1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
|
#!/bin/bash
# grep adapters from trimmomatic
if [ -a "$CONDA_PREFIX/share/trimmomatic/adapters" ]; then
cat $CONDA_PREFIX/share/trimmomatic/adapters/* > config/adapters.fa
adapter_path=$CONDA_PREFIX/share/trimmomatic/adapters/;
else
cat $CONDA_PREFIX/../../../share/trimmomatic/adapters/* > config/adapters.fa
adapter_path=$CONDA_PREFIX/../../../share/trimmomatic/adapters/;
fi
mkdir -p $CONDA_PREFIX/opt/qcumber/
cp -r * $CONDA_PREFIX/opt/qcumber/
#sed -i.bak "1c\#!$PYTHON" $CONDA_PREFIX/opt/qcumber/QCumber-2
sed -i.bak "s#ADAPTER_PATH = \"\"#ADAPTER_PATH = \"$adapter_path\"#g" $CONDA_PREFIX/opt/qcumber/QCumber-2
ln -s $CONDA_PREFIX/opt/qcumber/QCumber-2 $CONDA_PREFIX/bin/
chmod u+x $CONDA_PREFIX/bin/QCumber-2
|
