diff options
Diffstat (limited to 'configure')
| -rwxr-xr-x | configure | 294 |
1 files changed, 254 insertions, 40 deletions
@@ -34,6 +34,199 @@ set -e +# Output of --help +# ---------------- +me=$0 # Executable file name. +help_print() { + + if [ x"$build_dir" = x ]; then + bdir_status="NOT SET" + else + bdir_status="$build_dir" + fi + + if [ x"$input_dir" = x ]; then + indir_status="NOT SET" + else + indir_status="$input_dir" + fi + + if [ x"$software_dir" = x ]; then + software_status="NOT SET" + else + software_status="$software_dir" + fi + + if [ $in_minmapsize = 0 ]; then + mm_status="NOT SET" + else + mm_status="$in_minmapsize" + fi + + if [ $jobs = "0" ]; then + jobs_status="NUMBER OF THREADS ON SYSTEM" + else + jobs_status=$jobs + fi + + if [ $existing_conf = 1 ]; then + ec_status="ACTIVATED" + else + ec_status="NOT SET" + fi + + # Print the output. + cat <<EOF +Usage: $me [OPTION]... + +Configure the reproducible paper template for this system (do local +settings). The local settings can be given on the command-line through the +options below. If not, the configure script will interactively ask for a +value to each one (with basic necessary background information printed +before them). Alternatively, if you have already configured this script for +your system, you can use the '--existing-conf' to use it and avoid +re-setting the values. + +RECOMMENDATION: If this is the first time you are running this pipeline, +please don't use the options and let the script explain each parameter in +full detail by simply running './configure'. + +The only mandatory value for this script is the local build directory. This +is where all the pipeline's outputs will be stored. Optionally, you can +also provide directories that host input data, or software source codes. If +the necessary files don't exist there, the template will automatically +download them. + +With the options below you can modify the default behavior. Just note that +you should not put an '=' sign between an option name and its value. + +Options: + + -b, --build-dir STR Top directory to build the project in. + Current value: $bdir_status + + -i, --input-dir STR Directory containing necessary input datasets. + Current value: $indir_status + + -s, --software-dir STR Directory containing necessary software tarballs. + Current value: $software_status + + -m, --minmapsize INT (Specific to Gnuastro) Number of bytes to avoid + using RAM, use HDD/SSD instead of memory. + Current value: $mm_status + + -j, --jobs INT Number of threads to use in building the software + during the pipeline. Note that on MacOS, currently + the first phase will be done on a single thread, + but higher-level software will be built in parallel. + Current value: $jobs_status + + -e, --existing-conf Use (possibly existing) local configuration. + Current value: $ec_status + + -h, --help Print this help list. + +Mandatory or optional arguments to long options are also mandatory or optional +for any corresponding short options. + +Reproducible paper template: https://gitlab.com/makhlaghi/reproducible-paper + +Report bugs to mohammad@akhlaghi.org +EOF +} + + + + + +# Parse the arguments +# ------------------- +jobs=0 +build_dir= +input_dir= +software_dir= +in_minmapsize=0 +existing_conf=0 +while [[ $# -gt 0 ]] +do + key="$1" + case $key in + -b|--build-dir) + build_dir="$2" + if [ x"$build_dir" = x ]; then + echo "No argument given to '--build-dir' ('-b')." + exit 1; + fi + shift # past argument + shift # past value + ;; + -i|--input-dir) + input_dir="$2" + if [ x"$input_dir" = x ]; then + echo "No argument given to '--input-dir' ('-i')." + exit 1; + fi + shift # past argument + shift # past value + ;; + -s|--software-dir) + software_dir="$2" + if [ x"$software_dir" = x ]; then + echo "No argument given to '--software-dir' ('-s')." + exit 1; + fi + shift # past argument + shift # past value + ;; + -m|--minmapsize) + in_minmapsize="$2" + if [ x"$in_minmapsize" = x ]; then + echo "No argument given to '--minmapsize' ('-m')." + exit 1; + fi + shift # past argument + shift # past value + ;; + -j|--jobs) + jobs="$2" + if [ x"$jobs" = x ]; then + echo "No argument given to '--jobs' ('-j')." + exit 1; + fi + shift # past argument + shift # past value + ;; + -e|--existing-conf) + existing_conf=1 + shift # past argument + ;; + + -h|-P|--help|--printparams) + help_print + exit 0 + ;; +# -V|--version) +# echo $version +# exit 0 +# ;; + *) # unknown option + cat <<EOF +Usage: $me [OPTION]... +'$1' isn't a recognized option. Aborted. + +Note that for this script, option names (short or long format) and values +must be separated by atleast one white-space character and MUST NOT have +an '=' between them. +EOF + exit 1 + ;; + esac +done + + + + + # Important internal locations # ---------------------------- # @@ -141,17 +334,7 @@ printnotice=yes rewritepconfig=yes rewritegconfig=yes if [ -f $pconf ] || [ -f $glconf ]; then - - # If it already exits, see what the user wants to do. - echo "Atleast one local configuration file already exists." - echo - while [ "$userread" != "y" -a "$userread" != "n" ] - do - read -p"Re-write existing configuration file(s) (y/n)? " userread - done - - # Set `rewriteconfig'. - if [ $userread = "n" ]; then + if [ $existing_conf = 1 ]; then printnotice=no if [ -f $pconf ]; then rewritepconfig=no; fi if [ -f $glconf ]; then rewritegconfig=no; fi @@ -220,10 +403,10 @@ if [ $rewritepconfig = yes ]; then !!!!!!!!!!!!!!!!!!!!!! Warning !!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! -Couldn't find GNU Wget. It is used for downloading necessary programs and -data if they aren't already present in the specified directories. Therefore -the pipeline will crash if the necessary files are not already present on -the system. +Couldn't find GNU Wget, or cURL on this system. These programs are used for +downloading necessary programs and data if they aren't already present (in +directories that you can specify with this configure script). Therefore if +the necessary files are not present, the pipeline will crash. !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! @@ -258,30 +441,36 @@ build directory in a very different address from this one (one that can be deleted and has large volume), while having easy access to it from here. EOF - bdir="" + bdir= junkname=pure-junk-974adfkj38 while [ x$bdir == x ] do - # Ask the user. - read -p"Please enter the top build directory: " inbdir + # Ask the user (if not already set on the command-line). + if [ x"$build_dir" = x ]; then + read -p"Please enter the top build directory: " build_dir + fi # If it exists, see if we can write in it. If not, try making it. - if [ -d $inbdir ]; then - if mkdir $inbdir/$junkname 2> /dev/null; then - bdir=$(absolute_dir $inbdir) + if [ -d $build_dir ]; then + if mkdir $build_dir/$junkname 2> /dev/null; then + bdir=$(absolute_dir $build_dir) echo " -- Build directory: '$bdir'" - rm -rf $inbdir/$junkname + rm -rf $build_dir/$junkname else - echo " -- Can't write in '$inbdir'" + echo " -- Can't write in '$build_dir'" fi else - if mkdir $inbdir 2> /dev/null; then - bdir=$(absolute_dir $inbdir) + if mkdir $build_dir 2> /dev/null; then + bdir=$(absolute_dir $build_dir) echo " -- Build directory set to (the newly created): '$bdir'" else - echo " -- Can't create '$inbdir'" + echo " -- Can't create '$build_dir'" fi fi + + # Reset `build_dir' to blank, so it continues asking when the + # previous value wasn't usable. + build_dir= done fi @@ -291,12 +480,16 @@ fi # Input directory # --------------- -indir=$optionaldir +if [ x"$input_dir" = x ]; then + indir=$optionaldir +else + indir=$input_dir +fi wfpc2name=$(awk '!/^#/ && $1=="WFPC2IMAGE" {print $3}' $pdir/INPUTS.mk) wfpc2md5=$(awk '!/^#/ && $1=="WFPC2MD5" {print $3}' $pdir/INPUTS.mk) wfpc2size=$(awk '!/^#/ && $1=="WFPC2SIZE" {print $3}' $pdir/INPUTS.mk) wfpc2url=$(awk '!/^#/ && $1=="WFPC2URL" {print $3}' $pdir/INPUTS.mk) -if [ $rewritepconfig = yes ]; then +if [ $rewritepconfig = yes ] && [ x"$input_dir" = x ]; then cat <<EOF ---------------------------------- @@ -338,12 +531,16 @@ fi # Dependency tarball directory # ---------------------------- -if [ $rewritepconfig = yes ]; then +if [ x"$software_dir" = x ]; then ddir=$optionaldir +else + ddir=$software_dir +fi +if [ $rewritepconfig = yes ] && [ x"$software_dir" = x ]; then cat <<EOF --------------------------------------- -(OPTIONAL) Dependency tarball directory +(OPTIONAL) Software tarball directory --------------------------------------- To ensure an identical build environment, the pipeline will use its own @@ -369,9 +566,18 @@ fi # Memory mapping minimum size # --------------------------- -if [ $rewritegconfig = yes ]; then - defaultminmapsize=10000000000 - minmapsize=$defaultminmapsize +# +# This option is specific to GNU Astronomy Utilities. It is primarily +# included here as a demonstration option for software that need special +# local settings (that are irrelevant to their processing, but necessary to +# set based on local settings). If you do not use Gnuastro, please remove +# this option from this script. +if [ x"$in_minmapsize" = x ]; then + minmapsize=10000000000 +else + minmapsize=$in_minmapsize +fi +if [ $rewritegconfig = yes ] && [ $in_minmapsize = 0 ]; then cat <<EOF --------------------------- @@ -738,13 +944,21 @@ fi # Build Basic dependencies # ------------------------ # -# Since the system might not have GNU Coreutils at this stage, we'll just -# default to 4 threads if the actual number isn't found. This is because -# some versions of Make complain about not having enough 'pipe' (memory) on -# some systems. After some searching, I found out its because of too many -# threads. -if which nproc > /dev/null 2>/dev/null; then numthreads=$(nproc --all); -else numthreads=1; +# Since the system might not have GNU Make at this stage, and other Make +# implementations can't deal with parallel build properly, we'll just +# default to 1 thread. This is because some versions of Make complain about +# not having enough 'pipe' (memory) on some systems. After some searching, +# I found out its because of too many threads. GNU Make will be present on +# GNU systems (that have `nproc', part of GNU Coreutils). So to simplify +# the test for GNU Make, we'll just try running `nproc'. +if which nproc > /dev/null 2>/dev/null; then + if [ $jobs = 0 ]; then + numthreads=$(nproc --all); + else + numthreads=$jobs + fi +else + numthreads=1; fi make -f reproduce/src/make/dependencies-basic.mk \ rpath_command=$rpath_command \ |