Adding KRAKEN_NUM_THREADS support

CHANGELOG

@@ -7,7 +7,8 @@ v0.10.5-beta:
 * Included full sequence descriptions when using "--[un]classified-out"
 * Reduced memory usage of db_shrink (Build step 2 / kraken-build --shrink)
 * Reduced memory usage of db_sort (Build step 3)
-* Support added for KRAKEN_DB_PATH and KRAKEN_DEFAULT_DB env. variables
+* Support added for KRAKEN_NUM_THREADS, KRAKEN_DB_PATH, and KRAKEN_DEFAULT_DB
+  env. variables
 * Added kraken-translate for getting taxonomic names for each sequence
 
 v0.10.4-beta:

README

@@ -307,7 +307,7 @@ on the output of "kraken", like so:
   kraken-translate --db $DBNAME sequences.kraken > sequences.labels
 
 (The same database used to run kraken should be used to translate the
-output; see DATABASE ENVIRONMENT VARIABLES below for ways to reduce
+output; see KRAKEN ENVIRONMENT VARIABLES below for ways to reduce
 redundancy on the command line.)
 
 The file sequences.labels generated by the above example is a text file
@@ -638,13 +638,18 @@ in sensitivity that must be taken into account when deciding on the
 threshold to use for your own project.
 
 
-DATABASE ENVIRONMENT VARIABLES
+KRAKEN ENVIRONMENT VARIABLES
 ==============================
 
 The Kraken programs (with the exception of kraken-build) support the
-use of two environment variables to help in reducing command line
+use of some environment variables to help in reducing command line
 lengths:
 
+  - KRAKEN_NUM_THREADS: this variable is only used by "kraken"; if the
+    "--threads" option is not supplied to kraken, then the value of this
+    variable (if it is set) will be used as the number of threads to run
+    kraken.
+
   - KRAKEN_DB_PATH: much like the PATH variable is used for executables
     by your shell, KRAKEN_DB_PATH is a colon-separated list of directories
     that will be searched for the database you name if the named database

scripts/kraken

@@ -46,7 +46,7 @@ my $min_hits = 1;
 my $fasta_input = 0;
 my $fastq_input = 0;
 my $db_prefix;
-my $threads = 1;
+my $threads;
 my $preload = 0;
 my $gunzip = 0;
 my $bunzip2 = 0;
@@ -73,6 +73,10 @@ GetOptions(
   "bzip2-compressed" => \$bunzip2
 );
 
+if (! defined $threads) {
+  $threads = $ENV{"KRAKEN_NUM_THREADS"} || 1;
+}
+
 if (! @ARGV) {
   print STDERR "Need to specify input filenames!\n";
   usage();