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biology/bio-mocha: Update to 1.20

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Numerous bug fixes and enhancements since 1.16

Reported by:    portscout
This commit is contained in:
Jason W. Bacon 2024-10-09 17:22:39 -05:00
parent 384625e2db
commit f3b6d6f5f4
4 changed files with 24 additions and 26 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

11
biology/bio-mocha/Makefile
View file

@ -1,8 +1,9 @@
PORTNAME= bio-mocha
DISTVERSION= 1.16
DISTVERSION= 1.20
CATEGORIES= biology
MASTER_SITES= https://software.broadinstitute.org/software/mocha/
DISTFILES+= ${PORTNAME}_${DISTVERSION}-20221221.tar.gz
# Get this right, or ports will download bcftools in it's place via tuple
DISTFILES+= ${PORTNAME}_${DISTVERSION}-20240505.tar.gz
MAINTAINER= jwb@FreeBSD.org
COMMENT= Bcftools plugin for mosaic chromosomal alteration analysis
@ -10,8 +11,8 @@ WWW= https://software.broadinstitute.org/software/mocha/
LICENSE= MIT
BUILD_DEPENDS= bash:shells/bash htslib>=1.21:biology/htslib
LIB_DEPENDS= libhts.so:biology/htslib
BUILD_DEPENDS= bash:shells/bash
RUN_DEPENDS= bcftools>=${PORTVERSION}:biology/bcftools
USES= autoreconf gmake localbase perl5 python:env shebangfix
@ -20,7 +21,7 @@ USE_PERL5= test
GH_ACCOUNT= samtools
GH_PROJECT= bcftools
GH_TAGNAME= 1.16
GH_TAGNAME= 1.21
GNU_CONFIGURE= yes
SHEBANG_FILES= misc/* test/test.pl
@ -42,8 +43,6 @@ do-install:
${STAGEDIR}${PREFIX}/libexec/bcftools
${INSTALL_PROGRAM} ${WRKSRC}/plugins/mochatools.so \
${STAGEDIR}${PREFIX}/libexec/bcftools
${INSTALL_PROGRAM} ${WRKSRC}/plugins/trio-phase.so \
${STAGEDIR}${PREFIX}/libexec/bcftools
(cd ${WRKSRC}/MoCha && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR})
.include <bsd.port.mk>

10
biology/bio-mocha/distinfo
View file

@ -1,5 +1,5 @@
TIMESTAMP = 1672095342
SHA256 (bio-mocha_1.16-20221221.tar.gz) = 576cbdda53760f353fc8fd989751716b1d4f8c5e1921f838c263476282cced86
SIZE (bio-mocha_1.16-20221221.tar.gz) = 68625
SHA256 (samtools-bcftools-1.16_GH0.tar.gz) = c44c85a04e058e1f1eceeb712106031100bbd700b8ff3f623f7ff872469a4ba3
SIZE (samtools-bcftools-1.16_GH0.tar.gz) = 3432435
TIMESTAMP = 1727475837
SHA256 (bio-mocha_1.20-20240505.tar.gz) = 3beeb7f046b491fed162dfedd83a29b3eebb165fb1f2a25f44df7fa2f063793b
SIZE (bio-mocha_1.20-20240505.tar.gz) = 66752
SHA256 (samtools-bcftools-1.20-1.21_GH0.tar.gz) = 7484695c5d833fb1a89c2b886ec302db0514ba3c8e5ef7397b9302fa8bd37f8d
SIZE (samtools-bcftools-1.20-1.21_GH0.tar.gz) = 3665160

14
biology/bio-mocha/files/patch-Makefile
View file

@ -1,6 +1,6 @@
--- Makefile.orig 2021-03-17 09:16:18 UTC
--- Makefile.orig 2024-09-12 15:06:36 UTC
+++ Makefile
@@ -58,13 +58,14 @@ pluginpath = $(plugindir)
@@ -59,13 +59,14 @@ misc_bindir = $(bindir)
# Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS)
misc_bindir = $(bindir)
@ -22,12 +22,12 @@
PROGRAMS = bcftools
MISC_SCRIPTS = \
@@ -142,7 +143,7 @@ print-version:
ifdef USE_GPL
@@ -144,7 +145,7 @@ ifdef USE_GPL
main.o : EXTRA_CPPFLAGS += -DUSE_GPL
OBJS += polysomy.o peakfit.o
- GSL_LIBS ?= -lgsl -lcblas
+ GSL_LIBS ?= -lgslcblas
ifndef GSL_LIBS
- GSL_LIBS += -lgsl -lcblas
+ GSL_LIBS += -lgslcblas
endif
endif
print-%:

1
biology/bio-mocha/pkg-plist
View file

@ -1,7 +1,6 @@
libexec/bcftools/extendFMT.so
libexec/bcftools/mocha.so
libexec/bcftools/mochatools.so
libexec/bcftools/trio-phase.so
%%DATADIR%%/mocha_plot.R
%%DATADIR%%/pileup_plot.R
%%DATADIR%%/summary_plot.R