commit: b542f8b8e105b98240945504b7f73ff9abf7a1a3
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Thu Feb 4 07:07:20 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Thu Feb 4 07:07:20 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b542f8b8
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 <AT> riseup.net>
sci-biology/stacks/files/stacks-make-install.patch | 83 ++++++++++++++++++++++
.../{stacks-1.44.ebuild => stacks-2.55.ebuild} | 31 ++++----
2 files changed, 98 insertions(+), 16 deletions(-)
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 $(TEST_LOGS:.log=.trs)
diff --git a/sci-biology/stacks/stacks-1.44.ebuild
b/sci-biology/stacks/stacks-2.55.ebuild
similarity index 69%
rename from sci-biology/stacks/stacks-1.44.ebuild
rename to sci-biology/stacks/stacks-2.55.ebuild
index 3106657e9..4d7095d4f 100644
--- a/sci-biology/stacks/stacks-1.44.ebuild
+++ b/sci-biology/stacks/stacks-2.55.ebuild
@@ -1,11 +1,9 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=7
-AUTOTOOLS_AUTORECONF=yes
-
-inherit flag-o-matic eutils perl-module webapp autotools
+inherit flag-o-matic perl-module webapp autotools
DESCRIPTION="Analyze restriction enzyme data, draw gen. maps, population
genomics"
HOMEPAGE="http://creskolab.uoregon.edu/stacks";
@@ -14,7 +12,9 @@
SRC_URI="http://creskolab.uoregon.edu/stacks/source/${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"
}
