CVS commit: pkgsrc/biology/haplohseq

["Jason Bacon" <bacon%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   bacon
Date:           Sat Oct 12 12:19:52 UTC 2024

Added Files:
        pkgsrc/biology/haplohseq: DESCR Makefile PLIST distinfo
        pkgsrc/biology/haplohseq/files: haplohseq-example.in

Log Message:
biology/haplohseq: Identify regions of allelic imbalance

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.


To generate a diff of this commit:
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/haplohseq/DESCR \
    pkgsrc/biology/haplohseq/Makefile pkgsrc/biology/haplohseq/PLIST \
    pkgsrc/biology/haplohseq/distinfo
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/haplohseq/files/haplohseq-example.in

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

Added files:

Index: pkgsrc/biology/haplohseq/DESCR
diff -u /dev/null pkgsrc/biology/haplohseq/DESCR:1.1
--- /dev/null   Sat Oct 12 12:19:52 2024
+++ pkgsrc/biology/haplohseq/DESCR      Sat Oct 12 12:19:51 2024
@@ -0,0 +1,5 @@
+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.
Index: pkgsrc/biology/haplohseq/Makefile
diff -u /dev/null pkgsrc/biology/haplohseq/Makefile:1.1
--- /dev/null   Sat Oct 12 12:19:52 2024
+++ pkgsrc/biology/haplohseq/Makefile   Sat Oct 12 12:19:51 2024
@@ -0,0 +1,41 @@
+# $NetBSD: Makefile,v 1.1 2024/10/12 12:19:51 bacon Exp $
+
+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"
Index: pkgsrc/biology/haplohseq/PLIST
diff -u /dev/null pkgsrc/biology/haplohseq/PLIST:1.1
--- /dev/null   Sat Oct 12 12:19:52 2024
+++ pkgsrc/biology/haplohseq/PLIST      Sat Oct 12 12:19:51 2024
@@ -0,0 +1,9 @@
+@comment $NetBSD: PLIST,v 1.1 2024/10/12 12:19:51 bacon Exp $
+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
Index: pkgsrc/biology/haplohseq/distinfo
diff -u /dev/null pkgsrc/biology/haplohseq/distinfo:1.1
--- /dev/null   Sat Oct 12 12:19:52 2024
+++ pkgsrc/biology/haplohseq/distinfo   Sat Oct 12 12:19:51 2024
@@ -0,0 +1,5 @@
+$NetBSD: distinfo,v 1.1 2024/10/12 12:19:51 bacon Exp $
+
+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

Index: pkgsrc/biology/haplohseq/files/haplohseq-example.in
diff -u /dev/null pkgsrc/biology/haplohseq/files/haplohseq-example.in:1.1
--- /dev/null   Sat Oct 12 12:19:52 2024
+++ pkgsrc/biology/haplohseq/files/haplohseq-example.in Sat Oct 12 12:19:51 2024
@@ -0,0 +1,37 @@
+#!/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