haplohseq: Remove: Committed and no active development

[Jason W. Bacon (via pkgsrc-wip) <commit-notify%pkgsrc.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Sat Oct 12 07:22:32 2024 -0500
Changeset:	6ea6de3660c3a28522dd53e928c76f349a2d605a

Modified Files:
	Makefile
Removed Files:
	haplohseq/DESCR
	haplohseq/Makefile
	haplohseq/PLIST
	haplohseq/distinfo
	haplohseq/files/haplohseq-example.in

Log Message:
haplohseq: Remove: Committed and no active development

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=6ea6de3660c3a28522dd53e928c76f349a2d605a

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

diffstat:
 Makefile                             |  1 -
 haplohseq/DESCR                      |  5 -----
 haplohseq/Makefile                   | 41 ------------------------------------
 haplohseq/PLIST                      |  9 --------
 haplohseq/distinfo                   |  5 -----
 haplohseq/files/haplohseq-example.in | 37 --------------------------------
 6 files changed, 98 deletions(-)

diffs:
diff --git a/Makefile b/Makefile
index 2c12e31447..5ebd8afdef 100644
--- a/Makefile
+++ b/Makefile
@@ -1450,7 +1450,6 @@ SUBDIR+=	hal
 SUBDIR+=	halfempty
 SUBDIR+=	hammer
 SUBDIR+=	hanazono-ttf
-SUBDIR+=	haplohseq
 SUBDIR+=	hare
 SUBDIR+=	harec
 SUBDIR+=	harmony
diff --git a/haplohseq/DESCR b/haplohseq/DESCR
deleted file mode 100644
index 0b2c07f64d..0000000000
--- a/haplohseq/DESCR
+++ /dev/null
@@ -1,5 +0,0 @@
-Haplohseq identifies regions of allelic imbalance (AI) in sequencing
-data obtained from impure samples where AI events exist in a
-potentially low proportion of cells in the sample.  Input to the
-software includes a VCF file of genotypes and estimated phased
-genotypes.
diff --git a/haplohseq/Makefile b/haplohseq/Makefile
deleted file mode 100644
index 66232fc3fd..0000000000
--- a/haplohseq/Makefile
+++ /dev/null
@@ -1,41 +0,0 @@
-# $NetBSD$
-
-DISTNAME=	haplohseq-0.1.2.2
-CATEGORIES=	biology
-MASTER_SITES=	${MASTER_SITE_GITHUB:=outpaddling/}
-GITHUB_PROJECT=	haplohseq
-GITHUB_TAG=	e4892945eced075a5bb98f208786cdf85eb3d82a
-
-OWNER=		bacon%NetBSD.org@localhost
-HOMEPAGE=	https://sites.google.com/site/integrativecancergenomics/software/haplohseq
-COMMENT=	Identify regions of allelic imbalance
-LICENSE=	mit
-
-SUBST_CLASSES+=		test
-SUBST_STAGE.test=	pre-configure
-SUBST_SED.test=		-e 's|\.\./haplohseq|haplohseq|'
-SUBST_SED.test+=	-e 's|python|${PYTHONBIN}|'
-SUBST_FILES.test=	example/example_run.sh
-
-USE_LANGUAGES=	c c++
-USE_TOOLS+=	gmake pax
-MAKE_FILE=	makefile
-
-EXAMPLESDIR=	${PREFIX}/share/examples/haplohseq
-
-INSTALLATION_DIRS=	share/examples/haplohseq
-
-post-patch:
-	${SED} -e "s|%%EXAMPLESDIR%%|${EXAMPLESDIR}|" \
-		${FILESDIR}/haplohseq-example.in > ${WRKDIR}/haplohseq-example
-
-post-install:
-	${INSTALL_SCRIPT} ${WRKDIR}/haplohseq-example ${DESTDIR}${PREFIX}/bin
-	(cd ${WRKSRC} && pax -rw example ldmap scripts ${DESTDIR}${EXAMPLESDIR})
-
-do-test:
-	(cd ${WRKSRC}/build/test && ${SH} ${WRKSRC}/src/test/run-tests)
-
-.include "../../devel/boost-libs/buildlink3.mk"
-.include "../../lang/python/application.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/haplohseq/PLIST b/haplohseq/PLIST
deleted file mode 100644
index fca48e502f..0000000000
--- a/haplohseq/PLIST
+++ /dev/null
@@ -1,9 +0,0 @@
-@comment $NetBSD$
-bin/haplohseq
-bin/haplohseq-example
-share/examples/haplohseq/example/example_input/tumor_exome.vcf
-share/examples/haplohseq/example/example_run.sh
-share/examples/haplohseq/ldmap/hg19.exome.ldmap
-share/examples/haplohseq/scripts/haplohseq_plot.R
-share/examples/haplohseq/scripts/ldmap.py
-share/examples/haplohseq/scripts/simple_phaser.py
diff --git a/haplohseq/distinfo b/haplohseq/distinfo
deleted file mode 100644
index f5c0aef75a..0000000000
--- a/haplohseq/distinfo
+++ /dev/null
@@ -1,5 +0,0 @@
-$NetBSD$
-
-BLAKE2s (haplohseq-0.1.2.2-e4892945eced075a5bb98f208786cdf85eb3d82a.tar.gz) = dbd48a3854197dbf71189a56bdd0075ce8e6a78bca92b58673ae2770eae3daa6
-SHA512 (haplohseq-0.1.2.2-e4892945eced075a5bb98f208786cdf85eb3d82a.tar.gz) = 8de2c75d4e443eab79f520d43bd2e0c238dca798bf53cc7821d6fe8bdf94f3d3ae3b9319b9b21aae10dab6b52e5c1e81380380c456a240bfcfa8863b83c5feff
-Size (haplohseq-0.1.2.2-e4892945eced075a5bb98f208786cdf85eb3d82a.tar.gz) = 12085199 bytes
diff --git a/haplohseq/files/haplohseq-example.in b/haplohseq/files/haplohseq-example.in
deleted file mode 100644
index 0cb2a5bee1..0000000000
--- a/haplohseq/files/haplohseq-example.in
+++ /dev/null
@@ -1,37 +0,0 @@
-#!/bin/sh -e
-
-##########################################################################
-#   Script description:
-#       Run haplohseq example
-#
-#   https://sites.google.com/site/integrativecancergenomics/software/haplohseq
-#       
-#   History:
-#   Date        Name        Modification
-#   2019-11-13  Jason Bacon Begin
-##########################################################################
-
-usage()
-{
-    printf "Usage: $0 directory\n"
-    exit 1
-}
-
-
-##########################################################################
-#   Main
-##########################################################################
-
-if [ $# != 1 ]; then
-    usage
-fi
-
-dir="$1"
-
-if [ -e "$dir" ]; then
-    printf "'$dir' already exists.  Please remove it or specify another.\n"
-    exit 1
-fi
-cp -R %%EXAMPLESDIR%% "$dir"
-cd "$dir/example"
-sh ./example_run.sh