ddocent: Set SHELL to bash for consistent behavior from GNU parallel

[Jason W Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason W Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Sun Apr 15 07:02:46 2018 -0500
Changeset:	2ab2c057868ab5b075a607beeb0226c0f19647bf

Modified Files:
	ddocent/distinfo
	ddocent/patches/patch-dDocent

Log Message:
ddocent: Set SHELL to bash for consistent behavior from GNU parallel

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=2ab2c057868ab5b075a607beeb0226c0f19647bf

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 ddocent/distinfo              |  2 +-
 ddocent/patches/patch-dDocent | 24 +++++++++++++++++-------
 2 files changed, 18 insertions(+), 8 deletions(-)

diffs:
diff --git a/ddocent/distinfo b/ddocent/distinfo
index 4467da2f9b..34d882ca9d 100644
--- a/ddocent/distinfo
+++ b/ddocent/distinfo
@@ -4,4 +4,4 @@ SHA1 (dDocent-2.2.25.tar.gz) = 5bdb9419a7d6770114d1bb363fcf1af07d49190b
 RMD160 (dDocent-2.2.25.tar.gz) = a33107f9d3269f647f9970b0bfcd14e15bca9575
 SHA512 (dDocent-2.2.25.tar.gz) = d7ba86d363b50dba648bb7b26e4e3c0306b3b5735e9cdea95a8d00164e12649781f325ae3fe8fba14ed76fa6478ecdf3263b07002cd8df3067fb0359e657765a
 Size (dDocent-2.2.25.tar.gz) = 336804 bytes
-SHA1 (patch-dDocent) = 9505cfea35854ff83eefe7c16c59a03c362ed6b3
+SHA1 (patch-dDocent) = d81a3d26e7ea01305c29d79d4ee688dae9fdef34
diff --git a/ddocent/patches/patch-dDocent b/ddocent/patches/patch-dDocent
index 919767d8b6..a1e8b393da 100644
--- a/ddocent/patches/patch-dDocent
+++ b/ddocent/patches/patch-dDocent
@@ -1,10 +1,20 @@
 $NetBSD$
 
-# Locate tools installed via pkgsrc
+# Use pkgsrc trimmomatic path, support additional platforms
 
---- dDocent.orig	2018-03-06 14:22:03 UTC
+--- dDocent.orig	2017-11-29 17:09:13.000000000 +0000
 +++ dDocent
-@@ -27,15 +27,15 @@ do
+@@ -1,6 +1,9 @@
+ #!/usr/bin/env bash
+ export LC_ALL=en_US.UTF-8
+ 
++# GNU Parallel uses $SHELL and has issues with [t]csh
++export SHELL=%%PREFIX%%/bin/bash
++
+ ##########dDocent##########
+ VERSION='2.2.25'
+ #This script serves as an interactive bash wrapper to QC, assemble, map, and call SNPs from double digest RAD (SE or PE), ezRAD (SE or PE) data, or SE RAD data.
+@@ -27,15 +30,15 @@ do
  	fi
  done
  
@@ -24,7 +34,7 @@ $NetBSD$
  	else
      echo "The file listing adapters (included with trimmomatic) is not installed or is not in your" '$PATH'"."
      NUMDEP=$((NUMDEP + 1))
-@@ -80,6 +80,7 @@ FREEB=(`freebayes | grep -oh 'v[0-9].*' 
+@@ -80,6 +83,7 @@ FREEB=(`freebayes | grep -oh 'v[0-9].*'
          	exit 1
          fi         	
  VCFTV=$(vcftools | grep VCF | grep -oh '[0-9]*[a-z]*)$' | sed 's/[a-z)]//')
@@ -32,7 +42,7 @@ $NetBSD$
  	if [ "$VCFTV" -lt "10" ]; then
          	echo "The version of VCFtools installed in your" '$PATH' "is not optimized for dDocent."
          	echo "Please install at least version 0.1.11"
-@@ -89,7 +90,7 @@ VCFTV=$(vcftools | grep VCF | grep -oh '
+@@ -89,7 +93,7 @@ VCFTV=$(vcftools | grep VCF | grep -oh '
          elif [ "$VCFTV" -ge "12" ]; then
                  VCFGTFLAG="--max-missing"
  	fi
@@ -41,7 +51,7 @@ $NetBSD$
  	if [ "$BWAV" -lt "13" ]; then
          	echo "The version of bwa installed in your" '$PATH' "is not optimized for dDocent."
          	echo "Please install at least version 0.7.13"
-@@ -747,7 +748,14 @@ else
+@@ -747,7 +751,14 @@ else
  fi
  
  #Tries to get number of processors, if not asks user
@@ -57,7 +67,7 @@ $NetBSD$
  NUMProc=$(($NUMProc + 0)) 
  
  echo "dDocent detects $NUMProc processors available on this system."
-@@ -764,7 +772,15 @@ if [ $NUMProc -lt 1 ]; then
+@@ -764,7 +775,15 @@ if [ $NUMProc -lt 1 ]; then
  fi
  
  #Tries to get maximum system memory, if not asks user