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stringtie: Transcript assembly and quantification for RNA-seq
Module Name: pkgsrc-wip
Committed By: Jason W. Bacon <bacon%NetBSD.org@localhost>
Pushed By: outpaddling
Date: Wed Jul 19 07:55:40 2023 -0500
Changeset: 9e6291afd2410d011021bcf4ac74d20a0d713d68
Modified Files:
Makefile
Added Files:
stringtie/DESCR
stringtie/Makefile
stringtie/PLIST
stringtie/distinfo
stringtie/patches/patch-Makefile
stringtie/patches/patch-samtools-0.1.18_Makefile
Log Message:
stringtie: Transcript assembly and quantification for RNA-seq
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.
Citation:
Pertea et al. (2015) StringTie enables improved reconstruction of a
transcriptome from RNA-seq reads.
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=9e6291afd2410d011021bcf4ac74d20a0d713d68
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
Makefile | 1 +
stringtie/DESCR | 8 ++++++
stringtie/Makefile | 34 ++++++++++++++++++++++++
stringtie/PLIST | 2 ++
stringtie/distinfo | 7 +++++
stringtie/patches/patch-Makefile | 32 ++++++++++++++++++++++
stringtie/patches/patch-samtools-0.1.18_Makefile | 14 ++++++++++
7 files changed, 98 insertions(+)
diffs:
diff --git a/Makefile b/Makefile
index 8460be725a..86c09f9dfa 100644
--- a/Makefile
+++ b/Makefile
@@ -5328,6 +5328,7 @@ SUBDIR+= stracciatella
SUBDIR+= stratagus
SUBDIR+= stress
SUBDIR+= stress-ng
+SUBDIR+= stringtie
SUBDIR+= strongswan
SUBDIR+= structure
SUBDIR+= stumpwm
diff --git a/stringtie/DESCR b/stringtie/DESCR
new file mode 100644
index 0000000000..e90779f03d
--- /dev/null
+++ b/stringtie/DESCR
@@ -0,0 +1,8 @@
+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.
+Citation:
+Pertea et al. (2015) StringTie enables improved reconstruction of a
+transcriptome from RNA-seq reads.
+Nature Biotechnology 33: 290-295 doi:10.1038/nbt.3122
diff --git a/stringtie/Makefile b/stringtie/Makefile
new file mode 100644
index 0000000000..da68342726
--- /dev/null
+++ b/stringtie/Makefile
@@ -0,0 +1,34 @@
+# $NetBSD$
+#
+###########################################################
+# Generated by fbsd2pkg #
+# Wed Jul 19 07:41:21 CDT 2023 #
+###########################################################
+
+###########################################################
+# Unconverted and partially converted FreeBSD port syntax:
+
+# TEST_DEPENDS= bash:shells/bash \
+# curl:ftp/curl
+# Unknown tool: USE_TOOLS= compiler:c++11-lang
+#TEST_TARGET= test
+
+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
+
+USE_LANGUAGES= c c++
+USE_TOOLS+= gmake
+BUILD_TARGET= release
+
+INSTALLATION_DIRS= bin
+
+do-install:
+ ${INSTALL_PROGRAM} ${WRKSRC}/stringtie ${DESTDIR}${PREFIX}/bin
+
+.include "../../mk/bsd.pkg.mk"
diff --git a/stringtie/PLIST b/stringtie/PLIST
new file mode 100644
index 0000000000..af819f4e12
--- /dev/null
+++ b/stringtie/PLIST
@@ -0,0 +1,2 @@
+@comment $NetBSD$
+bin/stringtie
diff --git a/stringtie/distinfo b/stringtie/distinfo
new file mode 100644
index 0000000000..f2e3e5cb82
--- /dev/null
+++ b/stringtie/distinfo
@@ -0,0 +1,7 @@
+$NetBSD$
+
+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
diff --git a/stringtie/patches/patch-Makefile b/stringtie/patches/patch-Makefile
new file mode 100644
index 0000000000..663ea39c58
--- /dev/null
+++ b/stringtie/patches/patch-Makefile
@@ -0,0 +1,32 @@
+$NetBSD$
+
+# 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)
+ ${RM} core.*
diff --git a/stringtie/patches/patch-samtools-0.1.18_Makefile b/stringtie/patches/patch-samtools-0.1.18_Makefile
new file mode 100644
index 0000000000..78dd162631
--- /dev/null
+++ b/stringtie/patches/patch-samtools-0.1.18_Makefile
@@ -0,0 +1,14 @@
+$NetBSD$
+
+# 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 \
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