sci-biology/phusion: allmost corrected build process

Package-Manager: Portage-2.3.3, Repoman-2.3.1

1 files changed, 20 insertions, 2 deletions

diff --git a/sci-biology/phusion/phusion-2.1c.ebuild b/sci-biology/phusion/phusion-2.1c.ebuild
index 83b3f546b..35bd43425 100644
--- a/sci-biology/phusion/phusion-2.1c.ebuild
+++ b/sci-biology/phusion/phusion-2.1c.ebuild
@@ -4,7 +4,7 @@
 
 EAPI=5
 
-inherit eutils
+inherit eutils flag-o-matic toolchain-funcs
 
 DESCRIPTION="Whole genome shotgun assembler using phrap (for Sanger-based reads)"
 HOMEPAGE="http://www.sanger.ac.uk/resources/software/phusion/"
@@ -15,7 +15,13 @@ LICENSE="all-rights-reserved" # temporarily placed value
 # Availability
 # Phusion is undergoing a rewrite of the code to make this a portable package. It will be made available free of charge to academic sites, but requires licensing for commercial use. For more information please contact the authors.
 SLOT="0"
-KEYWORDS=""
+KEYWORDS="" # compile process does not exit upon errors
+# one file does not compile
+# x86_64-pc-linux-gnu-gcc  -O2 -pipe -maes -mpclmul -mpopcnt -mavx -march=native  -o contigoverlap  contigoverlap.o  -lm
+# contigoverlap.o: In function `HashFasta':
+# contigoverlap.c:(.text+0xbb1): relocation truncated to fit: R_X86_64_PC32 against symbol `n_Entry' defined in COMMON section in contigoverlap.o
+# contigoverlap.o: In function `Reads_Overlap':
+# contigoverlap.c:(.text+0x2637): relocation truncated to fit: R_X86_64_32S against symbol `qinfo' defined in COMMON section in contigoverlap.o
 IUSE=""
 
 DEPEND="app-shells/tcsh"
@@ -30,6 +36,18 @@ S="${WORKDIR}"/"phusion_pipeline_v2.1c"
 
 src_prepare(){
 	cp -pf "${EPREFIX}"/usr/bin/phrap src/phrap/phrap.manylong || die
+	# prevent file collision with sci-biology/shrimp-2.2.3 and sci-biology/phusion2-3.0
+	sed -e "s#fasta2fastq#fasta2fastq_"${PN}"#" -i src/fasta2fastq/fasta2fastq.c \
+		src/fasta2fastq/Makefile || die
+	sed -e "s#ctgreads.pl#ctgreads_"${PN}".pl#" -i src/Tcsh_scripts/*.csh || die
+	mv src/fasta2fastq/fasta2fastq.c src/fasta2fastq/fasta2fastq_"${PN}".c || die
+	mv src/Perl_scripts/ctgreads.pl src/Perl_scripts/ctgreads_"${PN}".pl || die
+	find . -name Makefile | while read f; do
+		sed -e "s/^CC =/CC = $(tc-getCC) #/" -i "$f" || die
+		sed -e "s/^ CFLAGS2 =/ CFLAGS2 = ${CFLAGS} #/" -i "$f" || die
+		sed -e "s/^CFLAGS =/CFLAGS = ${CFLAGS} #/" -i "$f" || die
+		sed -e "s/^ CFLAGS =/ CFLAGS = ${CFLAGS} #/" -i "$f" || die
+	done
 }
 
 src_compile(){