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|
#!/usr/bin/env bash
set -e
rootdir=$PWD
unamestr=$(uname)
# Check if the OS seems to be Linux. This should be informative to
# Windows/Mac users that are trying to install this, despite it being
# developed for Linux. There is a VM avilable for Mac/Windows.
if [ "$unamestr" != "Linux" ]
then
echo "Operating system does not appear to be Linux: uname says it's '$unamestr'"
if [ "$1" = "force" ]
then
echo "'force' option used, carrying on anyway. Best of luck to you..."
else
echo "
If you *really* want to try installing anyway, run this:
./install.sh force
If you're using a Mac or Windows, then the recommended way to run REAPR is
to use the virtual machine."
exit 1
fi
fi
echo "------------------------------------------------------------------------------
Checking prerequisites
------------------------------------------------------------------------------
"
echo "Checking Perl modules..."
modules_ok=1
for module in File::Basename File::Copy File::Spec File::Spec::Link Getopt::Long List::Util
do
set +e
perl -M$module -e 1 2>/dev/null
if [ $? -eq 0 ]
then
echo " OK $module"
else
echo " NOT FOUND: $module"
modules_ok=0
fi
set -e
done
if [ $modules_ok -ne 1 ]
then
echo "Some Perl modules were not found - please install them. Cannot continue"
exit 1
else
echo "... Perl modules all OK"
fi
echo
echo "Looking for R..."
if type -P R
then
echo "... found R OK"
else
echo "Didn't find R. It needs to be installed and in your path. Cannot continue"
fi
cd third_party
echo "
------------------------------------------------------------------------------
Compiling cmake
------------------------------------------------------------------------------
"
cd cmake
./bootstrap --prefix $PWD
make
cd ..
echo "
------------------------------------------------------------------------------
cmake compiled
------------------------------------------------------------------------------
"
echo "
------------------------------------------------------------------------------
Compiling Bamtools
------------------------------------------------------------------------------
"
cd bamtools
mkdir build
cd build
$rootdir/third_party/cmake/bin/cmake ..
make
cd $rootdir
echo "
------------------------------------------------------------------------------
Bamtools compiled
------------------------------------------------------------------------------
"
echo "
------------------------------------------------------------------------------
Compiling Tabix
------------------------------------------------------------------------------
"
cd third_party/tabix
make
cd ..
echo "
------------------------------------------------------------------------------
Tabix compiled
------------------------------------------------------------------------------
"
echo "
------------------------------------------------------------------------------
Compiling snpomatic
------------------------------------------------------------------------------
"
cd snpomatic
make
cd ..
echo "
------------------------------------------------------------------------------
snpomatic compiled
------------------------------------------------------------------------------
"
echo "
------------------------------------------------------------------------------
Compiling samtools
------------------------------------------------------------------------------
"
cd samtools
make
echo "
------------------------------------------------------------------------------
samtools compiled
------------------------------------------------------------------------------
"
echo "
------------------------------------------------------------------------------
Compiling Reapr
------------------------------------------------------------------------------
"
cd $rootdir/src
make
cd ..
ln -s src/reapr.pl reapr
echo "
Reapr compiled
All done!
Run
./reapr
for usage.
Read the manual
manual.pdf
for full instructions
"
|
