[med-svn] [stacks] 01/01: Fix script executable paths to debian install dir

[Kevin Murray]

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daube-guest pushed a commit to branch master
in repository stacks.

commit 750b9f1e1ae8a4183029960da3d04910c39b21d1
Author: Kevin Murray <kdmfoss at gmail.com>
Date:   Fri Oct 21 21:44:20 2016 +1100

    Fix script executable paths to debian install dir
---
 debian/changelog                |  6 ++++++
 debian/patches/script-exe-paths | 38 ++++++++++++++++++++++++++++++++++++++
 debian/patches/series           |  1 +
 3 files changed, 45 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 195be8e..e3c5aa0 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+stacks (1.42-2) UNRELEASED; urgency=medium
+
+  * Fix script executable paths to reflect debian install directory
+
+ -- Kevin Murray <kdmfoss at gmail.com>  Fri, 21 Oct 2016 21:44:40 +1100
+
 stacks (1.42-1) unstable; urgency=medium
 
   * New upstream version
diff --git a/debian/patches/script-exe-paths b/debian/patches/script-exe-paths
new file mode 100644
index 0000000..95fb420
--- /dev/null
+++ b/debian/patches/script-exe-paths
@@ -0,0 +1,38 @@
+Description: Fix script exe_paths
+ denovo_map.pl and other stacks scripts hard-code the binary paths to the
+ installation directory. However, we move these binaries to /usr/lib/stacks/bin,
+ which breaks these scripts. This hard-codes the binary path to the correct
+ location.
+Author: Kevin Murray <spam at kdmurray.id.au>
+Last-Update: 2016-10-21
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -175,10 +175,10 @@
+ 	$(MAKE) all "CXXFLAGS=-g -Wall -DDEBUG -std=gnu++0x"
+ 
+ install-data-hook:
+-	sed -e 's,_VERSION_,$(VERSION),' -e 's,_BINDIR_,$(bindir)/,g' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' $(DESTDIR)$(bindir)/denovo_map.pl > $(DESTDIR)$(bindir)/denovo_map.pl.subst
++	sed -e 's,_VERSION_,$(VERSION),' -e 's,_BINDIR_,/usr/lib/stacks/bin/,g' -e 's,_PKGDATADIR_,$(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
++	sed -e 's,_VERSION_,$(VERSION),' -e 's,_BINDIR_,/usr/lib/stacks/bin/,g' -e 's,_PKGDATADIR_,$(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 -e 's,_VERSION_,$(VERSION),' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' $(DESTDIR)$(bindir)/export_sql.pl > $(DESTDIR)$(bindir)/export_sql.pl.subst
+@@ -199,11 +199,11 @@
+ 	sed -e 's,_VERSION_,$(VERSION),' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' $(DESTDIR)$(bindir)/load_sequences.pl > $(DESTDIR)$(bindir)/load_sequences.pl.subst
+ 	mv $(DESTDIR)$(bindir)/load_sequences.pl.subst $(DESTDIR)$(bindir)/load_sequences.pl
+ 	chmod +x $(DESTDIR)$(bindir)/load_sequences.pl
+-	sed -e 's,_VERSION_,$(VERSION),' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' -e 's,_BINDIR_,$(bindir)/,g' \
++	sed -e 's,_VERSION_,$(VERSION),' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' -e 's,_BINDIR_,/usr/lib/stacks/bin/,g' \
+ 		$(DESTDIR)$(bindir)/stacks_export_notify.pl > $(DESTDIR)$(bindir)/stacks_export_notify.pl.subst
+ 	mv $(DESTDIR)$(bindir)/stacks_export_notify.pl.subst $(DESTDIR)$(bindir)/stacks_export_notify.pl
+ 	chmod +x $(DESTDIR)$(bindir)/stacks_export_notify.pl
+-	sed -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' -e 's,_BINDIR_,$(bindir)/,g' \
++	sed -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' -e 's,_BINDIR_,/usr/lib/stacks/bin/,g' \
+ 		$(DESTDIR)$(pkgdatadir)/php/constants.php.dist > $(DESTDIR)$(pkgdatadir)/php/constants.php.dist.subst
+ 	mv $(DESTDIR)$(pkgdatadir)/php/constants.php.dist.subst $(DESTDIR)$(pkgdatadir)/php/constants.php.dist
+ 	echo $(VERSION) > $(DESTDIR)$(pkgdatadir)/php/version.php
diff --git a/debian/patches/series b/debian/patches/series
index e8bf59d..04dcad4 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
 constants.php.patch
 email-settings.patch
+script-exe-paths

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