Repackaging DB2 DOCK38

The following is a script for repackaging 3D pipeline results. First, here is the script:

#!/bin/bash
# make_tarballs.bash

# required parameter
TARBALL_SOURCE=$1
TARBALL_REPACK_DEST=$2

TARBALL_SOURCE=$(realpath $TARBALL_SOURCE)
TARBALL_REPACK_DEST=$(realpath $TARBALL_REPACK_DEST)

[ -z $TARBALL_SOURCE ] && echo "need to provide TARBALL_SOURCE as 1st arg!" && exit 1
[ -z $TARBALL_REPACK_DEST ] && echo "need to provide TARBALL_REPACK_DEST as 2nd arg!" && exit 1

# optional parameters
WORKING_DIRECTORY=${WORKING_DIRECTORY-/tmp/$(whoami)}
PACKAGES_PER_PACKAGE=${PACKAGES_PER_PACKAGE-100}
PACKAGE_TYPE=${PACKAGE_TYPE-db2.gz}
PACKAGE_TYPE_SHORT=$(echo $PACKAGE_TYPE | cut -d'.' -f1)

echo WORKING_DIRECTORY=$WORKING_DIRECTORY
mkdir -p $WORKING_DIRECTORY && cd $WORKING_DIRECTORY
mkdir -p output working tarball_split_list

echo finding
find $TARBALL_SOURCE -name '*.tar.gz' > tarball_list.txt
echo splitting
split -l $PACKAGES_PER_PACKAGE tarball_list.txt tarball_split_list/
echo working
cd working
for f in ../tarball_split_list/*; do
        for tb in $(cat $f); do
                ! [ -z $VERBOSE ] && echo tar --transform='s/^.*\///' -xf $tb '*.'$PACKAGE_TYPE 2>/dev/null
                tar --transform='s/^.*\///' -xf $tb '*.'$PACKAGE_TYPE 2>/dev/null
        done
        ! [ -z $VERBOSE ] && echo tar -czf $(basename $f).$PACKAGE_TYPE.tar.gz '*.'$PACKAGE_TYPE
        tar -czf $(basename $f).$PACKAGE_TYPE_SHORT.tar.gz *.$PACKAGE_TYPE
        mv $(basename $f).$PACKAGE_TYPE_SHORT.tar.gz $TARBALL_REPACK_DEST
        rm *.$PACKAGE_TYPE
        echo $(basename $f)
done
cd ..
echo Done! Results in $PWD/output

Now, an example usage:

[user@gimel5 ~] bash make_tarballs.bash /nfs/exb/zinc22/tarballs/H17P200_H19P400.smi.batch-3d.d/out/aaa.d
finding
splitting
working
aa
ab
ac
ad
ae
af
ag
ah
ai
aj
Done! Results in /tmp/user/output

For docking from ligands built using our pipeline with default options, running this script unmodified is sufficient for creating appropriately sized packages for docking. You may wish to edit WORKING_DIRECTORY if your files total more than 50G in size- /tmp is not usually any larger than this!