From c5b92799b1a74511d8efb5dccc56adafd42ab113 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Sat, 24 May 2025 08:46:13 +0200
Subject: [PATCH] Detect number of cores

---
 data/cds/sp_chlorodb/.DS_Store | Bin 6148 -> 0 bytes
 detectors/cds/bin/go_cds.sh    |  10 ++++++++--
 2 files changed, 8 insertions(+), 2 deletions(-)
 delete mode 100644 data/cds/sp_chlorodb/.DS_Store

diff --git a/data/cds/sp_chlorodb/.DS_Store b/data/cds/sp_chlorodb/.DS_Store
deleted file mode 100644
index be8b350d5ff08759647a74402685afad60c471e5..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 6148
zcmeHKyK2Kw3_WU{66lh#<Nby73rtA%()>Va9O&R;sGHqee>+Ey78~QWLy$l^zUNAQ
zoZ-p>AiGPm1vUWIbVdAVn49ja&+IOk6;bpaO@C_NyRMyOE)!Z?;e-xfIFIWqG`OJ0
z_n3UZCo>zI(V`!3tni8#9I?gol<x6i+3lEKex2M&1yX@jAQeajZe9WQY_;{HW5!e<
z6-WjC6wvdb&=u>z!O@Nm1{(p06=^eG+blsWN)YS7!I2D2yp-sr5+jCqIr$QKb>QIW
z<&YRYB%UlWp@==5_b-+XsU0(>0;#}MfqP$WwErLI3-kZ9C|9XKDsWQ@NVPxicl@O2
zt+S8QUR&sI^j~AHr88J7CR!`zLR<0ED6i->_v^sH(aOnNIWd0(RF||=;6D_&0#9Km
AH~;_u

diff --git a/detectors/cds/bin/go_cds.sh b/detectors/cds/bin/go_cds.sh
index 144ea83..1895151 100755
--- a/detectors/cds/bin/go_cds.sh
+++ b/detectors/cds/bin/go_cds.sh
@@ -22,6 +22,12 @@
 THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
 source "${THIS_DIR}/../../../scripts/bash_init.sh"
 
+if [[ -z "$ANNOT_MAXCPU" ]] ; then
+  Threads=$(nproc)
+else
+  Threads=$ANNOT_MAXCPU
+fi
+
 needarg 1
 
 Fasta=$1; shift
@@ -74,7 +80,7 @@ if [[ "$cdsdetection_pass1" == "yes" ]] ; then
         echo tcsh -f $PROG_DIR/do_exonerate.csh Pass1 $Fasta $f $AnnotFile $DbRoot/models $temp
         done
     fi
-    done ) | parallel -j 8
+    done ) | parallel -j $Threads
 
     mv $temp/genome.cds.fasta $Genome.cds_pass1.fasta 
 fi
@@ -103,7 +109,7 @@ if [[ "$cdsdetection_pass3" == "yes" ]] ; then
           echo tcsh -f $PROG_DIR/do_exonerate.csh Pass3 $Fasta $f $AnnotFile $DbRoot/models $temp
         done
     fi
-    done) | parallel -j 8
+    done) | parallel -j $Threads
     mv $temp/genome.cds.fasta $Genome.cds_pass2.fasta 
 fi