sci-biology/stacks: version bump, EAPI bump

does not install yet: access denied
so no keywords for now

Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>

3 files changed, 99 insertions, 17 deletions

diff --git a/sci-biology/stacks/Manifest b/sci-biology/stacks/Manifest
index a71ef0cc2..51adfa214 100644
--- a/sci-biology/stacks/Manifest
+++ b/sci-biology/stacks/Manifest
@@ -1 +1 @@
-DIST stacks-1.44.tar.gz 904141 BLAKE2B 787bfdc3ab44519dfb5372f13de9f629b8d5b67b999b0a4d4555b3071ffc392682ad4afd2fcbf1fba96ee491930901379ae8063cfc46278df613c20b76a92341 SHA512 fd89b8fab3519e9b7c6387574cc13e46800a97627f580e5d5a9841e8d09327ff1de2b91d4e6de78748febcdd9314c0f4ac827f8cbcacdd17aca347e1541eb867
+DIST stacks-2.55.tar.gz 11716625 BLAKE2B ab359095a546a6ae946fd4196f7955b1e6f294c5ade94e1474984c435c3f2dd468fe8665afbcf201b567d2dd84b999bfc8f9ff7a6dd2712e6be0d4b0d609f0f6 SHA512 eb517f5d9a677095efe3000d0e88ee3be3a6abb725290a0fb1cdb9113a4f19d929dd8eb0d8ce3fd3f9d8234fc0b936523f06d754d5c428381fd97fcebbe89a0b
diff --git a/sci-biology/stacks/files/stacks-make-install.patch b/sci-biology/stacks/files/stacks-make-install.patch
new file mode 100644
index 000000000..e5011dfcf
--- /dev/null
+++ b/sci-biology/stacks/files/stacks-make-install.patch
@@ -0,0 +1,83 @@
+diff --git a/Makefile.am b/Makefile.am
+index 7ff8a2b..e6e4682 100644
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -104,19 +104,20 @@ debug:
+ 	$(MAKE) all "CXXFLAGS=-g -Wall -DDEBUG -Og"
+ 
+ install-data-hook:
+-	sed -e 's,_VERSION_,$(VERSION),' -e 's,_BINDIR_,$(bindir)/,g' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' $(DESTDIR)$(bindir)/denovo_map.pl > $(DESTDIR)$(bindir)/denovo_map.pl.subst
+-	mv $(DESTDIR)$(bindir)/denovo_map.pl.subst $(DESTDIR)$(bindir)/denovo_map.pl
+-	chmod +x $(DESTDIR)$(bindir)/denovo_map.pl
+-	sed -e 's,_VERSION_,$(VERSION),' -e 's,_BINDIR_,$(bindir)/,g' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' $(DESTDIR)$(bindir)/ref_map.pl > $(DESTDIR)$(bindir)/ref_map.pl.subst
+-	mv $(DESTDIR)$(bindir)/ref_map.pl.subst $(DESTDIR)$(bindir)/ref_map.pl
+-	chmod +x $(DESTDIR)$(bindir)/ref_map.pl
+-	sed -i.bkp -e 's,_VERSION_,$(VERSION),' $(DESTDIR)$(bindir)/stacks-integrate-alignments
+-	sed -i.bkp -e 's,_VERSION_,$(VERSION),' $(DESTDIR)$(bindir)/stacks-samtools-tview
+-	rm -f $(DESTDIR)$(bindir)/stacks-integrate-alignments.bkp
+-	rm -f $(DESTDIR)$(bindir)/stacks-samtools-tview.bkp
+-	chmod +x $(DESTDIR)$(bindir)/stacks-integrate-alignments
+-	chmod +x $(DESTDIR)$(bindir)/stacks-dist-extract
+-	chmod +x $(DESTDIR)$(bindir)/stacks-gdb
++	echo "Skipped"
++	##sed -e 's,_VERSION_,$(VERSION),' -e 's,_BINDIR_,$(bindir)/,g' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' $(DESTDIR)$(bindir)/denovo_map.pl > $(DESTDIR)$(bindir)/denovo_map.pl.subst
++	##mv $(DESTDIR)$(bindir)/denovo_map.pl.subst $(DESTDIR)$(bindir)/denovo_map.pl
++	##chmod +x $(DESTDIR)$(bindir)/denovo_map.pl
++	##sed -e 's,_VERSION_,$(VERSION),' -e 's,_BINDIR_,$(bindir)/,g' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' $(DESTDIR)$(bindir)/ref_map.pl > $(DESTDIR)$(bindir)/ref_map.pl.subst
++	##mv $(DESTDIR)$(bindir)/ref_map.pl.subst $(DESTDIR)$(bindir)/ref_map.pl
++	##chmod +x $(DESTDIR)$(bindir)/ref_map.pl
++	##sed -i.bkp -e 's,_VERSION_,$(VERSION),' $(DESTDIR)$(bindir)/stacks-integrate-alignments
++	##sed -i.bkp -e 's,_VERSION_,$(VERSION),' $(DESTDIR)$(bindir)/stacks-samtools-tview
++	##rm -f $(DESTDIR)$(bindir)/stacks-integrate-alignments.bkp
++	##rm -f $(DESTDIR)$(bindir)/stacks-samtools-tview.bkp
++	##chmod +x $(DESTDIR)$(bindir)/stacks-integrate-alignments
++	##chmod +x $(DESTDIR)$(bindir)/stacks-dist-extract
++	##chmod +x $(DESTDIR)$(bindir)/stacks-gdb
+ 	##sed -e 's,_VERSION_,$(VERSION),' -e 's,_BINDIR_,$(DESTDIR)$(bindir)/,g' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' $(DESTDIR)$(bindir)/denovo_map.py > $(DESTDIR)$(bindir)/denovo_map.py.subst
+ 	##mv $(DESTDIR)$(bindir)/denovo_map.py.subst $(DESTDIR)$(bindir)/denovo_map.py
+ 	##chmod +x $(DESTDIR)$(bindir)/denovo_map.py
+diff --git a/Makefile.in b/Makefile.in
+index ca1c64f..2c85268 100644
+--- a/Makefile.in
++++ b/Makefile.in
+@@ -819,10 +819,7 @@ install-binPROGRAMS: $(bin_PROGRAMS)
+ 	  END { for (d in files) print "f", d, files[d] }' | \
+ 	while read type dir files; do \
+ 	    if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \
+-	    test -z "$$files" || { \
+-	      echo " $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files '$(DESTDIR)$(bindir)$$dir'"; \
+-	      $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files "$(DESTDIR)$(bindir)$$dir" || exit $$?; \
+-	    } \
++	    test -z "$$files" || { echo "Skipped" } \
+ 	; done
+ 
+ uninstall-binPROGRAMS:
+@@ -1006,10 +1003,7 @@ install-dist_binSCRIPTS: $(dist_bin_SCRIPTS)
+ 	  END { for (d in files) print "f", d, files[d] }' | \
+ 	while read type dir files; do \
+ 	     if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \
+-	     test -z "$$files" || { \
+-	       echo " $(INSTALL_SCRIPT) $$files '$(DESTDIR)$(bindir)$$dir'"; \
+-	       $(INSTALL_SCRIPT) $$files "$(DESTDIR)$(bindir)$$dir" || exit $$?; \
+-	     } \
++	     test -z "$$files" || { echo "Skipped" } \
+ 	; done
+ 
+ uninstall-dist_binSCRIPTS:
+@@ -1600,15 +1594,7 @@ install-am: all-am
+ 
+ installcheck: installcheck-recursive
+ install-strip:
+-	if test -z '$(STRIP)'; then \
+-	  $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+-	    install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+-	      install; \
+-	else \
+-	  $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+-	    install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+-	    "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'" install; \
+-	fi
++	echo "Skipped"
+ mostlyclean-generic:
+ 	-test -z "$(TEST_LOGS)" || rm -f $(TEST_LOGS)
+ 	-test -z "$(TEST_LOGS:.log=.trs)" || rm -f $(TEST_LOGS:.log=.trs)
diff --git a/sci-biology/stacks/stacks-1.44.ebuild b/sci-biology/stacks/stacks-2.55.ebuild
index 3106657e9..4d7095d4f 100644
--- a/sci-biology/stacks/stacks-1.44.ebuild
+++ b/sci-biology/stacks/stacks-2.55.ebuild
@@ -1,11 +1,9 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-AUTOTOOLS_AUTORECONF=yes
-
-inherit flag-o-matic eutils perl-module webapp autotools
+inherit flag-o-matic perl-module webapp autotools
 
 DESCRIPTION="Analyze restriction enzyme data, draw gen. maps, population genomics"
 HOMEPAGE="http://creskolab.uoregon.edu/stacks"
@@ -14,7 +12,9 @@ SRC_URI="http://creskolab.uoregon.edu/stacks/source/${P}.tar.gz"
 LICENSE="GPL-3"
 # SLOT="0" # webapp ebuilds do not set SLOT
 KEYWORDS=""
-IUSE=""
+
+# No rule to make target test
+RESTRICT="test"
 
 DEPEND="
 	>=sci-libs/htslib-1.3.1:0
@@ -27,8 +27,12 @@ RDEPEND="${DEPEND}
 	>=dev-lang/php-5
 	dev-perl/DBD-mysql"
 
+PATCHES=(
+	"${FILESDIR}/${PN}-make-install.patch"
+)
+
 src_prepare(){
-	sed -e 's/SUBDIRS = htslib/SUBDIRS = /' -i Makefile.am || die
+	default
 	#mycppflags=`pkg-config --cflags htslib` # is blocked by bug #601366
 	if [ -z "$mycppflags" ]; then mycppflags="."; fi
 	sed -e "s#-I./htslib/htslib#-I/usr/include/bam -I${mycppflags}#" -i configure.ac || die
@@ -36,20 +40,15 @@ src_prepare(){
 }
 
 src_configure() {
-	econf --enable-bam --enable-sparsehash
+	econf
 	webapp_src_preinst
-	sed -i 's#/usr/lib/libbam.a#-lbam#;#./htslib/libhts.a#-lhts#' Makefile || die
-}
-
-src_compile(){
-	rm -rf htslib # zap bundled htslib-1.3.1
-	emake DESTDIR="${D}"
+	sed -e 's#/usr/lib/libbam.a#-lbam#;#./htslib/libhts.a#-lhts#' -i Makefile || die
 }
 
 src_install() {
-	emake install DESTDIR="${D}"
+	emake install DESTDIR="${ED}"
 	mydoc="Changes README TODO INSTALL"
-	perl-module_src_install DESTDIR="${D}"
+	perl-module_src_install DESTDIR="${ED}"
 	webapp_src_install || die "Failed running webapp_src_install"
 }