pkgsrc-WIP-changes archive
[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index][Old Index]
Import rsem-1.2.30 as wip/rsem.
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
+
Home |
Main Index |
Thread Index |
Old Index