Just a heads up, we don't have a huge amount of space on this machine, ~750 GB for the git repos. We can include some data in the projects, but really big datasets will need to remain elsewhere. For anyone new to Git, this is a fairly good place to start: http://gitref.org/index.html Documentation for Gitlab is available here: http://doc.gitlab.com/

Commit ee09486f authored by Khalid Kunji's avatar Khalid Kunji

Added static builds and falls back to them when there is no user compiled binary

parent f2490849
No preview for this file type
......@@ -205,7 +205,7 @@ then
fi
;;
v )
echo "GIGI-Quick version: 1.01"
echo "GIGI-Quick version: 1.03"
echo "If you intended to activate verbose output, that flag is now capitalized: '-V'"
exit 0
;;
......@@ -261,15 +261,48 @@ gigi_split="./SPLIT/gigisplit"
gigi_merge="./MERGE/gigimerge"
cd "${gigi%/*}"
export gigi="$(pwd)"/GIGI
if [ -x "$(pwd)"/GIGI ]
then
export gigi="$(pwd)"/GIGI
echo "Using user compiled GIGI"
elif [ $(getconf LONG_BIT) -eq 64 ]
then
export gigi="$(pwd)"/GIGI-static-64
echo "Using static 64 bit GIGI"
else
export gigi="$(pwd)"/GIGI-static-32
echo "Using static 32 bit GIGI"
fi
cd "$parent_path"
cd "${gigi_split%/*}"
export gigi_split="$(pwd)"/gigisplit
if [ -x "$(pwd)"/gigisplit ]
then
export gigi_split="$(pwd)"/gigisplit
echo "Using user compiled gigisplit"
elif [ $(getconf LONG_BIT) -eq 64 ]
then
export gigi_split="$(pwd)"/gigisplit-static-64
echo "Using static 64 bit gigisplit"
else
export gigi_split="$(pwd)"/gigisplit-static-32
echo "Using static 32 bit gigisplit"
fi
cd "$parent_path"
cd "${gigi_merge%/*}"
export gigi_merge="$(pwd)"/gigimerge
if [ -x "$(pwd)"/gigimerge ]
then
export gigi_merge="$(pwd)"/gigimerge
echo "Using user compiled gigimerge"
elif [ $(getconf LONG_BIT) -eq 64 ]
then
export gigi_merge="$(pwd)"/gigimerge-static-64
echo "Using static 64 bit gigimerge"
else
export gigi_merge="$(pwd)"/gigimerge-static-32
echo "Using static 32 bit gigimerge"
fi
if [ ${verbose} ]
then
......
......@@ -43,7 +43,7 @@ then
j=0
while IFS= read -r line; do
if (( i++ >= queue_length )); then
timeout --preserve-status 5 wait -n # wait for any job to complete. New in 4.3
wait -n # wait for any job to complete. New in 4.3
fi
if [ -e "${output_folder}/${run_name}/gigi_output/${j}/impute.geno" ]
then
......
export parent_path=$( cd "$(dirname $(readlink -f "${BASH_SOURCE[0]}"))" ; pwd -P )
command -v cmake >/dev/null 2>&1 || { echo >&2 \
"Cmake is required to build the make files but is not installed or not in the path. See README. Aborting."; exit 1; }
echo "Parent Path: " "${parent_path}"
cd "$parent_path"
......
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