[med-svn] [repeatmasker-recon] 03/05: patches for package

[Olivier Sallou]

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

osallou pushed a commit to branch master
in repository repeatmasker-recon.

commit 32ad686bc641c05cb782579d6e9eca7710f881a6
Author: Olivier Sallou <osallou at debian.org>
Date:   Fri Aug 21 21:08:43 2015 +0000

    patches for package
---
 debian/changelog                          |  2 ++
 debian/docs                               |  1 +
 debian/examples                           |  1 +
 debian/files                              |  1 -
 debian/install                            |  5 ++++
 debian/patches/0001-udpate-paths.patch    | 43 +++++++++++++++++++++++++++++++
 debian/patches/0002-fix_binary_name.patch | 22 ++++++++++++++++
 debian/patches/series                     |  2 ++
 debian/rules                              |  5 ++++
 9 files changed, 81 insertions(+), 1 deletion(-)

diff --git a/debian/changelog b/debian/changelog
index 1091fa9..918fdf6 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -3,5 +3,7 @@ repeatmasker-recon (1.08-1) unstable; urgency=low
   * Initial release (Closes: #XX)
     [ TODO ]
     d/watch
+    ITP
+    manpages?
 
  -- Olivier Sallou <osallou at debian.org>  Mon, 21 Aug 2015 10:57:33 +0000
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..6f5b6c7
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1 @@
+00README
diff --git a/debian/examples b/debian/examples
new file mode 100644
index 0000000..f37902f
--- /dev/null
+++ b/debian/examples
@@ -0,0 +1 @@
+Demos
diff --git a/debian/files b/debian/files
deleted file mode 100644
index 884bc54..0000000
--- a/debian/files
+++ /dev/null
@@ -1 +0,0 @@
-bio-rainbow_2.0.4-1_amd64.deb science optional
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..d859670
--- /dev/null
+++ b/debian/install
@@ -0,0 +1,5 @@
+bin/edgeredef usr/bin/
+bin/eledef usr/bin/
+bin/eleredef usr/bin/
+bin/famdef usr/bin/
+bin/imagespread usr/bin/
diff --git a/debian/patches/0001-udpate-paths.patch b/debian/patches/0001-udpate-paths.patch
new file mode 100644
index 0000000..5dfa0d8
--- /dev/null
+++ b/debian/patches/0001-udpate-paths.patch
@@ -0,0 +1,43 @@
+From: Olivier Sallou <osallou at debian.org>
+Date: Fri, 21 Aug 2015 21:02:20 +0000
+Subject: udpate paths
+
+---
+ scripts/recon.pl | 2 +-
+ src/Makefile     | 4 ++--
+ 2 files changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/scripts/recon.pl b/scripts/recon.pl
+index a3a3f97..634e8af 100755
+--- a/scripts/recon.pl
++++ b/scripts/recon.pl
+@@ -1,6 +1,6 @@
+ #! /usr/bin/perl
+ 
+-$path = "";
++$path = "/usr/bin";
+ 
+ if (!$path) {
+     die "Please modifiy this script to specify the path to the binaries.\n";
+diff --git a/src/Makefile b/src/Makefile
+index 3b709c1..da1fb7c 100644
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -5,7 +5,7 @@ VERSION = 1.08
+ 
+ ## where you want things installed
+ BINDIR  = ../bin
+-MANDIR  = $(HOME)/man
++MANDIR  = ../
+ 
+ ## sourcefiles
+ #SRCDIR = .
+@@ -18,7 +18,7 @@ CC = gcc
+ #  -pedantic clashes with -DMEMDEBUG??
+ #
+ #CFLAGS = -g -Wall -pedantic
+-CFLAGS = -O
++CFLAGS += -O
+ #CFLAGS = -g
+ #CFLAGS = -TARG:exc_max -64 -Ofast=ip27   #specific SGI Origin200  compiler#
+ 
diff --git a/debian/patches/0002-fix_binary_name.patch b/debian/patches/0002-fix_binary_name.patch
new file mode 100644
index 0000000..59975bc
--- /dev/null
+++ b/debian/patches/0002-fix_binary_name.patch
@@ -0,0 +1,22 @@
+From: Olivier Sallou <osallou at debian.org>
+Date: Fri, 21 Aug 2015 21:40:19 +0000
+Subject: fix_binary_name
+
+Use Debian renamed recon.pl to repeatmasker-recon
+---
+ Demos/README | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/Demos/README b/Demos/README
+index 6da320e..9c4b773 100644
+--- a/Demos/README
++++ b/Demos/README
+@@ -21,7 +21,7 @@ The empty directory of output is where you can run the RECON package
+ on this example (after installation, of course).  Within the output 
+ directory, type
+ 
+-../../scripts/recon.pl ../input/seqnames ../input/elegans.msps 1
++repeatmasker-recon ../input/seqnames ../input/elegans.msps 1
+ 
+ The process will generate several directories to store the output.  All
+ these directories, except for the summary directory stores intermediate
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..2446656
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,2 @@
+0001-udpate-paths.patch
+0002-fix_binary_name.patch
diff --git a/debian/rules b/debian/rules
index 7c8da2d..6a97a55 100755
--- a/debian/rules
+++ b/debian/rules
@@ -25,11 +25,16 @@ override_dh_auto_build:
 	cd src; make
 
 override_dh_auto_install:
+	mkdir -p bin
 	cd src; make install
 	dh_install
+	cp scripts/recon.pl debian/repeatmasker-recon/usr/bin/repeatmasker-recon
+	cp scripts/MSPCollect.pl debian/repeatmasker-recon/usr/bin/MSPCollect
+
 
 override_dh_clean:
 	cd src; make clean
+	rm -rf bin
 	dh_clean
 
 override_dh_installman:

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