[med-svn] [Git][med-team/lofreq][master] 3 commits: No long lines in yaml file

[Steffen Möller]

Steffen Möller pushed to branch master at Debian Med / lofreq


Commits:
4c4b1cb3 by Steffen Moeller at 2018-04-30T23:06:33+02:00
No long lines in yaml file

- - - - -
24557efd by Steffen Moeller at 2018-04-30T23:11:33+02:00
Added d/watch file

- - - - -
6d9659ab by Steffen Moeller at 2018-04-30T23:18:47+02:00
uthash still ref'ed in configure.ac

- - - - -


3 changed files:

- debian/patches/external-htslib.patch
- debian/upstream/metadata
- + debian/watch


Changes:

=====================================
debian/patches/external-htslib.patch
=====================================
--- a/debian/patches/external-htslib.patch
+++ b/debian/patches/external-htslib.patch
@@ -6,11 +6,42 @@ Description: Allow linking to external htslib
 Author: Afif Elghraoui <afif at ghraoui.name>
 Forwarded: no
 Last-Update: 2015-12-24
---- lofreq.orig/src/lofreq/Makefile.am
-+++ lofreq/src/lofreq/Makefile.am
-@@ -29,4 +29,4 @@
+Index: lofreq-2.1.3.1/src/lofreq/Makefile.am
+===================================================================
+--- lofreq-2.1.3.1.orig/src/lofreq/Makefile.am
++++ lofreq-2.1.3.1/src/lofreq/Makefile.am
+@@ -29,4 +29,4 @@ viterbi.c viterbi.h
  
  # note: order matters
  #lofreq_LDADD = @htslib_dir@/libhts.a @samtools_dir@/libbam.a
 -lofreq_LDADD = @HTSLIB@/libhts.a @SAMTOOLS@/libbam.a ../cdflib90/libcdf.a
 +lofreq_LDADD = -L at HTSLIB@ -lhts @SAMTOOLS@/libbam.a ../cdflib90/libcdf.a
+Index: lofreq-2.1.3.1/Makefile.am
+===================================================================
+--- lofreq-2.1.3.1.orig/Makefile.am
++++ lofreq-2.1.3.1/Makefile.am
+@@ -9,10 +9,10 @@ if ENABLE_TOOLS
+ TOOLS = src/tools
+ endif
+ 
+-LICENSES = LICENSE src/cdflib90.README src/uthash/LICENSE
++LICENSES = LICENSE src/cdflib90.README
+ EXTRA_DIST = binary_installer.sh $(LICENSES)
+ 
+-SUBDIRS = src/cdflib90 src/uthash src/lofreq src/scripts $(TOOLS) 
++SUBDIRS = src/cdflib90 src/lofreq src/scripts $(TOOLS)
+ bug-tests: all
+ 	cd tests && $(SHELL) run_all.sh;
+ 
+Index: lofreq-2.1.3.1/configure.ac
+===================================================================
+--- lofreq-2.1.3.1.orig/configure.ac
++++ lofreq-2.1.3.1/configure.ac
+@@ -215,7 +215,6 @@ AC_DEFINE([_USE_KNETFILE], [1], [KNETFIL
+ 
+ AC_CONFIG_FILES(Makefile
+         src/cdflib90/Makefile   
+-        src/uthash/Makefile
+         src/lofreq/Makefile
+         src/scripts/Makefile        
+         src/tools/setup_conf.py        


=====================================
debian/upstream/metadata
=====================================
--- a/debian/upstream/metadata
+++ b/debian/upstream/metadata
@@ -1,6 +1,12 @@
 Reference:
-  Author: Andreas Wilm and Pauline Poh Kim Aw and Denis Bertrand and Grace Hui Ting Yeo and Swee Hoe Ong and Chang Hua Wong and Chiea Chuen Khor and Rosemary Petric and Martin Lloyd Hibberd and Niranjan Nagarajan
-  Title: "LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets"
+  Author: >
+   Andreas Wilm and Pauline Poh Kim Aw and Denis Bertrand and Grace Hui
+   Ting Yeo and Swee Hoe Ong and Chang Hua Wong and Chiea Chuen Khor
+   and Rosemary Petric and Martin Lloyd Hibberd and Niranjan Nagarajan
+  Title: >
+   LoFreq: a sequence-quality aware, ultra-sensitive variant caller
+   for uncovering cell-population heterogeneity from high-throughput
+   sequencing datasets
   Journal: Nucleic Acids Research
   Year: 2012
   Volume: 40


=====================================
debian/watch
=====================================
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=4
+opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%lofreq-$1.tar.gz%" \
+   https://github.com/CSB5/lofreq/tags \
+   (?:.*?/)?v?(\d[\d.]*)\.tar\.gz debian uupdate



View it on GitLab: https://salsa.debian.org/med-team/lofreq/compare/abed31bab5ce3bcaedb611e67bfe106f8e0c9af8...6d9659ab3c552fb6db53e1b0f7f1b0077fd6e4e3

---
View it on GitLab: https://salsa.debian.org/med-team/lofreq/compare/abed31bab5ce3bcaedb611e67bfe106f8e0c9af8...6d9659ab3c552fb6db53e1b0f7f1b0077fd6e4e3
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