[med-svn] [hisat2] 01/01: improve reproducibility, setup watch, add remaining copyright holder

[Michael Crusoe]

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

misterc-guest pushed a commit to branch master
in repository hisat2.

commit bf7fc52dac85a8405518eb6510dad0ada69e10d0
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date:   Thu Aug 18 03:53:16 2016 -0700

    improve reproducibility, setup watch, add remaining copyright holder
---
 debian/copyright             |  1 +
 debian/patches/reproducibile | 53 ++++++++++++++++++++++++++++++++++++++++++++
 debian/watch                 | 40 ++-------------------------------
 3 files changed, 56 insertions(+), 38 deletions(-)

diff --git a/debian/copyright b/debian/copyright
index e5ff695..d593d78 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -6,6 +6,7 @@ Files: *
 Copyright: © 2011-2012, Ben Langmead <langmea at cs.jhu.edu>
            © 2013-2016, Daehwan Kim <infphilo at gmail.com>
            © 2015 Joe Paggi <jpaggi at mit.edu>
+           © 1999 N. Jesper Larsson <jesper at cs.lth.se>
 License: GPL-3+
 
 Files: fast_mutex.h
diff --git a/debian/patches/reproducibile b/debian/patches/reproducibile
index 6f6fd91..7eeece6 100644
--- a/debian/patches/reproducibile
+++ b/debian/patches/reproducibile
@@ -2,6 +2,59 @@ Author: Michael R. Crusoe
 Description: Make build reproducible
 --- hisat2.orig/Makefile
 +++ hisat2/Makefile
+@@ -26,7 +26,7 @@
+ CC = $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
+ CPP = $(GCC_PREFIX)/g++$(GCC_SUFFIX)
+ CXX = $(CPP)
+-HEADERS = $(wildcard *.h)
++HEADERS = $(sort $(wildcard *.h))
+ BOWTIE_MM = 1
+ BOWTIE_SHARED_MEM = 0
+ 
+@@ -130,7 +130,7 @@
+ HISAT2_CPPS_MAIN = $(SEARCH_CPPS) hisat2_main.cpp
+ HISAT2_BUILD_CPPS_MAIN = $(BUILD_CPPS) hisat2_build_main.cpp
+ 
+-SEARCH_FRAGMENTS = $(wildcard search_*_phase*.c)
++SEARCH_FRAGMENTS = $(sort $(wildcard search_*_phase*.c))
+ VERSION = $(shell cat VERSION)
+ 
+ # Convert BITS=?? to a -m flag
+@@ -183,14 +183,14 @@
+ 	hisat2-inspect-s-debug \
+ 	hisat2-inspect-l-debug
+ 
+-GENERAL_LIST = $(wildcard scripts/*.sh) \
+-	$(wildcard scripts/*.pl) \
+-	$(wildcard *.py) \
++GENERAL_LIST = $(sort $(wildcard scripts/*.sh)) \
++	$(sort $(wildcard scripts/*.pl)) \
++	$(sort $(wildcard *.py)) \
+ 	doc/manual.inc.html \
+ 	doc/README \
+ 	doc/style.css \
+-	$(wildcard example/index/*.ht2) \
+-	$(wildcard example/reads/*.fa) \
++	$(sort $(wildcard example/index/*.ht2)) \
++	$(sort $(wildcard example/reads/*.fa)) \
+ 	example/reference/22_20-21M.fa \
+ 	example/reference/22_20-21M.snp \
+ 	$(PTHREAD_PKG) \
+@@ -213,10 +213,10 @@
+ # the Windows FIND tool instead.
+ FIND=$(shell which find)
+ 
+-SRC_PKG_LIST = $(wildcard *.h) \
+-	$(wildcard *.hh) \
+-	$(wildcard *.c) \
+-	$(wildcard *.cpp) \
++SRC_PKG_LIST = $(sort $(wildcard *.h)) \
++	$(sort $(wildcard *.hh)) \
++	$(sort $(wildcard *.c)) \
++	$(sort $(wildcard *.cpp)) \
+ 	doc/strip_markdown.pl \
+ 	Makefile \
+ 	$(GENERAL_LIST)
 @@ -233,10 +233,13 @@
  
  both-debug: hisat2-align-s-debug hisat2-align-l-debug hisat2-build-s-debug hisat2-build-l-debug
diff --git a/debian/watch b/debian/watch
index 5d88692..49f1af9 100644
--- a/debian/watch
+++ b/debian/watch
@@ -1,39 +1,3 @@
 version=3
-
-# Uncomment to examine a Webpage
-# <Webpage URL> <string match>
-#http://www.example.com/downloads.php #PACKAGE#-(.*)\.tar\.gz
-
-# Uncomment to examine a Webserver directory
-#http://www.example.com/pub/#PACKAGE#-(.*)\.tar\.gz
-
-# Uncommment to examine a FTP server
-#ftp://ftp.example.com/pub/#PACKAGE#-(.*)\.tar\.gz debian uupdate
-
-# Uncomment to find new files on sourceforge
-# http://sf.net/#PACKAGE#/#PACKAGE#-(\d[\d\.]+)\.(?:tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))
-
-# Uncomment to find new files on Github
-#  - when using releases:
-# https://github.com/#GITHUBUSER#/#PACKAGE#/releases .*/archive/#PREFIX#(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
-#  - when using tags
-# https://github.com/#GITHUBUSER#/#PACKAGE#/tags .*/#PREFIX#(\d.*)\.(?:tgz|tbz2|txz|tar\.(?:gz|bz2|xz))
-# Remark: frequently you can do s/#PREFIX#/v?/ since 'v' or nothing is quite common but there are other prefixes possible
-
-# PyPi repository of Python modules
-#  see https://lists.debian.org/debian-python/2015/02/msg00027.html
-# http://pypi.debian.net/#module#/#module#-(.+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
-
-# Bitbucket
-# https://bitbucket.org/<user>/<project>/downloads .*/(\d\S*)\.tar\.gz
-
-# Gitlab
-# opts=filenamemangle=s/.*\.tar\.gz\?ref=v?(\d\S*)/<project>-$1\.tar\.gz/g \
-#  https://gitlab.com/<user>/<project>/tags .*archive\.tar\.gz\?ref=v?(\d\S*)
-
-# if tweaking of source is needed
-# \
-# debian debian/get-orig-source
-
-# if you need to repack and choose +dfsg prefix
-# opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,compress=xz" \
+opts=pasv \
+      ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-([0-9.]+)-source.zip

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