Better defaults / auto cpu ram

bin/shovill

@@ -13,7 +13,7 @@ use POSIX qw(strftime);
 
 # Globals
 my $EXE = basename($PROGRAM_NAME);
-my $VERSION = "1.0.7";
+my $VERSION = "1.0.8";
 my $AUTHOR = "Torsten Seemann";
 my $URL = "https://github.com/tseemann/shovill";
 my $BAM = "$EXE.bam";
@@ -28,7 +28,7 @@ my $KMER_READ_FRAC = 0.75;    # ensure max kmer below this prop of read length
 my $MIN_BQ = 3;               # for trimming and stats and pilon
 my $MIN_MQ = 60;              # for pilon
 my $MIN_FLASH_OVERLAP = 20;   # for stitching
-my $MIN_RAM_GB = 4;           # for all tools
+my $MIN_RAM_GB = 2;           # for all tools
 my $TRIMOPT = "ILLUMINACLIP:$ADAPTERS:1:30:11 LEADING:$MIN_BQ TRAILING:$MIN_BQ MINLEN:30 TOPHRED33";
 
 my @CMDLINE = ($0, @ARGV);    # save this for printing to log later
@@ -62,6 +62,10 @@ if ($ENV{TRAVIS} eq 'true') {
   delete $VERSION{'skesa'};
 }
 
+# Hardware stats
+my $CORES = num_cpus();
+my $MEMORY = avail_ram_gb();
+
 # Options
 my(@Options, $version,
              $outdir, $force, $cpus, $tmpdir, $keepfiles, $namefmt,
@@ -78,10 +82,6 @@ msg("Written by $AUTHOR");
 msg("Homepage is $URL");
 msg("Operating system is $OSNAME");
 msg("Perl version is $PERL_VERSION");
-
-# Hardware stats
-my $CORES = num_cpus();
-my $MEMORY = avail_ram_gb();
 msg("Machine has $CORES CPU cores and $MEMORY GB RAM");
 
 # Check options
@@ -689,8 +689,8 @@ sub setOptions {
     {OPT=>"keepfiles!", VAR=>\$keepfiles, DEFAULT=>0,    DESC=>"Keep intermediate files"},
     "RESOURCES",
     {OPT=>"tmpdir=s",   VAR=>\$tmpdir,    DEFAULT=>$ENV{TMPDIR} || '', DESC=>"Fast temporary directory"},
-    {OPT=>"cpus=i",     VAR=>\$cpus,      DEFAULT=>$ENV{SHOVILL_CPUS} || 8, DESC=>"Number of CPUs to use (0=ALL)"},
-    {OPT=>"ram=f",      VAR=>\$ram,       DEFAULT=>$ENV{SHOVILL_RAM} || 16,  DESC=>"Try to keep RAM usage below this many GB"},
+    {OPT=>"cpus=i",     VAR=>\$cpus,      DEFAULT=>$ENV{SHOVILL_CPUS} || $CORES, DESC=>"Number of CPUs to use (0=ALL)"},
+    {OPT=>"ram=f",      VAR=>\$ram,       DEFAULT=>$ENV{SHOVILL_RAM} || min(16,$MEMORY),  DESC=>"Try to keep RAM usage below this many GB"},
     "ASSEMBLER",
     {OPT=>"assembler=s",VAR=>\$assembler, DEFAULT=>$ENV{SHOVILL_ASSEMBLER} || 'spades', DESC=>"Assembler: ".join(' ', keys %ASSEMBLER) },
     {OPT=>"opts=s",     VAR=>\$opts,      DEFAULT=>'',   DESC=>"Extra assembler options in quotes eg. spades: \"--untrusted-contigs locus.fna\" ..."},

test/test.sh

@@ -14,7 +14,7 @@ $SHOVILL --version
 $SHOVILL --check
 $SHOVILL --help
 ! $SHOVILL --doesnotexist
-$SHOVILL --outdir "$OUTDIR" --R1 "$TESTDIR/R1.fq.gz" --R2 "$TESTDIR/R2.fq.gz" \
-	--ram 3 --cpus 8 --depth 25 --force
-grep '>' "$OUTDIR/contigs.fa"
 rm -frv "$OUTDIR"
+$SHOVILL --outdir "$OUTDIR" --R1 "$TESTDIR/R1.fq.gz" --R2 "$TESTDIR/R2.fq.gz" \
+	 --depth 25 --force --trim
+grep '>' "$OUTDIR/contigs.fa" | head