[med-svn] [Git][med-team/lumpy-sv][master] Changes for 0.3.1+dfsg-8
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Thu Oct 30 19:58:55 GMT 2025
Nilesh Patra pushed to branch master at Debian Med / lumpy-sv
Commits:
34123b61 by Nilesh Patra at 2025-10-31T01:14:05+05:30
Changes for 0.3.1+dfsg-8
- - - - -
8 changed files:
- debian/changelog
- debian/control
- + debian/patches/cleanup-bin.patch
- + debian/patches/do-not-override-dpkg-flags.patch
- debian/patches/fix_shebang.patch
- debian/patches/lumpyexpress.config.patch
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,18 @@
+lumpy-sv (0.3.1+dfsg-8) unstable; urgency=medium
+
+ * Team Upload.
+ * Add patch to not override dpkg provided c/cxxflags (Closes: #1119475)
+ * Remove generated bam files post installation (Closes: #1047978)
+ * Remove B-D on python3, dh-python and avoid using this debhelper.
+ This works on makefile instead
+ * Update shebang patch to fixup python3 shebangs
+ * Bump Standards-Version to 4.7.2 (no changes needed)
+ * Drop Redundant "Rules-Requires-Root: no"
+ * Drop myself from uploaders
+ * Drop python3:Depends
+
+ -- Nilesh Patra <nilesh at debian.org> Fri, 31 Oct 2025 00:58:42 +0530
+
lumpy-sv (0.3.1+dfsg-7) unstable; urgency=medium
* Fix watch file
=====================================
debian/control
=====================================
@@ -1,11 +1,9 @@
Source: lumpy-sv
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>, Nilesh Patra <nilesh at debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
- dh-python,
- python3,
libbamtools-dev,
libfastahack-dev,
libgzstream-dev,
@@ -14,18 +12,15 @@ Build-Depends: debhelper-compat (= 13),
libssl-dev,
libcurl4-gnutls-dev,
samtools,
- python3-pysam
-Standards-Version: 4.6.1
+Standards-Version: 4.7.2
Vcs-Browser: https://salsa.debian.org/med-team/lumpy-sv
Vcs-Git: https://salsa.debian.org/med-team/lumpy-sv.git
Homepage: https://github.com/arq5x/lumpy-sv
-Rules-Requires-Root: no
Package: lumpy-sv
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
- ${python3:Depends},
samblaster,
samtools,
python3,
=====================================
debian/patches/cleanup-bin.patch
=====================================
@@ -0,0 +1,19 @@
+--- a/src/filter/Makefile
++++ b/src/filter/Makefile
+@@ -2,3 +2,6 @@
+ all:
+ $(CC) $(CFLAGS) $(CPPFLAGS) -g -I/usr/include/htslib -o lumpy_filter filter.c -lhts -lcrypto -lcurl -lpthread -lz $(LDFLAGS)
+
++clean:
++ rm -vf lumpy_filter
++
+--- a/Makefile
++++ b/Makefile
+@@ -97,6 +97,7 @@
+ clean:
+ @echo "Cleaning up."
+ @rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
++ $(MAKE) --no-print-directory -C src/filter/ clean
+ #rm -Rf $(BT_ROOT)/lib
+ #rm -f $(BT_ROOT)/src/api/*.o
+ #rm -f $(BT_ROOT)/src/api/internal/*.o
=====================================
debian/patches/do-not-override-dpkg-flags.patch
=====================================
@@ -0,0 +1,24 @@
+Description: Do not override dpkg provided c/cxxflags
+Author: Nilesh Patra <nilesh at iki.fi>
+Last-Update: 2025-10-30
+--- a/Makefile
++++ b/Makefile
+@@ -22,8 +22,8 @@
+ endif
+ #export CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC -DDEBUG -D_DEBUG -DTRACE
+ #export CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC
+-export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC
+-export LIBS = -lz -L $(ZLIB_PATH)
++export CXXFLAGS += -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC $(CPPFLAGS)
++export LIBS += -lz -L $(ZLIB_PATH)
+ #export BT_ROOT = src/utils/BamTools/
+ export MKFILE_DIR = $(dir $(abspath $(lastword $(MAKEFILE_LIST))))
+
+--- a/src/filter/Makefile
++++ b/src/filter/Makefile
+@@ -1,4 +1,4 @@
+
+ all:
+- $(CC) -g -I/usr/include/htslib -o lumpy_filter filter.c -lhts -lcrypto -lcurl -lpthread -lz
++ $(CC) $(CFLAGS) $(CPPFLAGS) -g -I/usr/include/htslib -o lumpy_filter filter.c -lhts -lcrypto -lcurl -lpthread -lz $(LDFLAGS)
+
=====================================
debian/patches/fix_shebang.patch
=====================================
@@ -58,3 +58,91 @@ Description: Remove additional hash sign
if [ -z $5 ]
then
+--- a/scripts/bedpe_sort.py
++++ b/scripts/bedpe_sort.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ import sys
+ import numpy as np
+ from operator import itemgetter
+--- a/scripts/check_sorting.py
++++ b/scripts/check_sorting.py
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python
++#!/usr/bin/python3
+ import sys
+ import subprocess
+ import os
+--- a/scripts/get_coverages.py
++++ b/scripts/get_coverages.py
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python
++#!/usr/bin/python3
+ import sys
+ import subprocess
+ import os
+--- a/scripts/cnvanator_to_bedpes.py
++++ b/scripts/cnvanator_to_bedpes.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ import sys
+ from optparse import OptionParser
+
+--- a/scripts/extractSplitReads_BwaMem
++++ b/scripts/extractSplitReads_BwaMem
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+
+ import sys
+ import getopt
+--- a/scripts/l_merge.py
++++ b/scripts/l_merge.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python -u
++#!/usr/bin/env python3 -u
+ from operator import add
+ import time
+ import sys
+--- a/scripts/l_sort.py
++++ b/scripts/l_sort.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ import sys
+ import numpy as np
+ import glob
+--- a/scripts/pairend_distro.py
++++ b/scripts/pairend_distro.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ # (c) 2012 - Ryan M. Layer
+ # Hall Laboratory
+ # Quinlan Laboratory
+--- a/scripts/prob_bedpe_to_bedgraph.py
++++ b/scripts/prob_bedpe_to_bedgraph.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ import sys
+ import numpy as np
+
+--- a/scripts/vcfToBedpe
++++ b/scripts/vcfToBedpe
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+
+ import argparse, sys
+ import math, time, re
+--- a/scripts/get_exclude_regions.py
++++ b/scripts/get_exclude_regions.py
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python
++#!/usr/bin/python3
+ import sys
+ import subprocess
+ import os
=====================================
debian/patches/lumpyexpress.config.patch
=====================================
@@ -4,7 +4,7 @@ Description: Adapt paths to Debian locations
--- a/scripts/lumpyexpress
+++ b/scripts/lumpyexpress
-@@ -62,14 +62,14 @@ source_binaries() {
+@@ -62,14 +62,14 @@
else
echo "Config file $1 not found. Attempting to auto-source executables"
# general
@@ -21,7 +21,7 @@ Description: Adapt paths to Debian locations
# For testing if the full BAM is actually a CRAM!
HEXDUMP=`which hexdump || true`
-@@ -92,8 +92,8 @@ check_python_modules() {
+@@ -92,8 +92,8 @@
PYTHON_TEST=$1
echo -e "\nChecking for required python modules ($PYTHON_TEST)..."
@@ -32,7 +32,7 @@ Description: Adapt paths to Debian locations
}
## usage
-@@ -126,7 +126,7 @@ options:
+@@ -126,7 +126,7 @@
# set defaults
LUMPY_DIR=`dirname $0`
@@ -41,7 +41,7 @@ Description: Adapt paths to Debian locations
THREADS=1
ANNOTATE=0
MIN_SAMPLE_WEIGHT=4
-@@ -228,17 +228,17 @@ source_binaries $CONFIG
+@@ -228,17 +228,17 @@
if [[ -z "$LUMPY" ]]
then
usage
@@ -62,7 +62,7 @@ Description: Adapt paths to Debian locations
exit 1
fi
-@@ -259,7 +259,7 @@ then
+@@ -259,7 +259,7 @@
SAMSORT="$SAMTOOLS sort -m 1G -T "
else
usage
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,5 @@
use_debian_packaged_libs.patch
lumpyexpress.config.patch
fix_shebang.patch
+do-not-override-dpkg-flags.patch
+cleanup-bin.patch
=====================================
debian/rules
=====================================
@@ -8,7 +8,7 @@ include /usr/share/dpkg/default.mk
export DEB_BUILD_MAINT_OPTIONS=hardening=+all
%:
- dh $@ --with python3
+ dh $@
### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected
#override_dh_auto_test:
@@ -21,6 +21,4 @@ override_dh_install:
cat debian/missing-sources/sr.pos_sorted.sam |samtools view -Sb - > data/sr.pos_sorted.bam
dh_install
rm -f debian/$(DEB_SOURCE)*/usr/share/$(DEB_SOURCE)/scripts/lumpyexpress.config
-
-override_dh_python3:
- dh_python3 --shebang=/usr/bin/python3
+ rm -f data/pe.pos_sorted.bam data/sr.pos_sorted.bam
View it on GitLab: https://salsa.debian.org/med-team/lumpy-sv/-/commit/34123b617d9667c24746c4918c468fbfca17e37d
--
View it on GitLab: https://salsa.debian.org/med-team/lumpy-sv/-/commit/34123b617d9667c24746c4918c468fbfca17e37d
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