Import rsem-1.2.30 as wip/rsem.

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: Import rsem-1.2.30 as wip/rsem.
From: Jason Bacon <bacon4000%gmail.com@localhost>
Date: Wed, 11 May 2016 12:35:24 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Wed May 11 07:35:24 2016 -0500
Changeset:	418c2fedaa5ce084fe77f6fc9d5565cec7fe1a0f

Added Files:
	rsem/DESCR
	rsem/Makefile
	rsem/PLIST
	rsem/TODO
	rsem/distinfo
	rsem/patches/patch-Makefile
	rsem/patches/patch-samtools-1.3_Makefile
	rsem/patches/patch-samtools-1.3_htslib-1.3_Makefile

Log Message:
Import rsem-1.2.30 as wip/rsem.

RSEM is a software package for estimating gene and isoform expression levels
from RNA-Seq data.

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=418c2fedaa5ce084fe77f6fc9d5565cec7fe1a0f

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

diffstat:
 rsem/DESCR                                         |  2 +
 rsem/Makefile                                      | 75 ++++++++++++++++++
 rsem/PLIST                                         | 28 +++++++
 rsem/TODO                                          |  1 +
 rsem/distinfo                                      |  8 ++
 rsem/patches/patch-Makefile                        | 91 ++++++++++++++++++++++
 rsem/patches/patch-samtools-1.3_Makefile           | 55 +++++++++++++
 .../patches/patch-samtools-1.3_htslib-1.3_Makefile | 14 ++++
 8 files changed, 274 insertions(+)

diffs:
diff --git a/rsem/DESCR b/rsem/DESCR
new file mode 100644
index 0000000..71419b3
--- /dev/null
+++ b/rsem/DESCR
@@ -0,0 +1,2 @@
+RSEM is a software package for estimating gene and isoform expression levels
+from RNA-Seq data.
diff --git a/rsem/Makefile b/rsem/Makefile
new file mode 100644
index 0000000..d607946
--- /dev/null
+++ b/rsem/Makefile
@@ -0,0 +1,75 @@
+# $NetBSD$
+#
+###########################################################
+#                  Generated by fbsd2pkg                  #
+#              Sun May  1 07:19:47 CDT 2016               #
+###########################################################
+# Test new versions with Trinity before upgrading
+
+#DISTVERSIONPREFIX=v
+
+DISTNAME=	rsem-${PORTVERSION}
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=deweylab/}
+GITHUB_PROJECT=	RSEM
+GITHUB_TAG=	v${PORTVERSION}
+
+MAINTAINER=	bacon4000%gmail.com@localhost
+HOMEPAGE=	http://deweylab.biostat.wisc.edu/rsem/README.html
+COMMENT=	RNA-Seq by Expectation-Maximization
+LICENSE=	gnu-gpl-v3
+
+# Test and change if necessary.
+# MAKE_JOBS_SAFE=	no
+
+USE_LANGUAGES=	c c++
+# Gmake is for bundled samtools, which contains modifications for rsem.
+# Should be unbundled in the future.
+USE_TOOLS+=	gmake perl:run
+REPLACE_PERL=	convert-sam-for-rsem \
+                extract-transcript-to-gene-map-from-trinity \
+                rsem-calculate-expression \
+                rsem-control-fdr \
+                rsem-generate-data-matrix \
+                rsem-generate-ngvector \
+                rsem-plot-transcript-wiggles \
+                rsem-prepare-reference \
+                rsem-run-ebseq \
+                rsem_perl_utils.pm
+REPLACE_PYTHON=	rsem-refseq-extract-primary-assembly \
+		rsem-gff3-to-gtf
+
+SUBST_CLASSES+=		rscript
+SUBST_STAGE.rscript=	post-patch
+SUBST_SED.rscript=	-e "s|\#!/usr/bin/env Rscript|${PREFIX}/bin/Rscript|g"
+SUBST_FILES.rscript=	rsem-gen-transcript-plots \
+			rsem-plot-model
+
+SUBST_CLASSES+=		siteperl
+SUBST_STAGE.siteperl=	post-patch
+SUBST_SED.siteperl+=	-e 's|use lib $$FindBin::RealBin|use lib "${SITE_PERL}"|'
+SUBST_FILES.siteperl+=	${WRKSRC}/rsem*
+
+# Make sure all rsem programs use libexec/rsem/samtools
+SUBST_CLASSES+=		samdir
+SUBST_STAGE.samdir=	post-patch
+SUBST_SED.samdir+=	-e 's|samtools|${PREFIX}/libexec/rsem/samtools|g'
+SUBST_FILES.samdir+=	${WRKSRC}/rsem-calculate-expression
+SUBST_FILES.samdir+=	${WRKSRC}/rsem-plot-transcript-wiggles
+
+WRKSRC=		${WRKDIR}/RSEM-${PORTVERSION}
+MAKE_ENV=	libexecdir=${PREFIX}/libexec \
+		perl_mod_dir=${SITE_PERL}
+
+FETCH_USING=	curl
+
+PORTVERSION=	1.2.30
+SITE_PERL=	${PREFIX}/share/rsem
+
+post-install:
+	${RM} -rf ${DESTDIR}${PREFIX}/bin/samtools-*
+
+.include "../../math/R/buildlink3.mk"
+.include "../../lang/python/application.mk"
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/rsem/PLIST b/rsem/PLIST
new file mode 100644
index 0000000..0b8f0b4
--- /dev/null
+++ b/rsem/PLIST
@@ -0,0 +1,28 @@
+@comment $NetBSD$
+bin/convert-sam-for-rsem
+bin/extract-transcript-to-gene-map-from-trinity
+bin/rsem-bam2readdepth
+bin/rsem-bam2wig
+bin/rsem-build-read-index
+bin/rsem-calculate-credibility-intervals
+bin/rsem-calculate-expression
+bin/rsem-extract-reference-transcripts
+bin/rsem-generate-data-matrix
+bin/rsem-gen-transcript-plots
+bin/rsem-get-unique
+bin/rsem-gff3-to-gtf
+bin/rsem-parse-alignments
+bin/rsem-plot-model
+bin/rsem-plot-transcript-wiggles
+bin/rsem-prepare-reference
+bin/rsem-preref
+bin/rsem-refseq-extract-primary-assembly
+bin/rsem-run-em
+bin/rsem-run-gibbs
+bin/rsem-sam-validator
+bin/rsem-scan-for-paired-end-reads
+bin/rsem-simulate-reads
+bin/rsem-synthesis-reference-transcripts
+bin/rsem-tbam2gbam
+libexec/rsem/samtools
+share/rsem/rsem_perl_utils.pm
diff --git a/rsem/TODO b/rsem/TODO
new file mode 100644
index 0000000..b2e3b56
--- /dev/null
+++ b/rsem/TODO
@@ -0,0 +1 @@
+Clean up and test.
diff --git a/rsem/distinfo b/rsem/distinfo
new file mode 100644
index 0000000..690399e
--- /dev/null
+++ b/rsem/distinfo
@@ -0,0 +1,8 @@
+$NetBSD$
+
+SHA1 (rsem-1.2.30.tar.gz) = dfe0cc7a503af2a976923432b266a8b589b264ca
+RMD160 (rsem-1.2.30.tar.gz) = b6843ac7c5db828a40d23568cc7f13507756d91c
+Size (rsem-1.2.30.tar.gz) = 9192827 bytes
+SHA1 (patch-Makefile) = 0fdd585d4ccb70a56a589e8ac280f7d63f1d9840
+SHA1 (patch-samtools-1.3_Makefile) = 6c9094bc8e0af85fede6d1db6af36e2da2a3e2e0
+SHA1 (patch-samtools-1.3_htslib-1.3_Makefile) = 036026001b4d34b1b03db763f334782fd4a9751a
diff --git a/rsem/patches/patch-Makefile b/rsem/patches/patch-Makefile
new file mode 100644
index 0000000..20f2a56
--- /dev/null
+++ b/rsem/patches/patch-Makefile
@@ -0,0 +1,91 @@
+$NetBSD$
+
+# Respect the environment
+--- Makefile.orig	2016-03-07 07:49:06 UTC
++++ Makefile
+@@ -1,5 +1,9 @@
+-SAMTOOLS = samtools-1.3
+-HTSLIB = htslib-1.3
++# Use ?= to allow overriding standard variables with make arguments or
++# environment variables.  This eliminates the need to edit the Makefile for
++# different platforms and allows package managers to control automated builds.
++
++SAMTOOLS ?= samtools-1.3
++HTSLIB ?= htslib-1.3
+ 
+ ifneq ($(cygwin), true)
+   SAMTOOLS_MAKEFILE = Makefile
+@@ -7,31 +11,36 @@ else
+   SAMTOOLS_MAKEFILE = Makefile.cygwin
+ endif
+ 
+-# overridable, defaulting to local copy
+-BOOST = .
++# Overridable, defaulting to local copy
++BOOST ?= .
+ 
+ # Compilation variables
+-CXX = g++
+-CXXFLAGS = -std=gnu++98 -Wall -I. -I$(BOOST) -I$(SAMTOOLS)/$(HTSLIB)
+-CPPFLAGS =
++CXX ?= g++
++# Allow overriding non-portable flags
++CXXFLAGS ?= -Wall
++CXXFLAGS += -std=gnu++98 -I. -I$(BOOST) -I$(SAMTOOLS)/$(HTSLIB)
++CPPFLAGS ?=
+ 
+-LDFLAGS =
+-LDLIBS =
++LDFLAGS ?=
++LDLIBS ?=
+ 
+ # Installation variables
+-INSTALL = install
+-INSTALL_PROGRAM = $(INSTALL) -p
+-INSTALL_DATA = $(INSTALL) -p -m 644
+-INSTALL_DIR = $(INSTALL) -d
+-STRIP ?=strip
++INSTALL ?= install
++INSTALL_PROGRAM ?= $(INSTALL) -p
++INSTALL_DATA ?= $(INSTALL) -p -m 644
++INSTALL_DIR ?= $(INSTALL) -d
++STRIP ?= strip
+ 
+-prefix ?= /usr/local
+-exec_prefix = $(prefix)
++# PREFIX, not prefix, is used by most package managers
++PREFIX ?= /usr/local
++exec_prefix = $(PREFIX)
+ bindir = $(exec_prefix)/bin
++libexecdir ?= $(bindir)
++perl_mod_dir ?= $(bindir)
+ 
+ # Auxiliary variables for compilation
+-SAMHEADERS = $(SAMTOOLS)/$(HTSLIB)/htslib/sam.h
+-SAMLIBS = $(SAMTOOLS)/$(HTSLIB)/libhts.a
++SAMHEADERS ?= $(SAMTOOLS)/$(HTSLIB)/htslib/sam.h
++SAMLIBS ?= $(SAMTOOLS)/$(HTSLIB)/libhts.a
+ CONFIGURE = ./configure
+ 
+ OBJS1 = parseIt.o
+@@ -158,12 +167,15 @@ ebseq :
+ 
+ # Install RSEM
+ install : $(PROGRAMS) $(SCRIPTS) $(SAMTOOLS)/samtools rsem_perl_utils.pm
+-	$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(bindir)/$(SAMTOOLS)
++	$(INSTALL_DIR) \
++		$(DESTDIR)$(bindir) \
++		$(DESTDIR)$(libexecdir)/rsem \
++		$(DESTDIR)$(perl_mod_dir)
+ 	$(foreach prog,$(PROGRAMS),$(INSTALL_PROGRAM) $(prog) $(DESTDIR)$(bindir)/$(prog) ; $(STRIP) $(DESTDIR)$(bindir)/$(prog) ;)
+-	$(INSTALL_PROGRAM) $(SAMTOOLS)/samtools $(DESTDIR)$(bindir)/$(SAMTOOLS)/samtools
+-	$(STRIP) $(DESTDIR)$(bindir)/$(SAMTOOLS)/samtools
+-	$(foreach script,$(SCRIPTS),$(INSTALL_PROGRAM) $(script) $(DESTDIR)$(bindir)/$(script) ;)
+-	$(INSTALL_DATA) rsem_perl_utils.pm $(DESTDIR)$(bindir)/rsem_perl_utils.pm
++	$(INSTALL_PROGRAM) $(SAMTOOLS)/samtools $(DESTDIR)$(libexecdir)/rsem
++	$(STRIP) $(DESTDIR)$(libexecdir)/rsem/samtools
++	$(foreach script,$(SCRIPTS),$(INSTALL_PROGRAM) $(script) $(DESTDIR)$(bindir) ;)
++	$(INSTALL_DATA) rsem_perl_utils.pm $(DESTDIR)$(perl_mod_dir)
+ 
+ # Clean
+ clean :
diff --git a/rsem/patches/patch-samtools-1.3_Makefile b/rsem/patches/patch-samtools-1.3_Makefile
new file mode 100644
index 0000000..4f7c9ea
--- /dev/null
+++ b/rsem/patches/patch-samtools-1.3_Makefile
@@ -0,0 +1,55 @@
+$NetBSD$
+
+# Respect the environment
+--- samtools-1.3/Makefile.orig	2016-03-07 07:49:06 UTC
++++ samtools-1.3/Makefile
+@@ -21,10 +21,10 @@
+ # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ # DEALINGS IN THE SOFTWARE.
+ 
+-CC       = gcc
+-CPPFLAGS =
+-CFLAGS   = -g -Wall -O2
+-LDFLAGS  =
++CC       ?= gcc
++CPPFLAGS ?=
++CFLAGS   ?= -g -Wall -O2
++LDFLAGS  ?=
+ LIBS     =
+ 
+ DFLAGS=     -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE
+@@ -39,18 +39,18 @@ AOBJS=      bam_index.o bam_plcmd.o sam_
+             bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o \
+             bam_quickcheck.o bam_addrprg.o
+ 
+-prefix      = /usr/local
+-exec_prefix = $(prefix)
++PREFIX      ?= /usr/local
++exec_prefix = $(PREFIX)
+ bindir      = $(exec_prefix)/bin
+ datarootdir = $(prefix)/share
+ mandir      = $(datarootdir)/man
+ man1dir     = $(mandir)/man1
+ 
+ MKDIR_P = mkdir -p
+-INSTALL = install -p
+-INSTALL_PROGRAM = $(INSTALL)
+-INSTALL_DATA    = $(INSTALL) -m 644
+-INSTALL_DIR     = $(MKDIR_P) -m 755
++INSTALL ?= install -p
++INSTALL_PROGRAM ?= $(INSTALL)
++INSTALL_DATA    ?= $(INSTALL) -m 644
++INSTALL_DIR     ?= $(MKDIR_P) -m 755
+ 
+ 
+ PROGRAMS = samtools
+@@ -83,7 +83,8 @@ all: $(PROGRAMS) $(BUILT_MISC_PROGRAMS) 
+ # TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally
+ ALL_CPPFLAGS = $(DFLAGS) -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS)
+ ALL_LDFLAGS  = -rdynamic $(HTSLIB_LDFLAGS) $(LDFLAGS)
+-ALL_LIBS     = -lz -ldl $(LIBS)
++LDL_LIB      ?= -ldl
++ALL_LIBS     = -lz $(LDL_LIB) $(LIBS)
+ 
+ # Usually config.mk and config.h are generated by running configure
+ # or config.status, but if those aren't used create defaults here.
diff --git a/rsem/patches/patch-samtools-1.3_htslib-1.3_Makefile b/rsem/patches/patch-samtools-1.3_htslib-1.3_Makefile
new file mode 100644
index 0000000..766ac90
--- /dev/null
+++ b/rsem/patches/patch-samtools-1.3_htslib-1.3_Makefile
@@ -0,0 +1,14 @@
+$NetBSD$
+
+# Respect the environment
+--- samtools-1.3/htslib-1.3/Makefile.orig	2016-03-07 07:49:06 UTC
++++ samtools-1.3/htslib-1.3/Makefile
+@@ -22,7 +22,7 @@
+ # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ # DEALINGS IN THE SOFTWARE.
+ 
+-CC     = gcc
++CC     ?= gcc
+ AR     = ar
+ RANLIB = ranlib
+
Prev by Date: Add new package trimmomatic to Makefile
Next by Date: Add new package rsem to Makefile
Previous by Thread: Add new package trimmomatic to Makefile
Next by Thread: Add new package rsem to Makefile
Indexes:
Home | Main Index | Thread Index | Old Index