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commit: b542f8b8e105b98240945504b7f73ff9abf7a1a3 |
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Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> |
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AuthorDate: Thu Feb 4 07:07:20 2021 +0000 |
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Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> |
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CommitDate: Thu Feb 4 07:07:20 2021 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b542f8b8 |
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|
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sci-biology/stacks: version bump, EAPI bump |
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|
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does not install yet: access denied |
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so no keywords for now |
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|
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Package-Manager: Portage-3.0.14, Repoman-3.0.2 |
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Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net> |
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|
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sci-biology/stacks/files/stacks-make-install.patch | 83 ++++++++++++++++++++++ |
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.../{stacks-1.44.ebuild => stacks-2.55.ebuild} | 31 ++++---- |
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2 files changed, 98 insertions(+), 16 deletions(-) |
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|
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diff --git a/sci-biology/stacks/files/stacks-make-install.patch b/sci-biology/stacks/files/stacks-make-install.patch |
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new file mode 100644 |
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index 000000000..e5011dfcf |
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--- /dev/null |
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+++ b/sci-biology/stacks/files/stacks-make-install.patch |
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@@ -0,0 +1,83 @@ |
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+diff --git a/Makefile.am b/Makefile.am |
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+index 7ff8a2b..e6e4682 100644 |
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+--- a/Makefile.am |
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++++ b/Makefile.am |
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+@@ -104,19 +104,20 @@ debug: |
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+ $(MAKE) all "CXXFLAGS=-g -Wall -DDEBUG -Og" |
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+ |
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+ install-data-hook: |
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+- sed -e 's,_VERSION_,$(VERSION),' -e 's,_BINDIR_,$(bindir)/,g' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' $(DESTDIR)$(bindir)/denovo_map.pl > $(DESTDIR)$(bindir)/denovo_map.pl.subst |
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+- mv $(DESTDIR)$(bindir)/denovo_map.pl.subst $(DESTDIR)$(bindir)/denovo_map.pl |
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+- chmod +x $(DESTDIR)$(bindir)/denovo_map.pl |
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+- 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 |
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+- mv $(DESTDIR)$(bindir)/ref_map.pl.subst $(DESTDIR)$(bindir)/ref_map.pl |
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+- chmod +x $(DESTDIR)$(bindir)/ref_map.pl |
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+- sed -i.bkp -e 's,_VERSION_,$(VERSION),' $(DESTDIR)$(bindir)/stacks-integrate-alignments |
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+- sed -i.bkp -e 's,_VERSION_,$(VERSION),' $(DESTDIR)$(bindir)/stacks-samtools-tview |
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+- rm -f $(DESTDIR)$(bindir)/stacks-integrate-alignments.bkp |
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+- rm -f $(DESTDIR)$(bindir)/stacks-samtools-tview.bkp |
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+- chmod +x $(DESTDIR)$(bindir)/stacks-integrate-alignments |
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+- chmod +x $(DESTDIR)$(bindir)/stacks-dist-extract |
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+- chmod +x $(DESTDIR)$(bindir)/stacks-gdb |
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++ echo "Skipped" |
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++ ##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 |
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++ ##mv $(DESTDIR)$(bindir)/denovo_map.pl.subst $(DESTDIR)$(bindir)/denovo_map.pl |
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++ ##chmod +x $(DESTDIR)$(bindir)/denovo_map.pl |
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++ ##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 |
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++ ##mv $(DESTDIR)$(bindir)/ref_map.pl.subst $(DESTDIR)$(bindir)/ref_map.pl |
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++ ##chmod +x $(DESTDIR)$(bindir)/ref_map.pl |
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++ ##sed -i.bkp -e 's,_VERSION_,$(VERSION),' $(DESTDIR)$(bindir)/stacks-integrate-alignments |
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++ ##sed -i.bkp -e 's,_VERSION_,$(VERSION),' $(DESTDIR)$(bindir)/stacks-samtools-tview |
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++ ##rm -f $(DESTDIR)$(bindir)/stacks-integrate-alignments.bkp |
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++ ##rm -f $(DESTDIR)$(bindir)/stacks-samtools-tview.bkp |
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++ ##chmod +x $(DESTDIR)$(bindir)/stacks-integrate-alignments |
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++ ##chmod +x $(DESTDIR)$(bindir)/stacks-dist-extract |
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++ ##chmod +x $(DESTDIR)$(bindir)/stacks-gdb |
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+ ##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 |
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+ ##mv $(DESTDIR)$(bindir)/denovo_map.py.subst $(DESTDIR)$(bindir)/denovo_map.py |
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+ ##chmod +x $(DESTDIR)$(bindir)/denovo_map.py |
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+diff --git a/Makefile.in b/Makefile.in |
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+index ca1c64f..2c85268 100644 |
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+--- a/Makefile.in |
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++++ b/Makefile.in |
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+@@ -819,10 +819,7 @@ install-binPROGRAMS: $(bin_PROGRAMS) |
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+ END { for (d in files) print "f", d, files[d] }' | \ |
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+ while read type dir files; do \ |
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+ if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \ |
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+- test -z "$$files" || { \ |
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+- echo " $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files '$(DESTDIR)$(bindir)$$dir'"; \ |
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+- $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files "$(DESTDIR)$(bindir)$$dir" || exit $$?; \ |
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+- } \ |
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++ test -z "$$files" || { echo "Skipped" } \ |
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+ ; done |
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+ |
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+ uninstall-binPROGRAMS: |
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+@@ -1006,10 +1003,7 @@ install-dist_binSCRIPTS: $(dist_bin_SCRIPTS) |
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+ END { for (d in files) print "f", d, files[d] }' | \ |
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+ while read type dir files; do \ |
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+ if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \ |
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+- test -z "$$files" || { \ |
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+- echo " $(INSTALL_SCRIPT) $$files '$(DESTDIR)$(bindir)$$dir'"; \ |
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+- $(INSTALL_SCRIPT) $$files "$(DESTDIR)$(bindir)$$dir" || exit $$?; \ |
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+- } \ |
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++ test -z "$$files" || { echo "Skipped" } \ |
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+ ; done |
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+ |
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+ uninstall-dist_binSCRIPTS: |
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+@@ -1600,15 +1594,7 @@ install-am: all-am |
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+ |
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+ installcheck: installcheck-recursive |
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+ install-strip: |
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+- if test -z '$(STRIP)'; then \ |
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+- $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \ |
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+- install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \ |
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+- install; \ |
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+- else \ |
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+- $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \ |
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+- install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \ |
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+- "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'" install; \ |
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+- fi |
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++ echo "Skipped" |
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+ mostlyclean-generic: |
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+ -test -z "$(TEST_LOGS)" || rm -f $(TEST_LOGS) |
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+ -test -z "$(TEST_LOGS:.log=.trs)" || rm -f $(TEST_LOGS:.log=.trs) |
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|
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diff --git a/sci-biology/stacks/stacks-1.44.ebuild b/sci-biology/stacks/stacks-2.55.ebuild |
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similarity index 69% |
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rename from sci-biology/stacks/stacks-1.44.ebuild |
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rename to sci-biology/stacks/stacks-2.55.ebuild |
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index 3106657e9..4d7095d4f 100644 |
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--- a/sci-biology/stacks/stacks-1.44.ebuild |
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+++ b/sci-biology/stacks/stacks-2.55.ebuild |
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@@ -1,11 +1,9 @@ |
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-# Copyright 1999-2017 Gentoo Foundation |
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+# Copyright 1999-2021 Gentoo Authors |
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# Distributed under the terms of the GNU General Public License v2 |
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|
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-EAPI=5 |
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+EAPI=7 |
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|
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-AUTOTOOLS_AUTORECONF=yes |
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- |
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-inherit flag-o-matic eutils perl-module webapp autotools |
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+inherit flag-o-matic perl-module webapp autotools |
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|
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DESCRIPTION="Analyze restriction enzyme data, draw gen. maps, population genomics" |
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HOMEPAGE="http://creskolab.uoregon.edu/stacks" |
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@@ -14,7 +12,9 @@ SRC_URI="http://creskolab.uoregon.edu/stacks/source/${P}.tar.gz" |
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LICENSE="GPL-3" |
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# SLOT="0" # webapp ebuilds do not set SLOT |
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KEYWORDS="" |
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-IUSE="" |
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+ |
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+# No rule to make target test |
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+RESTRICT="test" |
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|
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DEPEND=" |
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>=sci-libs/htslib-1.3.1:0 |
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@@ -27,8 +27,12 @@ RDEPEND="${DEPEND} |
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>=dev-lang/php-5 |
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dev-perl/DBD-mysql" |
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|
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+PATCHES=( |
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+ "${FILESDIR}/${PN}-make-install.patch" |
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+) |
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+ |
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src_prepare(){ |
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- sed -e 's/SUBDIRS = htslib/SUBDIRS = /' -i Makefile.am || die |
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+ default |
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#mycppflags=`pkg-config --cflags htslib` # is blocked by bug #601366 |
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if [ -z "$mycppflags" ]; then mycppflags="."; fi |
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sed -e "s#-I./htslib/htslib#-I/usr/include/bam -I${mycppflags}#" -i configure.ac || die |
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@@ -36,20 +40,15 @@ src_prepare(){ |
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} |
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|
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src_configure() { |
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- econf --enable-bam --enable-sparsehash |
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+ econf |
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webapp_src_preinst |
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- sed -i 's#/usr/lib/libbam.a#-lbam#;#./htslib/libhts.a#-lhts#' Makefile || die |
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-} |
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- |
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-src_compile(){ |
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- rm -rf htslib # zap bundled htslib-1.3.1 |
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- emake DESTDIR="${D}" |
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+ sed -e 's#/usr/lib/libbam.a#-lbam#;#./htslib/libhts.a#-lhts#' -i Makefile || die |
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} |
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|
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src_install() { |
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- emake install DESTDIR="${D}" |
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+ emake install DESTDIR="${ED}" |
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mydoc="Changes README TODO INSTALL" |
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- perl-module_src_install DESTDIR="${D}" |
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+ perl-module_src_install DESTDIR="${ED}" |
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webapp_src_install || die "Failed running webapp_src_install" |
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} |
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