[med-svn] [subread] 03/06: d/changelog: new upstream version 1.4.6-p5 d/rules: build instructions for documentation d/subread.docs: install pdf d/control: add texlive Build-Dependecies d/patches/fix_syntax.patch: partially applied by upstream

[Alex Mestiashvili]

This is an automated email from the git hooks/post-receive script.

malex-guest pushed a commit to branch master
in repository subread.

commit 18dd66793738f00e890a0a19c4fc74f5b2b374e1
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Sat Sep 5 12:35:58 2015 +0200

    d/changelog: new upstream version 1.4.6-p5
    d/rules: build instructions for documentation
    d/subread.docs: install pdf
    d/control: add texlive Build-Dependecies
    d/patches/fix_syntax.patch: partially applied by upstream
---
 debian/changelog                |  6 ++++++
 debian/control                  |  4 +++-
 debian/patches/fix_syntax.patch | 15 ---------------
 debian/rules                    |  7 +++++++
 debian/subread.docs             |  1 +
 5 files changed, 17 insertions(+), 16 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index e18b801..0cb8af8 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+subread (1.4.6-p5+dfsg-1) UNRELEASED; urgency=medium
+
+  * Imported Upstream version 1.4.6-p5+dfsg
+
+ -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de>  Sat, 05 Sep 2015 12:35:30 +0200
+
 subread (1.4.6-p4+dfsg-1) unstable; urgency=medium
 
   * d/patches/arch_specific_flags.patch: set the optimization level 
diff --git a/debian/control b/debian/control
index 5b3b497..ddbb62a 100644
--- a/debian/control
+++ b/debian/control
@@ -7,7 +7,9 @@ Testsuite: autopkgtest
 Priority: optional
 Build-Depends: debhelper (>= 9),
                zlib1g-dev,
-               help2man
+               help2man,
+               texlive-latex-extra,
+               texlive-bibtex-extra,
 Standards-Version: 3.9.6
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/subread.git
 Vcs-Git: git://anonscm.debian.org/debian-med/subread.git
diff --git a/debian/patches/fix_syntax.patch b/debian/patches/fix_syntax.patch
index 6147896..15487c3 100644
--- a/debian/patches/fix_syntax.patch
+++ b/debian/patches/fix_syntax.patch
@@ -1,6 +1,5 @@
 Description: Fix spelling errors
 Subject: spelling-error-in-binary subread-buildindex s/sucessfully/successfully/
- coverageCount s/coveage/coverage/
 Origin: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 --- subread.orig/src/index-builder.c
 +++ subread/src/index-builder.c
@@ -13,17 +12,3 @@ Origin: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
  	}
  
  	exit(param);
---- subread.orig/src/coverage_calc.c
-+++ subread/src/coverage_calc.c
-@@ -28,9 +28,9 @@
- 
- void calcCount_usage()
- {
--	SUBREADprintf("\ncoveageCount v%s\n\n", SUBREAD_VERSION);
-+	SUBREADprintf("\ncoverageCount v%s\n\n", SUBREAD_VERSION);
- 	SUBREADprintf("Counting the coverage of mapped reads at each location on the entire reference genome.\n\n");
--	SUBREADprintf("./ncoveageCount -i <sam_bam_input> -o <output_prefix>\n\n");
-+	SUBREADprintf("./coverageCount -i <sam_bam_input> -o <output_prefix>\n\n");
- }
- 
- void add_chro(char *sam_h)
diff --git a/debian/rules b/debian/rules
index cef5aab..dfbb6bd 100755
--- a/debian/rules
+++ b/debian/rules
@@ -9,6 +9,9 @@ pkg := $(shell dpkg-parsechangelog --show-field=Source)
 mandir := $(CURDIR)/debian/$(pkg)/usr/share/man/man1
 bindir := $(CURDIR)/bin
 utildir := $(CURDIR)/bin/utilities
+TEXDOC := SubreadUsersGuide.tex
+BIBDOC := SubreadUsersGuide.aux
+DOCDIR := doc
 
 DEB_HOST_ARCH := $(shell dpkg-architecture -qDEB_HOST_ARCH)
 EXTRA_CC_FLAGS = 
@@ -26,6 +29,10 @@ override_dh_clean:
 
 override_dh_auto_build:
 	cd src; make -f Makefile.Linux
+	cd $(DOCDIR) && pdflatex -synctex=1 -interaction=nonstopmode $(TEXDOC)
+	cd $(DOCDIR) && bibtex $(BIBDOC)
+	cd $(DOCDIR) && pdflatex -synctex=1 -interaction=nonstopmode $(TEXDOC)
+	cd $(DOCDIR) && pdflatex -synctex=1 -interaction=nonstopmode $(TEXDOC)
 	dh_auto_build
 
 override_dh_auto_test:
diff --git a/debian/subread.docs b/debian/subread.docs
index 71dfd5b..05bd242 100644
--- a/debian/subread.docs
+++ b/debian/subread.docs
@@ -1 +1,2 @@
 README.txt
+doc/SubreadUsersGuide.pdf

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/subread.git