[Debian-med-packaging] qcumber | Fix package to build successfully (!1)

[Andreas Tille]

On Mon, Feb 17, 2020 at 02:49:16PM +0000, Nilesh Patra wrote:
> @tille pushed.

Thanks.

> Need yout help in this package now.

Well, upstream recommends bioconda.  I've checked the bioconda
recipe, which says:



#!/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



I guess if we adapt the PATHes that could be our install
instruction.  Does this help?

Kind regards

        Andreas.

-- 
http://fam-tille.de