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 2ed206f3 authored by Khalid Kunji's avatar Khalid Kunji

regions

parent 0415ceff
......@@ -165,8 +165,30 @@ then
exit 1
fi
;;
r )
region_start="${@:1:1}"
shift
region_end="${@:1:1}"
shift
if [ "${queue_length:0:1}" == "-" ]
then
echo "Flags shouldn't follow each other separately (e.g. -o -n ./out 4), but instead should be joined (e.g. -on ./out 4) or totally separate (e.g. -o ./out -n 4)"
exit 1
fi
if [[ "${region_start}" && "${region_end}" ]]
then
echo "Region set successfully: "
echo "Start: " "${region_start}"
echo "End: " "${region_end}"
export region_start
export region_end
else
echo "-r flag given without region start and end, aborting."
exit 1
fi
;;
v )
echo "GIGI-Quick version: 0.99"
echo "GIGI-Quick version: 1.00"
echo "If you intended to activate verbose output, that flag is now capitalized: '-V'"
exit 0
;;
......
......@@ -23,7 +23,12 @@ else
echo "Long is: " "${long}"
fi
echo "SPLIT STEP, NUM CHUNKS: " "${num_chunks}"
$timecmd -o "${output_folder}/${run_name}/STATS/time${i}.log" -f'memory in kilobytes %M real %e user %U sys %S command %C' "${gigi_split}" "${param_file##*/}" "${num_chunks}" "${gigi_split_prefix}" "${long}" > "${output_folder}/${run_name}/LOGS/split.log"
if [[ "${region_start}" && "${region_end}" ]]
then
$timecmd -o "${output_folder}/${run_name}/STATS/time${i}.log" -f'memory in kilobytes %M real %e user %U sys %S command %C' "${gigi_split}" "${param_file##*/}" "${num_chunks}" "${gigi_split_prefix}" "${long}" "${region_start}" "${region_end}"> "${output_folder}/${run_name}/LOGS/split.log"
else
$timecmd -o "${output_folder}/${run_name}/STATS/time${i}.log" -f'memory in kilobytes %M real %e user %U sys %S command %C' "${gigi_split}" "${param_file##*/}" "${num_chunks}" "${gigi_split_prefix}" "${long}" > "${output_folder}/${run_name}/LOGS/split.log"
fi
echo "Split exit status: " "$?"
fi
cd "$parent_path"
......
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