git: 9b044f5d9ebc - main - biology/ddocent: Remove expired port
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Date: Wed, 30 Sep 2026 21:29:53 UTC
The branch main has been updated by rene:
URL: https://cgit.FreeBSD.org/ports/commit/?id=9b044f5d9ebce50ffe459b5249619856a6e6f9f9
commit 9b044f5d9ebce50ffe459b5249619856a6e6f9f9
Author: Rene Ladan <rene@FreeBSD.org>
AuthorDate: 2026-09-30 21:29:47 +0000
Commit: Rene Ladan <rene@FreeBSD.org>
CommitDate: 2026-09-30 21:29:47 +0000
biology/ddocent: Remove expired port
2026-09-30 biology/ddocent: No apparent interest, unable to maintain
---
MOVED | 1 +
biology/Makefile | 1 -
biology/ddocent/Makefile | 67 ----
biology/ddocent/distinfo | 3 -
biology/ddocent/files/ddocent-assembly-test | 366 ---------------------
.../ddocent/files/ddocent-assembly-test-cleanup | 8 -
biology/ddocent/files/patch-dDocent | 73 ----
.../ddocent/files/patch-scripts_ReferenceOpt.sh | 11 -
biology/ddocent/pkg-descr | 5 -
biology/ddocent/pkg-plist | 16 -
10 files changed, 1 insertion(+), 550 deletions(-)
diff --git a/MOVED b/MOVED
index f0ef1a5a10a3..dfb1c6ca9aa1 100644
--- a/MOVED
+++ b/MOVED
@@ -5680,3 +5680,4 @@ net-im/vesktop||2026-09-30|Has expired: Depends on expired devel/electron40
devel/electron40||2026-09-30|Has expired: EOLed upstream, switch to newer version
devel/lnphost||2026-09-30|Has expired: Deprecated upstream: Consider porting brickOS-bibo as a replacement
german/eric6||2026-09-30|Has expired: Depends on deprecated Qt5 WebEngine
+biology/ddocent||2026-09-30|Has expired: No apparent interest, unable to maintain
diff --git a/biology/Makefile b/biology/Makefile
index 1c0e65aeba22..f2f831af8e5b 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -44,7 +44,6 @@
SUBDIR += coverm
SUBDIR += cufflinks
SUBDIR += cytoscape
- SUBDIR += ddocent
SUBDIR += diamond
SUBDIR += dsr-pdb
SUBDIR += edlib
diff --git a/biology/ddocent/Makefile b/biology/ddocent/Makefile
deleted file mode 100644
index 535b0f270ffb..000000000000
--- a/biology/ddocent/Makefile
+++ /dev/null
@@ -1,67 +0,0 @@
-PORTNAME= dDocent
-DISTVERSIONPREFIX= v
-DISTVERSION= 2.7.8
-PORTREVISION= 5
-CATEGORIES= biology java perl5 python
-
-MAINTAINER= ports@FreeBSD.org
-COMMENT= Bash pipeline for RAD sequencing
-WWW= http://ddocent.com
-
-LICENSE= MIT
-
-DEPRECATED= No apparent interest, unable to maintain
-EXPIRATION_DATE=2026-09-30
-
-RUN_DEPENDS= mawk>=0:lang/mawk \
- gawk>=0:lang/gawk \
- coreutils>=0:sysutils/coreutils \
- gnuplot>=0:math/gnuplot \
- parallel>=0:sysutils/parallel \
- bash:shells/bash \
- bwa>=0.7.13:biology/bwa \
- cd-hit>=0:biology/cd-hit \
- samtools>=1.3:biology/samtools \
- vcftools>=0.1.15:biology/vcftools \
- trimmomatic>=0:biology/trimmomatic \
- bamtools>=0:biology/bamtools \
- stacks>=0:biology/stacks \
- rainbow>=0:biology/rainbow \
- trimadap>=0:biology/trimadap \
- seqtk>=0:biology/seqtk \
- bedtools>=2.26.0:biology/bedtools \
- pear-merger>=0:biology/pear-merger \
- vcflib>=0:biology/vcflib \
- freebayes:biology/freebayes \
- fastp:biology/fastp
-
-USES= java perl5 python shebangfix
-USE_GITHUB= yes
-
-SHEBANG_FILES= dDocent scripts/*.sh scripts/*.pl scripts/dDocent_filters
-GH_ACCOUNT= jpuritz
-
-NO_BUILD= yes
-NO_ARCH= yes
-
-do-install:
- @${MKDIR} ${STAGEDIR}${PREFIX}/bin
- ${INSTALL_SCRIPT} \
- ${WRKSRC}/dDocent \
- ${WRKSRC}/*.sh \
- ${FILESDIR}/ddocent-assembly-test \
- ${FILESDIR}/ddocent-assembly-test-cleanup \
- ${WRKSRC}/scripts/*.sh \
- ${WRKSRC}/scripts/*.pl \
- ${WRKSRC}/scripts/dDocent_filters \
- ${STAGEDIR}${PREFIX}/bin
-
-# These are on top of patch-dDocent, so don't apply them within the source
-# tree, or they'll get picked up by patch generators, and hard-code PREFIX.
-post-install:
- @${REINPLACE_CMD} -i '' \
- -e 's|SHELL=bash|SHELL=${LOCALBASE}/bin/bash|g' \
- -e 's|python|${PYTHON_CMD}|g' \
- ${STAGEDIR}${PREFIX}/bin/dDocent
-
-.include <bsd.port.mk>
diff --git a/biology/ddocent/distinfo b/biology/ddocent/distinfo
deleted file mode 100644
index addc264a5dd5..000000000000
--- a/biology/ddocent/distinfo
+++ /dev/null
@@ -1,3 +0,0 @@
-TIMESTAMP = 1556888100
-SHA256 (jpuritz-dDocent-v2.7.8_GH0.tar.gz) = 02aa297f602b55587782c959379cada8d8b0570973da75eb9f5786089a3ed485
-SIZE (jpuritz-dDocent-v2.7.8_GH0.tar.gz) = 345571
diff --git a/biology/ddocent/files/ddocent-assembly-test b/biology/ddocent/files/ddocent-assembly-test
deleted file mode 100644
index 7696b900cf04..000000000000
--- a/biology/ddocent/files/ddocent-assembly-test
+++ /dev/null
@@ -1,366 +0,0 @@
-#!/usr/bin/env bash
-
-set -e
-
-##########################################################################
-# Function description:
-# Pause until user presses return
-##########################################################################
-
-pause()
-{
- local junk
-
- printf "Press return to continue..."
- read junk
-}
-
-
-##########################################################################
-# Not necessary if invoking scripts with "bash script-name" as shown
-# in the dDocent tutorial, but supplied for completeness. Tutorial
-# scripts have also been patched upstream to usr /usr/bin/env, but
-# we won't assume they'll all stay that way.
-##########################################################################
-
-fix_bash_path()
-{
- # Don't echo these commands
- { set +x; } 2>/dev/null
- if [ $# != 1 ]; then
- printf "Usage: $0 script\n"
- exit 1
- fi
- sed -i.bak -e "s|#!/bin/bash|#!/usr/bin/env bash|g" $1
- set -x
-}
-
-
-##########################################################################
-# Main
-##########################################################################
-
-##########################################################################
-# Workarounds for running dDocent from FreeBSD ports and Pkgsrc.
-# Include this section in any scripts running dDocent commands.
-##########################################################################
-
-# Hack to allow remake_reference.sh, etc. to find trimmomatic.
-# trimmomatic.jar and adapter files are not an executables and should not
-# be in PATH according to filesystem hierarchy standards, but the dDocent
-# scripts are coded to look for them there, because that's how dDocent
-# installs the bundled Trimmomatic.
-if [ -e /usr/local/share/java/classes/trimmomatic.jar ]; then
- export PATH=${PATH}:/usr/local/share/java/classes:/usr/local/share/trimmomatic/adapters
-elif [ -e $PKGSRC/lib/java/trimmomatic.jar ]; then
- export PATH=${PATH}:$PKGSRC/lib/java:$PKGSRC/share/trimmomatic/adapters
-else
- printf "Error: Trimmomatic is not installed in a known location.\n" >> /dev/stderr
-fi
-
-if ! pwd | fgrep dDocent-test; then
- mkdir -p dDocent-test
- cd dDocent-test
-fi
-
-# remake_reference.sh and some other scripts use GNU extensions in awk
-# commands. Trick systems into using gawk to get around this without
-# having to patch every script.
-mkdir -p ddocent-bin
-ln -sf `which gawk` ddocent-bin/awk
-ln -sf `which python2.7` ddocent-bin/python
-export PATH=`pwd`/ddocent-bin:$PATH
-
-##########################################################################
-# Actual dDocent commands below
-##########################################################################
-
-##########################################################################
-# Command sequence from the dDocent tutorial on Github. See link below.
-##########################################################################
-
-cat << EOM
-
-This script runs the test commands described at
-
-http://ddocent.com/assembly
-
-You may want to follow along on this web page as the script runs. It will
-pause after each step to allow checking the output.
-
-EOM
-pause
-
-mkdir -p Data
-cd Data
-
-printf "Downloading and unpacking data.zip...\n"
-if [ -e data.zip ]; then
- mv data.zip /tmp/dDocent-data.zip
- rm -rf *
- mv /tmp/dDocent-data.zip data.zip
-else
- rm -rf *
- curl --insecure -L -o data.zip \
- 'https://www.dropbox.com/s/t09xjuudev4de72/data.zip?dl=0'
-fi
-
-# Hack: current data.zip contains data.zip. ??!
-if [ ! -e simRRLs2.py ]; then
- yes | unzip data.zip || true
-fi
-ls -l
-pause
-
-set -x
-head SimRAD.barcodes
-{ set +x; } 2>/dev/null
-pause
-
-set -x
-cut -f2 SimRAD.barcodes > barcodes
-head barcodes
-{ set +x; } 2>/dev/null
-pause
-
-set -x
-process_radtags -1 SimRAD_R1.fastq.gz -2 SimRAD_R2.fastq.gz -b barcodes \
- -e ecoRI --renz_2 mspI -r -i gzfastq
-ls | fgrep sample_ | head
-{ set +x; } 2>/dev/null
-pause
-
-set -x
-rm *rem*
-{ set +x; } 2>/dev/null
-pause
-
-{ set +x; } 2>/dev/null
-pause
-
-set -x
-Rename_for_dDocent.sh SimRAD.barcodes
-{ set +x; } 2>/dev/null
-
-set -x
-ls *.fq.gz
-{ set +x; } 2>/dev/null
-pause
-
-set -x
-ls *.F.fq.gz > namelist
-sed -i'' -e 's/.F.fq.gz//g' namelist
-AWK1='BEGIN{P=1}{if(P==1||P==2){gsub(/^[@]/,">");print}; if(P==4)P=0; P++}'
-AWK2='!/>/'
-AWK3='!/NNN/'
-PERLT='while (<>) {chomp; $z{$_}++;} while(($k,$v) = each(%z)) {print "$v\t$k\n";}'
-
-cat namelist | parallel --no-notice -j 8 "zcat {}.F.fq.gz | mawk '$AWK1' | mawk '$AWK2' > {}.forward"
-cat namelist | parallel --no-notice -j 8 "zcat {}.R.fq.gz | mawk '$AWK1' | mawk '$AWK2' > {}.reverse"
-cat namelist | parallel --no-notice -j 8 "paste -d '-' {}.forward {}.reverse | mawk '$AWK3' | sed 's/-/NNNNNNNNNN/' | perl -e '$PERLT' > {}.uniq.seqs"
-{ set +x; } 2>/dev/null
-pause
-
-set -x
-cat *.uniq.seqs > uniq.seqs
-for i in {2..20};
-do
-echo $i >> pfile
-done
-cat pfile | parallel --no-notice \
- "echo -n {}xxx && mawk -v x={} '\$1 >= x' uniq.seqs | wc -l" \
- | mawk '{gsub("xxx","\t",$0); print;}'| sort -g > uniqseq.data
-rm pfile
-{ set +x; } 2>/dev/null
-pause
-
-set -x
-more uniqseq.data
-{ set +x; } 2>/dev/null
-pause
-
-set -x
-gnuplot << \EOF
-set terminal dumb size 80, 30
-set autoscale
-set xrange [2:20]
-unset label
-set title "Number of Unique Sequences with More than X Coverage (Counted within individuals)"
-set xlabel "Coverage"
-set ylabel "Number of Unique Sequences"
-plot 'uniqseq.data' with lines notitle
-pause -1
-EOF
-{ set +x; } 2>/dev/null
-pause
-
-set -x
-parallel --no-notice -j 8 mawk -v x=4 \''$1 >= x'\' ::: *.uniq.seqs | cut -f2 | perl -e 'while (<>) {chomp; $z{$_}++;} while(($k,$v) = each(%z)) {print "$v\t$k\n";}' > uniqCperindv
-wc -l uniqCperindv
-{ set +x; } 2>/dev/null
-pause
-
-set -x
-for ((i = 2; i <= 10; i++));
-do
-echo $i >> ufile
-done
-
-cat ufile | parallel --no-notice "echo -n {}xxx && mawk -v x={} '\$1 >= x' uniqCperindv | wc -l" | mawk '{gsub("xxx","\t",$0); print;}'| sort -g > uniqseq.peri.data
-rm ufile
-{ set +x; } 2>/dev/null
-pause
-
-set -x
-gnuplot << \EOF
-set terminal dumb size 80, 30
-set autoscale
-unset label
-set title "Number of Unique Sequences present in more than X Individuals"
-set xlabel "Number of Individuals"
-set ylabel "Number of Unique Sequences"
-plot 'uniqseq.peri.data' with lines notitle
-pause -1
-EOF
-{ set +x; } 2>/dev/null
-pause
-
-set -x
-mawk -v x=4 '$1 >= x' uniqCperindv > uniq.k.4.c.4.seqs
-wc -l uniq.k.4.c.4.seqs
-{ set +x; } 2>/dev/null
-pause
-
-set -x
-cut -f2 uniq.k.4.c.4.seqs > totaluniqseq
-mawk '{c= c + 1; print ">Contig_" c "\n" $1}' totaluniqseq > uniq.fasta
-{ set +x; } 2>/dev/null
-pause
-
-set -x
-sed -e 's/NNNNNNNNNN/\t/g' uniq.fasta | cut -f1 > uniq.F.fasta
-{ set +x; } 2>/dev/null
-pause
-
-set -x
-cd-hit-est -i uniq.F.fasta -o xxx -c 0.8 -T 0 -M 0 -g 1
-{ set +x; } 2>/dev/null
-pause
-
-set -x
-mawk '{if ($1 ~ /Cl/) clus = clus + 1; else print $3 "\t" clus}' xxx.clstr | sed 's/[>Contig_,...]//g' | sort -g -k1 > sort.contig.cluster.ids
-paste sort.contig.cluster.ids totaluniqseq > contig.cluster.totaluniqseq
-sort -k2,2 -g contig.cluster.totaluniqseq | sed -e 's/NNNNNNNNNN/\t/g' > rcluster
-{ set +x; } 2>/dev/null
-pause
-
-set -x
-head rcluster
-{ set +x; } 2>/dev/null
-pause
-
-set -x
-cut -f2 rcluster | uniq | wc -l
-{ set +x; } 2>/dev/null
-pause
-
-set -x
-rainbow div -i rcluster -o rbdiv.out
-{ set +x; } 2>/dev/null
-pause
-
-set -x
-rainbow div -i rcluster -o rbdiv.out -f 0.5 -K 10
-{ set +x; } 2>/dev/null
-pause
-
-set -x
-rainbow merge -o rbasm.out -a -i rbdiv.out
-{ set +x; } 2>/dev/null
-pause
-
-set -x
-rainbow merge -o rbasm.out -a -i rbdiv.out -r 2
-{ set +x; } 2>/dev/null
-pause
-
-# If missing fdesc mount for bash, <(echo "E") will not work
-# cat rbasm.out <(echo "E") |sed 's/[0-9]*:[0-9]*://g' | mawk ' {
-set -x
-echo "E" > endfile
-cat rbasm.out endfile |sed 's/[0-9]*:[0-9]*://g' | mawk ' {
-if (NR == 1) e=$2;
-else if ($1 ~/E/ && lenp > len1) {c=c+1; print ">dDocent_Contig_" e "\n" seq2 "NNNNNNNNNN" seq1; seq1=0; seq2=0;lenp=0;e=$2;fclus=0;len1=0;freqp=0;lenf=0}
-else if ($1 ~/E/ && lenp <= len1) {c=c+1; print ">dDocent_Contig_" e "\n" seq1; seq1=0; seq2=0;lenp=0;e=$2;fclus=0;len1=0;freqp=0;lenf=0}
-else if ($1 ~/C/) clus=$2;
-else if ($1 ~/L/) len=$2;
-else if ($1 ~/S/) seq=$2;
-else if ($1 ~/N/) freq=$2;
-else if ($1 ~/R/ && $0 ~/0/ && $0 !~/1/ && len > lenf) {seq1 = seq; fclus=clus;lenf=len}
-else if ($1 ~/R/ && $0 ~/0/ && $0 ~/1/) {seq1 = seq; fclus=clus; len1=len}
-else if ($1 ~/R/ && $0 ~!/0/ && freq > freqp && len >= lenp || $1 ~/R/ && $0 ~!/0/ && freq == freqp && len > lenp) {seq2 = seq; lenp = len; freqp=freq}
-}' > rainbow.fasta
-{ set +x; } 2>/dev/null
-pause
-
-set -x
-cd-hit-est -i rainbow.fasta -o referenceRC.fasta -M 0 -T 0 -c 0.9
-{ set +x; } 2>/dev/null
-pause
-
-remake_reference.sh 4 4 0.90 PE 2
-{ set +x; } 2>/dev/null
-pause
-
-ReferenceOpt.sh
-
-bash ReferenceOpt.sh 4 8 4 8 PE 16
-{ set +x; } 2>/dev/null
-pause
-
-set -x
-bash remake_reference.sh 4 4 0.90 PE 2
-head reference.fasta
-{ set +x; } 2>/dev/null
-pause
-
-set -x
-wc -l reference.fasta
-{ set +x; } 2>/dev/null
-pause
-
-set -x
-mawk '/>/' reference.fasta | wc -l
-{ set +x; } 2>/dev/null
-pause
-
-set -x
-mawk '/^NAATT.*N*.*CCGN$/' reference.fasta | wc -l
-grep '^NAATT.*N*.*CCGN$' reference.fasta | wc -l
-{ set +x; } 2>/dev/null
-pause
-
-printf "Bonus Section: Optimize reference assemblies? (takes a long time) y/[n] "
-read bonus
-if [ 0$bonus = 0y ]; then
- set -x
- { set +x; } 2>/dev/null
- printf "Running dDocent to trim reads.\n"
- pause
- set -x
- cat << EOM | dDocent || true
-yes
-8
-10g
-yes
-no
-no
-no
-bacon@uwm.edu
-EOM
- RefMapOpt.sh 4 8 4 8 0.9 64 PE
- { set +x; } 2>/dev/null
- pause
- more mapping.results
- pause
-fi
diff --git a/biology/ddocent/files/ddocent-assembly-test-cleanup b/biology/ddocent/files/ddocent-assembly-test-cleanup
deleted file mode 100644
index 4189b3bb0355..000000000000
--- a/biology/ddocent/files/ddocent-assembly-test-cleanup
+++ /dev/null
@@ -1,8 +0,0 @@
-#!/bin/sh -e
-
-if pwd | fgrep dDocent-test; then
- rm -rf .*.bak Data ddocent-bin
-else
- printf "$0 can only be run in a dDocent-test directory.\n"
- exit 1
-fi
diff --git a/biology/ddocent/files/patch-dDocent b/biology/ddocent/files/patch-dDocent
deleted file mode 100644
index 1513c4138ef2..000000000000
--- a/biology/ddocent/files/patch-dDocent
+++ /dev/null
@@ -1,73 +0,0 @@
---- dDocent.orig 2019-05-03 12:59:20 UTC
-+++ dDocent
-@@ -1,5 +1,6 @@
- #!/usr/local/bin/bash
- export LC_ALL=en_US.UTF-8
-+# GNU Parallel uses $SHELL and has issues with [t]csh
- export SHELL=bash
-
- ##########dDocent##########
-@@ -83,7 +84,7 @@ VCFTV=$(vcftools | grep VCF | grep -oh '[0-9]*[a-z]*)$
- elif [ "$VCFTV" -ge "12" ]; then
- VCFGTFLAG="--max-missing"
- fi
--BWAV=$(bwa 2>&1 | mawk '/Versi/' | sed 's/Version: //g' | sed 's/0.7.//g' | sed 's/-.*//g' | cut -c 1-2)
-+BWAV=$(bwa 2>&1 | mawk '/Versi/' | sed 's/Version: //g' | sed 's/0.7.//g' | sed 's/a*-.*//g')
- if [ "$BWAV" -lt "13" ]; then
- echo "The version of bwa installed in your" '$PATH' "is not optimized for dDocent."
- echo "Please install at least version 0.7.13"
-@@ -481,7 +482,7 @@ if [ "$SNP" != "no" ]; then
- if ( cov < cutoff) {x="mapped."i".bed";print $1"\t"$2"\t"$3 > x}
- else {i=i+1; x="mapped."i".bed"; print $1"\t"$2"\t"$3 > x; cov=0}
- }'
-- ls mapped.*.bed | sed 's/mapped.//g' | sed 's/.bed//g' | shuf | parallel --bar --halt now,fail=1 --env call_genos2 --memfree $MAXMemory -j 4 --no-notice "call_genos2 {} 2> /dev/null"
-+ ls mapped.*.bed | sed 's/mapped.//g' | sed 's/.bed//g' | gshuf | parallel --bar --halt now,fail=1 --env call_genos2 --memfree $MAXMemory -j 4 --no-notice "call_genos2 {} 2> /dev/null"
- if [ -f "freebayes.error" ]; then
- echo -e "\n\n\nFreeBayes has failed when trying to finish a previously failed instance. Memory and processor settings need to be drastically reconfigured"
- ERROR3=1
-@@ -505,7 +506,7 @@ if [ "$SNP" != "no" ]; then
-
- rm freebayes.error freebayes.log &> /dev/null
-
-- ls mapped.*.bed | sed 's/mapped.//g' | sed 's/.bed//g' | shuf | parallel --bar --halt now,fail=5 --env call_genos --memfree $MAXMemory -j $NUMProc --no-notice "call_genos {} 2> /dev/null"
-+ ls mapped.*.bed | sed 's/mapped.//g' | sed 's/.bed//g' | gshuf | parallel --bar --halt now,fail=5 --env call_genos --memfree $MAXMemory -j $NUMProc --no-notice "call_genos {} 2> /dev/null"
-
-
- if [ -f "freebayes.error" ]; then
-@@ -541,7 +542,7 @@ if [ "$SNP" != "no" ]; then
- echo "Using FreeBayes to call SNPs again"
- NumP=$(( $NUMProc / 4 ))
- NumP=$(( $NumP * 3 ))
-- ls mapped.*.bed | sed 's/mapped.//g' | sed 's/.bed//g' | shuf | parallel --bar --halt now,fail=5 --env call_genos --memfree $MAXMemory -j $NumP --no-notice "call_genos {} 2> /dev/null"
-+ ls mapped.*.bed | sed 's/mapped.//g' | sed 's/.bed//g' | gshuf | parallel --bar --halt now,fail=5 --env call_genos --memfree $MAXMemory -j $NumP --no-notice "call_genos {} 2> /dev/null"
- fi
- fi
-
-@@ -575,7 +576,7 @@ if [ "$SNP" != "no" ]; then
- NumP=$(( $NumP / 4 ))
- NumP=$(( $NumP * 3 ))
- echo "Using FreeBayes to call SNPs again"
-- ls mapped.*.bed | sed 's/mapped.//g' | sed 's/.bed//g' | shuf | parallel --bar --halt now,fail=1 --env call_genos --memfree $MAXMemory -j $NumP --no-notice "call_genos {} 2> /dev/null"
-+ ls mapped.*.bed | sed 's/mapped.//g' | sed 's/.bed//g' | gshuf | parallel --bar --halt now,fail=1 --env call_genos --memfree $MAXMemory -j $NumP --no-notice "call_genos {} 2> /dev/null"
- fi
- fi
-
-@@ -1132,6 +1133,8 @@ fi
-
- if [[ "$OSTYPE" == "darwin"* ]]; then
- NUMProc=( `sysctl hw.ncpu | cut -f2 -d " " `)
-+elif [[ "$OSTYPE" == "FreeBSD" ]]; then
-+ NUMProc=( `sysctl -n hw.ncpu` )
- else
- NUMProc=( `grep -c ^processor /proc/cpuinfo 2> /dev/null` )
- fi
-@@ -1154,6 +1157,9 @@ fi
- #Tries to get maximum system memory, if not asks user
- if [[ "$OSTYPE" == "darwin"* ]]; then
- MAXMemory=0
-+elif [[ "$OSTYPE" == "FreeBSD" ]]; then
-+ MAXMemory=`sysctl -n hw.realmem`
-+ MAXMemory=$((MAXMemory / 1073741824))G
- else
- MAXMemory=$(($(grep -Po '(?<=^MemTotal:)\s*[0-9]+' /proc/meminfo | tr -d " ") / 1048576))
-
diff --git a/biology/ddocent/files/patch-scripts_ReferenceOpt.sh b/biology/ddocent/files/patch-scripts_ReferenceOpt.sh
deleted file mode 100644
index 784cfa5c9c6d..000000000000
--- a/biology/ddocent/files/patch-scripts_ReferenceOpt.sh
+++ /dev/null
@@ -1,11 +0,0 @@
---- scripts/ReferenceOpt.sh.orig 2019-05-03 12:58:47 UTC
-+++ scripts/ReferenceOpt.sh
-@@ -400,7 +400,7 @@ done
-
- cut -f4 -d " " kopt.data > plot.kopt.data
- gnuplot << \EOF
--set terminal dumb size 120, 30
-+set terminal dumb size 80, 30
- set autoscale
- unset label
- set title "Histogram of number of reference contigs"
diff --git a/biology/ddocent/pkg-descr b/biology/ddocent/pkg-descr
deleted file mode 100644
index a74299d2a8d0..000000000000
--- a/biology/ddocent/pkg-descr
+++ /dev/null
@@ -1,5 +0,0 @@
-dDocent is simple bash wrapper to QC, assemble, map, and call SNPs from almost
-any kind of RAD sequencing. If you have a reference already, dDocent can be
-used to call SNPs from almost any type of NGS data set. It is designed to run
-on Linux based machines with large memory capacity and multiple processing
-cores, and it can be modified for use on HPC.
diff --git a/biology/ddocent/pkg-plist b/biology/ddocent/pkg-plist
deleted file mode 100644
index 7f7306525447..000000000000
--- a/biology/ddocent/pkg-plist
+++ /dev/null
@@ -1,16 +0,0 @@
-bin/ErrorCount.sh
-bin/RefMapOpt.sh
-bin/ReferenceOpt.sh
-bin/Rename_SequenceFiles.sh
-bin/Rename_for_dDocent.sh
-bin/Rename_for_dDocent_with-INDEX.sh
-bin/dDocent
-bin/dDocent_filters
-bin/dDocent_ngs.sh
-bin/ddocent-assembly-test
-bin/ddocent-assembly-test-cleanup
-bin/filter_hwe_by_pop.pl
-bin/filter_missing_ind.sh
-bin/pop_missing_filter.sh
-bin/remake_reference.sh
-bin/remove.bad.hap.loci.sh