Update rsem to 1.3.2 (#15318)

Package uploads complete: [ci skip]
 - biocontainers/rsem:1.3.2--pl526r351hc0aa232_0
 - linux-64/rsem-1.3.2-pl526r351hc0aa232_0.tar.bz2
 - osx-64/rsem-1.3.2-pl526r351h43679fd_0.tar.bz2

recipes/rsem/01_fix_cxx_11.patch

@@ -0,0 +1,49 @@
+Fixes C++11: casting iostream to bool must be explicit
+
+diff -rNu RSEM-1.3.2.orig/buildReadIndex.cpp RSEM-1.3.2/buildReadIndex.cpp
+--- RSEM-1.3.2.orig/buildReadIndex.cpp	2019-04-06 15:04:25.000000000 -0600
++++ RSEM-1.3.2/buildReadIndex.cpp	2019-05-11 18:57:20.451993213 -0600
+@@ -37,15 +37,15 @@
+ 		streampos pos = fin.tellg();
+ 		success = true;
+
+-		success = (getline(fin, line));
++		success = (bool)(getline(fin, line));
+ 		if (!success) continue;
+-		success = (getline(fin, line));
++		success = (bool)(getline(fin, line));
+ 		if (!success) continue;
+
+ 		if (hasQ) {
+-			success = (getline(fin, line));
++			success = (bool)(getline(fin, line));
+ 			if (!success) continue;
+-			success = (getline(fin, line));
++			success = (bool)(getline(fin, line));
+ 			if (!success) continue;
+ 		}
+
+diff -rNu RSEM-1.3.2.orig/PairedEndHit.h RSEM-1.3.2/PairedEndHit.h
+--- RSEM-1.3.2.orig/PairedEndHit.h	2019-04-06 15:04:25.000000000 -0600
++++ RSEM-1.3.2/PairedEndHit.h	2019-05-11 18:57:51.399980833 -0600
+@@ -26,7 +26,7 @@
+
+ bool PairedEndHit::read(std::istream& in) {
+ 	conprb = 0.0;
+-    return (in>>sid>>pos>>insertL);
++    return (bool)(in>>sid>>pos>>insertL);
+ }
+
+ void PairedEndHit::write(std::ostream& out) {
+diff -rNu RSEM-1.3.2.orig/SingleHit.h RSEM-1.3.2/SingleHit.h
+--- RSEM-1.3.2.orig/SingleHit.h	2019-04-06 15:04:25.000000000 -0600
++++ RSEM-1.3.2/SingleHit.h	2019-05-11 18:59:11.543948700 -0600
+@@ -43,7 +43,7 @@
+
+ bool SingleHit::read(std::istream& in) {
+ 	conprb = 0.0;
+-	return (in>>sid>>pos);
++	return (bool)(in>>sid>>pos);
+ }
+
+ void SingleHit::write(std::ostream& out) {

recipes/rsem/02_fix_makefile.patch

@@ -0,0 +1,58 @@
+Removes vendored samtools and allows overriding compile flags
+
+diff -ru RSEM-1.3.2.orig/Makefile RSEM-1.3.2/Makefile
+--- RSEM-1.3.2.orig/Makefile	2019-04-06 15:04:25.000000000 -0600
++++ RSEM-1.3.2/Makefile	2019-05-11 19:02:37.320313844 -0600
+@@ -11,12 +11,12 @@
+ BOOST = .
+
+ # Compilation variables
+-CXX = g++
+-CXXFLAGS = -std=gnu++98 -Wall -I. -I$(BOOST) -I$(SAMTOOLS)/$(HTSLIB)
+-CPPFLAGS =
++CXX ?= g++
++CXXFLAGS ?= -std=gnu++98 -Wall -I. -I$(BOOST) -I$(SAMTOOLS)/$(HTSLIB)
++CPPFLAGS ?=
+
+-LDFLAGS =
+-LDLIBS =
++LDFLAGS ?=
++LDLIBS ?=
+
+ # Installation variables
+ INSTALL = install
+@@ -54,13 +54,11 @@
+
+ .PHONY : all ebseq pRSEM clean
+
+-all : $(PROGRAMS) $(SAMTOOLS)/samtools
++all : $(PROGRAMS)
+
+ $(SAMTOOLS)/samtools :
+ 	cd $(SAMTOOLS) && $(CONFIGURE) --without-curses && $(MAKE) -f $(SAMTOOLS_MAKEFILE) samtools
+
+-$(SAMLIBS) : $(SAMTOOLS)/samtools
+-
+
+ # Compile objects
+ $(OBJS1) :
+@@ -163,17 +161,14 @@
+
+
+ # Install RSEM
+-install : $(PROGRAMS) $(SCRIPTS) $(SAMTOOLS)/samtools rsem_perl_utils.pm
+-	$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(bindir)/$(SAMTOOLS)
++install : $(PROGRAMS) $(SCRIPTS) rsem_perl_utils.pm
++	$(INSTALL_DIR) $(DESTDIR)$(bindir)
+ 	$(foreach prog,$(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
+
+ # Clean
+ clean :
+ 	rm -f *.o *~ $(PROGRAMS)
+-	cd $(SAMTOOLS) && $(MAKE) clean-all
+ 	cd EBSeq && $(MAKE) clean
+ 	cd pRSEM && $(MAKE) clean

recipes/rsem/build.sh

@@ -1,113 +1,48 @@
-#!/usr/bin/env bash
-
-set -x -e
-
-pushd $SRC_DIR
-
-binaries="\
-convert-sam-for-rsem \
-EBSeq/rsem-for-ebseq-calculate-clustering-info \
-EBSeq/rsem-for-ebseq-find-DE \
-EBSeq/rsem-for-ebseq-generate-ngvector-from-clustering-info \
-extract-transcript-to-gene-map-from-trinity \
-rsem-bam2readdepth \
-rsem-bam2wig \
-rsem-build-read-index \
-rsem-calculate-credibility-intervals \
-rsem-calculate-expression \
-rsem-control-fdr \
-rsem-extract-reference-transcripts \
-rsem-generate-data-matrix \
-rsem-generate-ngvector \
-rsem-gen-transcript-plots \
-rsem-get-unique \
-rsem-gff3-to-gtf \
-rsem-parse-alignments \
-rsem-plot-model \
-rsem-plot-transcript-wiggles \
-rsem-prepare-reference \
-rsem-preref \
-rsem-refseq-extract-primary-assembly \
-rsem-run-ebseq \
-rsem-run-em \
-rsem-run-gibbs \
-rsem-sam-validator \
-rsem-scan-for-paired-end-reads \
-rsem-simulate-reads \
-rsem-synthesis-reference-transcripts \
-rsem-tbam2gbam \
-"
-
-export INCLUDE_PATH="${PREFIX}/include"
-export LIBRARY_PATH="${PREFIX}/lib"
-export LD_LIBRARY_PATH="${PREFIX}/lib"
-
-export LDFLAGS="-L${PREFIX}/lib"
-export CPPFLAGS="-I${PREFIX}/include"
-export CFLAGS="-I${PREFIX}/include"
-
-########################################################
-### Prepare Samtools/Htslib
-########################################################
-
-sed -i.bak 's/^CPPFLAGS =$//g' samtools-1.3/Makefile
-sed -i.bak 's/^LDFLAGS  =$//g' samtools-1.3/Makefile
-
-sed -i.bak 's/^CPPFLAGS =$//g' samtools-1.3/htslib-1.3/Makefile
-sed -i.bak 's/^LDFLAGS  =$//g' samtools-1.3/htslib-1.3/Makefile
-
-# varfilter.py in install fails because we don't install Python
-sed -i.bak 's#misc/varfilter.py##g' samtools-1.3/Makefile
-
-# Remove rdynamic which can cause build issues on OSX
-# https://sourceforge.net/p/samtools/mailman/message/34699333/
-sed -i.bak 's/ -rdynamic//g' samtools-1.3/Makefile
-sed -i.bak 's/ -rdynamic//g' samtools-1.3/htslib-1.3/configure
-
-########################################################
-### Build rsem
-########################################################
-
-INSTALLDIR=$PREFIX/lib/rsem
-BINDIR=$PREFIX/bin
-mkdir -p $BINDIR
-mkdir -p $INSTALLDIR
-
-make
-make ebseq
-
-for i in $binaries; do cp $i $INSTALLDIR && chmod +x $INSTALLDIR/$(basename $i); done
-for i in $binaries; do
-    echo "#!/usr/bin/env bash" > $BINDIR/$(basename $i);
-    echo 'DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )' >>  $BINDIR/$(basename $i);
-    echo '$DIR/../lib/rsem/'$(basename $i) '$@' >> $BINDIR/$(basename $i);
-    chmod +x $BINDIR/$(basename $i);
-done
-
-########################################################
-### Do Perl Things
-########################################################
-
-
+#!/usr/bin/bash
+set -x
+
+case `uname` in
+    Linux)
+	DSOSUF="so"
+	;;
+    Darwin)
+	DSOSUF="dylib"
+	;;
+    *)
+	echo "Unknown uname '`uname`'" >&2
+	exit 1
+esac
+
+# main binaries
+make \
+    CXX=$CXX \
+    CXXFLAGS="$CXXFLAGS" \
+    CPPFLAGS="$CPPFLAGS -I$PREFIX/include -I." \
+    SAMLIBS=$PREFIX/lib/libhts.$DSOSUF \
+    SAMHEADERS=$PREFIX/include/htslib/sam.h \
+    LDFLAGS="$LDFLAGS -L$PREFIX/lib" \
+    prefix="$PREFIX" \
+    install
+
+# EBSeq R scripts and one binary
+sed -i.bak 's|#!/usr/bin/env Rscript|#!'$(which Rscript)'|' EBSeq/rsem-*
+rm EBSeq/rsem-*.bak
+make -C EBSeq CXX="$CXX $CXXFLAGS $LDFLAGS" rsem-for-ebseq-calculate-clustering-info
+cp EBSeq/rsem-* $PREFIX/bin
+
+# Fix perl scripts and module
+# move all perl stuff into a separate dir
 mkdir -p perl-build/lib
-#mv *pl perl-build
-mv *.pm perl-build/lib
-mv rsem-calculate-expression perl-build
-mv rsem-control-fdr perl-build
-mv rsem-generate-data-matrix perl-build
-mv rsem-plot-transcript-wiggles perl-build
-mv rsem-prepare-reference perl-build
-mv rsem-run-ebseq perl-build
+mv $PREFIX/bin/rsem*.pm perl-build/lib
+for n in $PREFIX/bin/rsem-*; do
+    if head -n1 "$n" | grep -q "env perl"; then
+	mv -v "$n" perl-build
+    fi
+done
+mv rsem-control-fdr rsem-run-ebseq perl-build
 cp ${RECIPE_DIR}/Build.PL perl-build
-
 cd perl-build
-
+# now run perl install
 perl ./Build.PL
-
-# patch shebang line to make it shorter
-perl -i.bak -wpe 's[^#!.+][#!/usr/bin/env perl]' Build
-
-./Build manifest
-./Build install --installdirs site
-
-chmod u+rwx $PREFIX/bin/*
+perl ./Build manifest
+perl ./Build install --installdirs site

recipes/rsem/meta.yaml

@@ -1,44 +1,48 @@
-{% set version = "1.3.1" %}
+{% set version = "1.3.2" %}
 
 package:
   name: rsem
   version: {{ version }}
 
 source:
   url: https://github.com/deweylab/RSEM/archive/v{{ version }}.tar.gz
-  sha256: 93c749a03ac16e94b1aab94d032d4fd5687d3261316ce943ecb89d3ae3ec2e11
+  sha256: 7cf5538226330960415f759045fd6940fe39ed26955ba833e09dbfdf3332ec6b
+  patches:
+    - 01_fix_cxx_11.patch  # iostreams must be cast to bool explicitly
+    - 02_fix_makefile.patch  # de-vendor samtools and allow overriding *FLAGS
 
 build:
   rpaths:
     - lib/R/lib/
     - lib/
-  number: 1
+  number: 0
 
 requirements:
   build:
     - {{ compiler('c') }}
   host:
     - bioconductor-biobase
-    - boost
     - perl
     - perl-module-build
     - r-base
+    - samtools
+    - htslib
     - zlib
   run:
     - bioconductor-biobase
     - bioconductor-ebseq
-    - boost
+    - ucsc-bigwigsummary
     - perl
     - perl-module-build
     - r-base
-    - samtools 1.3
+    - samtools
     - zlib
 
 test:
   commands:
     - rsem-prepare-reference 2>&1 | grep reference_name > /dev/null
     - rsem-for-ebseq-find-DE 2>&1 | grep Usage > /dev/null
-    - rsem-bam2wig foo bar foobar 2>&1 | grep "fail to open file" > /dev/null
+    - rsem-bam2wig foo bar foobar 2>&1 | grep "Failed to open file" > /dev/null
     - which rsem-for-ebseq-calculate-clustering-info
 
 about: