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biology/fastp: Update to 0.26.0 

Improve adapter detection and trimming
Changes: https://github.com/OpenGene/fastp/releases
New maintainer: hayzam@alchemilla.io

Reported by:    portscout
This commit is contained in:
Jason W. Bacon 2025-06-07 07:28:25 -05:00
parent 1ff9ba0b92
commit b902f8f425
3 changed files with 14 additions and 11 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
biology/fastp/Makefile
View File

@ -1,9 +1,9 @@
PORTNAME= fastp
DISTVERSIONPREFIX= v
DISTVERSION= 0.25.0
DISTVERSION= 0.26.0
CATEGORIES= biology
MAINTAINER= jwb@FreeBSD.org
MAINTAINER= hayzam@alchemilla.io
COMMENT= Ultra-fast all-in-one FASTQ preprocessor
WWW= https://github.com/OpenGene/fastp

6
biology/fastp/distinfo
View File

@ -1,3 +1,3 @@
TIMESTAMP = 1748779414
SHA256 (OpenGene-fastp-v0.25.0_GH0.tar.gz) = 55fa7d9b8166200e901ff59a1825ba6455ec1a322d9465ce40aae6d145c3146f
SIZE (OpenGene-fastp-v0.25.0_GH0.tar.gz) = 164959
TIMESTAMP = 1749236354
SHA256 (OpenGene-fastp-v0.26.0_GH0.tar.gz) = ab5396f448bece92e599e4d3acc48751fc46f0f43333ca271d229aa95dc47c4e
SIZE (OpenGene-fastp-v0.26.0_GH0.tar.gz) = 166500

15
biology/fastp/files/patch-Makefile
View File

@ -1,4 +1,4 @@
--- Makefile.orig 2025-04-16 10:13:35 UTC
--- Makefile.orig 2025-06-06 00:03:48 UTC
+++ Makefile
@@ -7,6 +7,8 @@ LIBRARY_DIRS ?=
INCLUDE_DIRS ?=
@ -9,14 +9,15 @@
SRC := $(wildcard ${DIR_SRC}/*.cpp)
OBJ := $(patsubst %.cpp,${DIR_OBJ}/%.o,$(notdir ${SRC}))
@@ -15,15 +17,20 @@ CXX ?= g++
@@ -15,15 +17,21 @@ CXX ?= g++
BIN_TARGET := ${TARGET}
CXX ?= g++
-CXXFLAGS := -std=c++11 -pthread -g -O3 -MD -MP -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir)) ${CXXFLAGS}
+# Optional flags that the user can override by setting CXXFLAGS in the
+# env or make argument
+CXXFLAGS ?= -g -O3
+# env or make argument. -pthread is a link flag, and serves no purpose
+# in the compile command. It is handled by -lpthread in LIBS.
+CXXFLAGS ?= -g -O3 -MD -MP
+# Required flags
+CXXFLAGS += -std=c++11 -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir))
LIBS := -lisal -ldeflate -lpthread
@ -33,11 +34,13 @@
static:${OBJ}
$(CXX) $(OBJ) -o ${BIN_TARGET} $(STATIC_LD_FLAGS)
@@ -38,8 +45,13 @@ clean:
@@ -38,8 +46,15 @@ clean:
@rm -rf $(DIR_OBJ)
@rm -f $(TARGET)
+# Respect DESTDIR for staged installs (used by most package managers)
+# Respect DESTDIR for staged installs (used by most package managers).
+# DESTDIR is empty by default, so this will install directly to BINDIR
+# unless DESTDIR is supplied by the user.
install:
- install $(TARGET) $(BINDIR)/$(TARGET)
+ install $(TARGET) $(DESTDIR)$(BINDIR)/$(TARGET)