidvanzessen
parents:
diff changeset
11 echo "$input $species $locus $output"
010402c959aa Uploaded
davidvanzessen
parents:
diff changeset
12
14
dca3273a7291 Uploaded
davidvanzessen
parents: 12
diff changeset
13 java -Xmx64G -jar $IGBLASTWRP/igblastwrp.jar -S $species -R $locus ${input} $PWD/blasted_output 2>&1
12
010402c959aa Uploaded
davidvanzessen
parents:
diff changeset
14
010402c959aa Uploaded
davidvanzessen
parents:
diff changeset
15 Rscript --verbose $dir/igblast.r "$PWD/blasted_output.L2.txt" "$output" 2>&1