CVS commit: pkgsrc/biology/stringtie

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

Module Name:    pkgsrc
Committed By:   bacon
Date:           Sat Aug 12 14:58:35 UTC 2023

Added Files:
        pkgsrc/biology/stringtie: DESCR Makefile PLIST distinfo
        pkgsrc/biology/stringtie/patches: patch-Makefile
            patch-samtools-0.1.18_Makefile

Log Message:
biology/stringtie: RNA-Seq assembly and quantification

StringTie is a fast and highly efficient assembler of RNA-seq alignments
into potential transcripts. The input can be the alignments of raw reads
as usual; it also accepts longer assembled sequences. The output can be
processed by downstream software including Ballgown, Cuffdiff, etc.


To generate a diff of this commit:
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/stringtie/DESCR \
    pkgsrc/biology/stringtie/Makefile pkgsrc/biology/stringtie/PLIST \
    pkgsrc/biology/stringtie/distinfo
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/stringtie/patches/patch-Makefile \
    pkgsrc/biology/stringtie/patches/patch-samtools-0.1.18_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/stringtie/DESCR
diff -u /dev/null pkgsrc/biology/stringtie/DESCR:1.1
--- /dev/null   Sat Aug 12 14:58:35 2023
+++ pkgsrc/biology/stringtie/DESCR      Sat Aug 12 14:58:35 2023
@@ -0,0 +1,4 @@
+StringTie is a fast and highly efficient assembler of RNA-seq alignments into
+potential transcripts. The input can be the alignments of raw reads as usual;
+it also accepts longer assembled sequences. The output can be processed by
+downstream software including Ballgown, Cuffdiff, etc.
Index: pkgsrc/biology/stringtie/Makefile
diff -u /dev/null pkgsrc/biology/stringtie/Makefile:1.1
--- /dev/null   Sat Aug 12 14:58:35 2023
+++ pkgsrc/biology/stringtie/Makefile   Sat Aug 12 14:58:35 2023
@@ -0,0 +1,26 @@
+# $NetBSD: Makefile,v 1.1 2023/08/12 14:58:35 bacon Exp $
+
+DISTNAME=      stringtie-2.1.1
+CATEGORIES=    biology
+MASTER_SITES=  http://ccb.jhu.edu/software/stringtie/dl/
+
+OWNER=         bacon%NetBSD.org@localhost
+HOMEPAGE=      http://www.ccb.jhu.edu/software/stringtie/
+COMMENT=       Transcript assembly and quantification for RNA-seq
+LICENSE=       mit
+
+TEST_DEPENDS=  bash>0:../../shells/bash \
+               curl>0:../../www/curl
+TEST_TARGET=   test
+
+USE_LANGUAGES= c c++
+USE_TOOLS+=    gmake
+BUILD_TARGET=  release
+
+INSTALLATION_DIRS=     bin
+
+do-install:
+       ${INSTALL_PROGRAM} ${WRKSRC}/stringtie ${DESTDIR}${PREFIX}/bin
+
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
Index: pkgsrc/biology/stringtie/PLIST
diff -u /dev/null pkgsrc/biology/stringtie/PLIST:1.1
--- /dev/null   Sat Aug 12 14:58:35 2023
+++ pkgsrc/biology/stringtie/PLIST      Sat Aug 12 14:58:35 2023
@@ -0,0 +1,2 @@
+@comment $NetBSD: PLIST,v 1.1 2023/08/12 14:58:35 bacon Exp $
+bin/stringtie
Index: pkgsrc/biology/stringtie/distinfo
diff -u /dev/null pkgsrc/biology/stringtie/distinfo:1.1
--- /dev/null   Sat Aug 12 14:58:35 2023
+++ pkgsrc/biology/stringtie/distinfo   Sat Aug 12 14:58:35 2023
@@ -0,0 +1,7 @@
+$NetBSD: distinfo,v 1.1 2023/08/12 14:58:35 bacon Exp $
+
+BLAKE2s (stringtie-2.1.1.tar.gz) = b774942714f8798edf59c508c6e2375692676ef36ddfcb3d91468ccd057880b8
+SHA512 (stringtie-2.1.1.tar.gz) = 96f8d6bba0dd76f8f83fad71936c72f87e0004d82977b914e97d012b979bd61cf6900ff63a0f514204f56628751c7e752076978df12e019dd43b3495ab172081
+Size (stringtie-2.1.1.tar.gz) = 1969917 bytes
+SHA1 (patch-Makefile) = 36eaf391e0d856fe2be59fb34a8f06dbe400a8ef
+SHA1 (patch-samtools-0.1.18_Makefile) = 62cd4a780dd99bd8c55ff727ca6a7759c2bf379d

Index: pkgsrc/biology/stringtie/patches/patch-Makefile
diff -u /dev/null pkgsrc/biology/stringtie/patches/patch-Makefile:1.1
--- /dev/null   Sat Aug 12 14:58:35 2023
+++ pkgsrc/biology/stringtie/patches/patch-Makefile     Sat Aug 12 14:58:35 2023
@@ -0,0 +1,32 @@
+$NetBSD: patch-Makefile,v 1.1 2023/08/12 14:58:35 bacon Exp $
+
+# Respect ${MAKE}
+
+--- Makefile.orig      2020-01-26 03:31:12 UTC
++++ Makefile
+@@ -20,7 +20,7 @@ ifeq "$(GCCVER8)" "1"
+   BASEFLAGS += -Wno-class-memaccess
+ endif
+ 
+-LINKER  := $(if $(LINKER),$(LINKER),g++)
++LINKER  := $(if $(LINKER),$(LINKER),$(CXX))
+ 
+ LDFLAGS := $(if $(LDFLAGS),$(LDFLAGS),-g)
+ 
+@@ -151,7 +151,7 @@ rlink.o : rlink.h tablemaker.h $(GDIR)/G
+ tmerge.o : rlink.h tmerge.h
+ tablemaker.o : tablemaker.h rlink.h
+ ${BAM}/libbam.a: 
+-      cd ${BAM} && make lib
++      cd ${BAM} && ${MAKE} lib
+ stringtie: ${BAM}/libbam.a $(OBJS) stringtie.o
+       ${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
+       @echo
+@@ -167,6 +167,6 @@ clean:
+       ${RM} stringtie${EXE} stringtie.o*  $(OBJS)
+       ${RM} core.*
+ allclean cleanAll cleanall:
+-      cd ${BAM} && make clean
++      cd ${BAM} && ${MAKE} clean
+       ${RM} stringtie${EXE} stringtie.o* $(OBJS)
+       ${RM} core.*
Index: pkgsrc/biology/stringtie/patches/patch-samtools-0.1.18_Makefile
diff -u /dev/null pkgsrc/biology/stringtie/patches/patch-samtools-0.1.18_Makefile:1.1
--- /dev/null   Sat Aug 12 14:58:35 2023
+++ pkgsrc/biology/stringtie/patches/patch-samtools-0.1.18_Makefile     Sat Aug 12 14:58:35 2023
@@ -0,0 +1,14 @@
+$NetBSD: patch-samtools-0.1.18_Makefile,v 1.1 2023/08/12 14:58:35 bacon Exp $
+
+# Respect CC, CFLAGS
+
+--- samtools-0.1.18/Makefile.orig      2018-03-06 16:29:49 UTC
++++ samtools-0.1.18/Makefile
+@@ -1,5 +1,5 @@
+-CC=                   gcc
+-CFLAGS=               -g -Wall -fsigned-char -O2 #-m64 #-arch ppc
++CC?=                  gcc
++CFLAGS?=              -g -Wall -fsigned-char -O2 #-m64 #-arch ppc
+ DFLAGS=               -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 #-D_USE_KNETFILE 
+ KNETFILE_O=   knetfile.o
+ LOBJS=                bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \