CVS commit: pkgsrc/biology/bio-mocha

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

Module Name:    pkgsrc
Committed By:   bacon
Date:           Fri Oct 11 22:44:39 UTC 2024

Added Files:
        pkgsrc/biology/bio-mocha: DESCR Makefile PLIST distinfo
        pkgsrc/biology/bio-mocha/patches: patch-Makefile

Log Message:
biology/bio-mocha: Bcftools plugin for mCA analysis

MoChA is a bcftools plugin released under the MIT license for mosaic
chromosomal alteration detection and analysis from DNA microarray or
whole genome sequence data. It can be used both with Illumina and
Affymetrix data. It can also be used for detection of germline copy
number variants. Data can be prepared in usable file formats using the
gtc2vcf plugin.


To generate a diff of this commit:
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/bio-mocha/DESCR \
    pkgsrc/biology/bio-mocha/Makefile pkgsrc/biology/bio-mocha/PLIST \
    pkgsrc/biology/bio-mocha/distinfo
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/bio-mocha/patches/patch-Makefile

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

Added files:

Index: pkgsrc/biology/bio-mocha/DESCR
diff -u /dev/null pkgsrc/biology/bio-mocha/DESCR:1.1
--- /dev/null   Fri Oct 11 22:44:39 2024
+++ pkgsrc/biology/bio-mocha/DESCR      Fri Oct 11 22:44:39 2024
@@ -0,0 +1,6 @@
+MoChA is a bcftools plugin released under the MIT license for mosaic
+chromosomal alteration detection and analysis from DNA microarray or
+whole genome sequence data. It can be used both with Illumina and
+Affymetrix data. It can also be used for detection of germline copy
+number variants. Data can be prepared in usable file formats using the
+gtc2vcf plugin.
Index: pkgsrc/biology/bio-mocha/Makefile
diff -u /dev/null pkgsrc/biology/bio-mocha/Makefile:1.1
--- /dev/null   Fri Oct 11 22:44:39 2024
+++ pkgsrc/biology/bio-mocha/Makefile   Fri Oct 11 22:44:39 2024
@@ -0,0 +1,66 @@
+# $NetBSD: Makefile,v 1.1 2024/10/11 22:44:39 bacon Exp $
+
+DISTNAME=      bio-mocha-1.20
+CATEGORIES=    biology
+# Can't get ${MASTER_SITE_GITHUB:=samtools/} to work with additional distfile
+MASTER_SITES=  https://software.broadinstitute.org/software/mocha/
+MASTER_SITES+= https://github.com/samtools/bcftools/releases/download/${GH_TAG}/
+DISTFILES+=    bio-mocha_1.20-20240505.tar.gz
+DISTFILES+=    bcftools-1.21.tar.bz2
+GH_TAG=                1.21
+
+OWNER=         bacon%NetBSD.org@localhost
+HOMEPAGE=      https://software.broadinstitute.org/software/mocha/
+COMMENT=       Bcftools plugin for mosaic chromosomal alteration analysis
+LICENSE=       mit
+
+REPLACE_INTERPRETER+=  R
+REPLACE.R.old=         /usr/bin/env Rscript
+REPLACE.R.new=         ${PREFIX}/bin/Rscript
+REPLACE_FILES.R=       MoCha/*.R
+
+SUBST_CLASSES+=                version
+SUBST_STAGE.version=   pre-configure
+SUBST_SED.version=     -e "s|m4_esyscmd_s(\[./version.sh 2>/dev/null\])|[${PKGVERSION_NOREV}]|"
+SUBST_FILES.version=   configure.ac
+
+DEPENDS=       bash>=0:../../shells/bash
+DEPENDS+=      bcftools>=1.16:../../biology/bcftools
+
+USE_TOOLS+=    autoconf automake autoreconf bash gmake perl pax
+GNU_CONFIGURE= yes
+REPLACE_PERL=  misc/* test/test.pl
+
+WRKSRC=                ${WRKDIR}/bcftools-${GH_TAG}
+
+DATADIR=               ${PREFIX}/share/bio-mocha
+# FIXME: Why is share/bio-mocha only required on macOS?
+INSTALLATION_DIRS=     libexec/bcftools share/bio-mocha
+
+post-extract:
+       ${CP} ${WRKDIR}/*.c ${WRKDIR}/*.h ${WRKSRC}/plugins
+       ${MKDIR} ${WRKSRC}/MoCha
+       ${CP} ${WRKDIR}/*.R ${WRKSRC}/MoCha
+
+pre-configure:
+       cd ${WRKSRC} && autoreconf -if
+
+# One .so for each .c in the mocha distfile
+do-install:
+       ${INSTALL_PROGRAM} ${WRKSRC}/plugins/extendFMT.so \
+               ${DESTDIR}${PREFIX}/libexec/bcftools
+       ${INSTALL_PROGRAM} ${WRKSRC}/plugins/mocha.so \
+               ${DESTDIR}${PREFIX}/libexec/bcftools
+       ${INSTALL_PROGRAM} ${WRKSRC}/plugins/mochatools.so \
+               ${DESTDIR}${PREFIX}/libexec/bcftools
+       (cd ${WRKSRC}/MoCha && pax -rw . ${DESTDIR}${DATADIR})
+
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../math/gsl/buildlink3.mk"
+.include "../../lang/python/application.mk"
+.include "../../biology/htslib/buildlink3.mk"
+.include "../../math/R/buildlink3.mk"
+# Required for Linux, even though inherited from htslib
+.include "../../archivers/bzip2/buildlink3.mk"
+.include "../../archivers/xz/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
Index: pkgsrc/biology/bio-mocha/PLIST
diff -u /dev/null pkgsrc/biology/bio-mocha/PLIST:1.1
--- /dev/null   Fri Oct 11 22:44:39 2024
+++ pkgsrc/biology/bio-mocha/PLIST      Fri Oct 11 22:44:39 2024
@@ -0,0 +1,7 @@
+@comment $NetBSD: PLIST,v 1.1 2024/10/11 22:44:39 bacon Exp $
+libexec/bcftools/extendFMT.so
+libexec/bcftools/mocha.so
+libexec/bcftools/mochatools.so
+share/bio-mocha/mocha_plot.R
+share/bio-mocha/pileup_plot.R
+share/bio-mocha/summary_plot.R
Index: pkgsrc/biology/bio-mocha/distinfo
diff -u /dev/null pkgsrc/biology/bio-mocha/distinfo:1.1
--- /dev/null   Fri Oct 11 22:44:39 2024
+++ pkgsrc/biology/bio-mocha/distinfo   Fri Oct 11 22:44:39 2024
@@ -0,0 +1,9 @@
+$NetBSD: distinfo,v 1.1 2024/10/11 22:44:39 bacon Exp $
+
+BLAKE2s (bcftools-1.21.tar.bz2) = 517b73f84870fa967e6f7f6241c446131cc54229e7ee446110955e39dfbe2563
+SHA512 (bcftools-1.21.tar.bz2) = f8fb2e50a1a9e7a7e8a4f71d71d052f6019d54c60ae060d0abfbd01ab61a2c44e04e069c479ea9f6156513b54a611a9a46930a0ff4454019bb715fdb9558d07d
+Size (bcftools-1.21.tar.bz2) = 7982173 bytes
+BLAKE2s (bio-mocha_1.20-20240505.tar.gz) = 318b02176dfff73b88da45f7bd754921027307696ce4a124a934090539529efe
+SHA512 (bio-mocha_1.20-20240505.tar.gz) = 1aeeffb2383f7e6d223129ca58ca55823444275b0d0d759f9c8842dc5f3f4ff493af106c68bdc2c43840098691a357a53e18af4914f78584aad34edb58851991
+Size (bio-mocha_1.20-20240505.tar.gz) = 66752 bytes
+SHA1 (patch-Makefile) = 9dfe7b5dcf77deac6d248d7612440780ec8a3731

Index: pkgsrc/biology/bio-mocha/patches/patch-Makefile
diff -u /dev/null pkgsrc/biology/bio-mocha/patches/patch-Makefile:1.1
--- /dev/null   Fri Oct 11 22:44:39 2024
+++ pkgsrc/biology/bio-mocha/patches/patch-Makefile     Fri Oct 11 22:44:39 2024
@@ -0,0 +1,23 @@
+$NetBSD: patch-Makefile,v 1.1 2024/10/11 22:44:39 bacon Exp $
+
+# Respect pkgsrc env
+
+--- Makefile.orig      2021-03-19 17:42:33.842623449 +0000
++++ Makefile
+@@ -60,11 +60,11 @@ misc_bindir = $(bindir)
+ 
+ MKDIR_P = mkdir -p
+ INSTALL = install -p
+-INSTALL_DATA    = $(INSTALL) -m 644
+-INSTALL_DIR     = $(MKDIR_P) -m 755
+-INSTALL_MAN     = $(INSTALL_DATA)
+-INSTALL_PROGRAM = $(INSTALL)
+-INSTALL_SCRIPT  = $(INSTALL_PROGRAM)
++INSTALL_DATA    = ${BSD_INSTALL_DATA}
++INSTALL_DIR     = $(MKDIR_P)
++INSTALL_MAN     = ${BSD_INSTALL_MAN}
++INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM}
++INSTALL_SCRIPT  = ${BSD_INSTALL_SCRIPT}
+ 
+ PROGRAMS = bcftools
+ MISC_SCRIPTS = \