[med-svn] [Git][med-team/ragout][master] Another attempt at 2.2
Steffen Möller
gitlab at salsa.debian.org
Sat Jan 4 18:20:07 GMT 2020
Steffen Möller pushed to branch master at Debian Med / ragout
Commits:
c8991daa by Steffen Möller at 2020-01-04T19:08:56+01:00
Another attempt at 2.2
- - - - -
7 changed files:
- debian/changelog
- debian/control
- debian/patches/2to3.patch
- + debian/patches/adjustSetupParsingBinaries.patch
- debian/patches/series
- debian/ragout.install
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,14 +1,23 @@
-ragout (2.2-1) UNRELEASED; urgency=medium
+ragout (2.2-1) unstable; urgency=medium
+ [Andreas Tille]
* New upstream version
* debhelper-compat 12
* Standards-Version: 4.4.0
- * Use 2to3 to port to Python3
- Closes: #938330
- TODO: Does not work yet - see
- https://github.com/fenderglass/Ragout/issues/52
+ * Use 2to3 to port to Python3 (Closes: #938330)
+ also see https://github.com/fenderglass/Ragout/issues/52
+ [Steffen Moeller]
+ * Not having Python install binaries in setup.py, chaning
+ d/ragout.install accordingly
+ * bin/ragout was still about to invoke python2
+ * not allowing bin/ragout to change $PATH
+ * demoted sibelia to recommends runtime dependency as there are
+ modules that don't use it.
+ TODO: Find out what happened to
+ https://salsa.debian.org/med-team/sibelia
+ which is not in new or main.
- -- Andreas Tille <tille at debian.org> Thu, 05 Sep 2019 10:06:47 +0200
+ -- Steffen Moeller <moeller at debian.org> Sat, 04 Jan 2020 19:07:58 +0100
ragout (2.1.1+dfsg-1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -17,8 +17,9 @@ Architecture: any
Depends: ${shlibs:Depends},
${python3:Depends},
${misc:Depends},
- sibelia,
python3-networkx (>= 2.2)
+Recommends:
+ sibelia
Description: Reference-Assisted Genome Ordering UTility
Ragout (Reference-Assisted Genome Ordering UTility) is a tool for
chromosome-level scaffolding using multiple references. Given initial
=====================================
debian/patches/2to3.patch
=====================================
@@ -43,8 +43,10 @@ SyntaxError: invalid or missing encoding declaration for 'bin/ragout-maf2synteny
Reported upstream in: https://github.com/fenderglass/Ragout/issues/52
---- a/ragout/assembly_graph/assembly_refine.py
-+++ b/ragout/assembly_graph/assembly_refine.py
+Index: ragout/ragout/assembly_graph/assembly_refine.py
+===================================================================
+--- ragout.orig/ragout/assembly_graph/assembly_refine.py
++++ ragout/ragout/assembly_graph/assembly_refine.py
@@ -11,7 +11,7 @@ import re
import logging
from collections import namedtuple
@@ -72,8 +74,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52
queue.put(src)
visited = set([src])
parent = {src : src}
---- a/ragout/breakpoint_graph/breakpoint_graph.py
-+++ b/ragout/breakpoint_graph/breakpoint_graph.py
+Index: ragout/ragout/breakpoint_graph/breakpoint_graph.py
+===================================================================
+--- ragout.orig/ragout/breakpoint_graph/breakpoint_graph.py
++++ ragout/ragout/breakpoint_graph/breakpoint_graph.py
@@ -87,12 +87,10 @@ class BreakpointGraph(object):
def genomes_chrs_support(self, node_1, node_2):
if not self.bp_graph.has_edge(node_1, node_2):
@@ -155,8 +159,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52
fout.write(" [" + ", ".join(extra) + "]")
fout.write(";\n")
fout.write("}")
---- a/ragout/breakpoint_graph/chimera_detector.py
-+++ b/ragout/breakpoint_graph/chimera_detector.py
+Index: ragout/ragout/breakpoint_graph/chimera_detector.py
+===================================================================
+--- ragout.orig/ragout/breakpoint_graph/chimera_detector.py
++++ ragout/ragout/breakpoint_graph/chimera_detector.py
@@ -7,7 +7,7 @@ This module tries to detect missassemble
in input sequences and breaks them if neccesary
"""
@@ -209,8 +215,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52
for genome in common_genomes:
if chr_1[genome] != chr_2[genome]:
return False
---- a/ragout/breakpoint_graph/permutation.py
-+++ b/ragout/breakpoint_graph/permutation.py
+Index: ragout/ragout/breakpoint_graph/permutation.py
+===================================================================
+--- ragout.orig/ragout/breakpoint_graph/permutation.py
++++ ragout/ragout/breakpoint_graph/permutation.py
@@ -118,8 +118,7 @@ class PermutationContainer:
to_keep = target_blocks.intersection(reference_blocks)
else:
@@ -243,8 +251,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52
total_length = 0
total_covered = 0
for perm in genome_perms:
---- a/ragout/breakpoint_graph/repeat_resolver.py
-+++ b/ragout/breakpoint_graph/repeat_resolver.py
+Index: ragout/ragout/breakpoint_graph/repeat_resolver.py
+===================================================================
+--- ragout.orig/ragout/breakpoint_graph/repeat_resolver.py
++++ ragout/ragout/breakpoint_graph/repeat_resolver.py
@@ -51,7 +51,7 @@ def resolve_repeats(ref_perms, target_pe
next_block_id = 0
for perm in chain(ref_perms, target_perms):
@@ -400,19 +410,22 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52
if block.sign < 0:
left_context, right_context = (right_context[::-1],
---- a/ragout/main.py
-+++ b/ragout/main.py
+Index: ragout/ragout/main.py
+===================================================================
+--- ragout.orig/ragout/main.py
++++ ragout/ragout/main.py
@@ -36,10 +36,10 @@ from ragout.breakpoint_graph.chimera_det
from ragout.__version__ import __version__
#register backends
-import synteny_backend.sibelia
-+from . import synteny_backend.sibelia
- #import synteny_backend.cactus
+-#import synteny_backend.cactus
-import synteny_backend.maf
-import synteny_backend.hal
-+from . import synteny_backend.maf
-+from . import synteny_backend.hal
++from synteny_backend import sibelia
++#from synteny_backend import cactus
++from synteny_backend import maf
++from synteny_backend import hal
logger = logging.getLogger()
debugger = DebugConfig.get_instance()
@@ -425,8 +438,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52
scale = config.vals["blocks"][recipe["blocks"]]
else:
scale = recipe["blocks"]
---- a/ragout/newick/__init__.py
-+++ b/ragout/newick/__init__.py
+Index: ragout/ragout/newick/__init__.py
+===================================================================
+--- ragout.orig/ragout/newick/__init__.py
++++ ragout/ragout/newick/__init__.py
@@ -5,14 +5,14 @@ Copyright (C) 2003-2008, Thomas Mailund
'''
@@ -447,8 +462,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52
test_suite = unittest.TestSuite()
test_suite.addTest(lexertest.test_suite)
---- a/ragout/newick/lexer.py
-+++ b/ragout/newick/lexer.py
+Index: ragout/ragout/newick/lexer.py
+===================================================================
+--- ragout.orig/ragout/newick/lexer.py
++++ ragout/ragout/newick/lexer.py
@@ -8,7 +8,7 @@ rarely need to access it in your own mod
use the parser or tree modules, and from those most likely only the
objects loaded into the mail package. '''
@@ -465,8 +482,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52
- from lexertest import test_suite
+ from .lexertest import test_suite
unittest.TextTestRunner(verbosity=2).run(test_suite)
---- a/ragout/newick/lexertest.py
-+++ b/ragout/newick/lexertest.py
+Index: ragout/ragout/newick/lexertest.py
+===================================================================
+--- ragout.orig/ragout/newick/lexertest.py
++++ ragout/ragout/newick/lexertest.py
@@ -1,7 +1,7 @@
import unittest
@@ -477,8 +496,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52
class LexerTest(unittest.TestCase):
''' Test of the Lexer class. '''
---- a/ragout/newick/parser.py
-+++ b/ragout/newick/parser.py
+Index: ragout/ragout/newick/parser.py
+===================================================================
+--- ragout.orig/ragout/newick/parser.py
++++ ragout/ragout/newick/parser.py
@@ -5,7 +5,7 @@ Copyright (C) 2003-2008, Thomas Mailund
This module contains the functionality for grammatical analysis. '''
@@ -504,8 +525,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52
- from parsertest import test_suite
+ from .parsertest import test_suite
unittest.TextTestRunner(verbosity=2).run(test_suite)
---- a/ragout/newick/parsertest.py
-+++ b/ragout/newick/parsertest.py
+Index: ragout/ragout/newick/parsertest.py
+===================================================================
+--- ragout.orig/ragout/newick/parsertest.py
++++ ragout/ragout/newick/parsertest.py
@@ -1,7 +1,7 @@
import unittest
@@ -516,8 +539,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52
class ParserTest(unittest.TestCase):
''' Test of the _Parser class. '''
---- a/ragout/newick/tree.py
-+++ b/ragout/newick/tree.py
+Index: ragout/ragout/newick/tree.py
+===================================================================
+--- ragout.orig/ragout/newick/tree.py
++++ ragout/ragout/newick/tree.py
@@ -6,8 +6,8 @@ Copyright (C) 2003-2008, Thomas Mailund
This module contains the representation of trees and a parser for
creating trees from a Newick string or file. '''
@@ -536,8 +561,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52
- from treetest import test_suite
+ from .treetest import test_suite
unittest.TextTestRunner(verbosity=2).run(test_suite)
---- a/ragout/newick/treetest.py
-+++ b/ragout/newick/treetest.py
+Index: ragout/ragout/newick/treetest.py
+===================================================================
+--- ragout.orig/ragout/newick/treetest.py
++++ ragout/ragout/newick/treetest.py
@@ -1,9 +1,9 @@
import unittest
@@ -552,16 +579,20 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52
class BuilderTest(unittest.TestCase):
''' Test of the _TreeBuilder (and Leaf and Tree) class. '''
---- a/ragout/parsers/phylogeny_parser.py
-+++ b/ragout/parsers/phylogeny_parser.py
+Index: ragout/ragout/parsers/phylogeny_parser.py
+===================================================================
+--- ragout.orig/ragout/parsers/phylogeny_parser.py
++++ ragout/ragout/parsers/phylogeny_parser.py
@@ -66,4 +66,4 @@ def get_leaves_names(newick_str):
if tree is None:
return None
- return list(map(lambda n: n.identifier, tree.get_leaves()))
+ return list([n.identifier for n in tree.get_leaves()])
---- a/ragout/parsers/recipe_parser.py
-+++ b/ragout/parsers/recipe_parser.py
+Index: ragout/ragout/parsers/recipe_parser.py
+===================================================================
+--- ragout.orig/ragout/parsers/recipe_parser.py
++++ ragout/ragout/parsers/recipe_parser.py
@@ -72,12 +72,12 @@ def parse_ragout_recipe(filename):
if param_name == "blocks":
if value not in config.vals["blocks"]:
@@ -588,8 +619,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52
g_params.setdefault(def_key, def_val)
return recipe_dict
---- a/ragout/phylogeny/inferer.py
-+++ b/ragout/phylogeny/inferer.py
+Index: ragout/ragout/phylogeny/inferer.py
+===================================================================
+--- ragout.orig/ragout/phylogeny/inferer.py
++++ ragout/ragout/phylogeny/inferer.py
@@ -7,7 +7,7 @@ This module infers phylogenetic tree bas
breakpoints data
"""
@@ -608,8 +641,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52
taxas = list(map(Leaf, sorted(genomes)))
for t in taxas:
t.terminal = True
---- a/ragout/phylogeny/phylogeny.py
-+++ b/ragout/phylogeny/phylogeny.py
+Index: ragout/ragout/phylogeny/phylogeny.py
+===================================================================
+--- ragout.orig/ragout/phylogeny/phylogeny.py
++++ ragout/ragout/phylogeny/phylogeny.py
@@ -111,7 +111,7 @@ class Phylogeny:
edges = sorted(root.get_edges(), key=lambda e: e[2], reverse=True)
@@ -633,8 +668,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52
def _median(values):
---- a/ragout/scaffolder/merge_iters.py
-+++ b/ragout/scaffolder/merge_iters.py
+Index: ragout/ragout/scaffolder/merge_iters.py
+===================================================================
+--- ragout.orig/ragout/scaffolder/merge_iters.py
++++ ragout/ragout/scaffolder/merge_iters.py
@@ -229,10 +229,8 @@ class RearrangementProjector:
new_adj_graph.add_edge(u, v)
@@ -681,8 +718,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52
link_to_change = left_scf.contigs[left_pos].link
else:
not_found += 1
---- a/ragout/scaffolder/output_generator.py
-+++ b/ragout/scaffolder/output_generator.py
+Index: ragout/ragout/scaffolder/output_generator.py
+===================================================================
+--- ragout.orig/ragout/scaffolder/output_generator.py
++++ ragout/ragout/scaffolder/output_generator.py
@@ -60,11 +60,11 @@ class OutputGenerator:
seq_1, seq_2 = get_seq(cnt_1), get_seq(cnt_2)
@@ -728,8 +767,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52
contigs_n50 = _calc_n50(contigs_len, fragments_len)
scaffolds_n50 = _calc_n50(scaffolds_len, output_len)
---- a/ragout/scaffolder/scaffolder.py
-+++ b/ragout/scaffolder/scaffolder.py
+Index: ragout/ragout/scaffolder/scaffolder.py
+===================================================================
+--- ragout.orig/ragout/scaffolder/scaffolder.py
++++ ragout/ragout/scaffolder/scaffolder.py
@@ -35,7 +35,7 @@ def build_scaffolds(adjacencies, perm_co
contigs, contig_index = _make_contigs(perm_container)
scaffolds = _extend_scaffolds(adjacencies, contigs, contig_index,
@@ -762,8 +803,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52
new_contigs[i].link = new_contigs[i + 1].link
new_contigs[-1].link = Link(0, [])
scf.contigs = new_contigs
---- a/ragout/shared/datatypes.py
-+++ b/ragout/shared/datatypes.py
+Index: ragout/ragout/shared/datatypes.py
+===================================================================
+--- ragout.orig/ragout/shared/datatypes.py
++++ ragout/ragout/shared/datatypes.py
@@ -63,7 +63,7 @@ class Permutation:
def __str__(self):
return ("[{0}, {1}, {2}, b:{3}, e:{4}]"
@@ -785,8 +828,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52
def name(self):
return self.perm.name()
---- a/ragout/synteny_backend/cactus.py
-+++ b/ragout/synteny_backend/cactus.py
+Index: ragout/ragout/synteny_backend/cactus.py
+===================================================================
+--- ragout.orig/ragout/synteny_backend/cactus.py
++++ ragout/ragout/synteny_backend/cactus.py
@@ -64,7 +64,7 @@ def _make_permutations(recipe, output_di
else:
@@ -805,8 +850,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52
if genome != recipe["target"]:
file.write("*")
file.write("{0} {1}\n".format(genome, os.path.abspath(params["fasta"])))
---- a/ragout/synteny_backend/sibelia.py
-+++ b/ragout/synteny_backend/sibelia.py
+Index: ragout/ragout/synteny_backend/sibelia.py
+===================================================================
+--- ragout.orig/ragout/synteny_backend/sibelia.py
++++ ragout/ragout/synteny_backend/sibelia.py
@@ -70,7 +70,7 @@ class SibeliaBackend(SyntenyBackend):
if not os.path.isdir(block_dir):
os.mkdir(block_dir)
@@ -825,8 +872,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52
if "fasta" not in gen_params:
raise BackendException("FASTA file for '{0}' is not "
"specified".format(gen_name))
---- a/scripts/2geneorder.py
-+++ b/scripts/2geneorder.py
+Index: ragout/scripts/2geneorder.py
+===================================================================
+--- ragout.orig/scripts/2geneorder.py
++++ ragout/scripts/2geneorder.py
@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/python3
@@ -851,8 +900,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52
print(">{0}".format(genome))
for seq in seqs:
print(seq)
---- a/scripts/compare-assemblies.py
-+++ b/scripts/compare-assemblies.py
+Index: ragout/scripts/compare-assemblies.py
+===================================================================
+--- ragout.orig/scripts/compare-assemblies.py
++++ ragout/scripts/compare-assemblies.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.7
+#!/usr/bin/python3
@@ -907,8 +958,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52
for block_1, block_2 in zip(blocks[:-1], blocks[1:]):
graph.add_edge(-block_1, block_2, name=seq, color="green")
---- a/scripts/debug-report.py
-+++ b/scripts/debug-report.py
+Index: ragout/scripts/debug-report.py
+===================================================================
+--- ragout.orig/scripts/debug-report.py
++++ ragout/scripts/debug-report.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.7
+#!/usr/bin/python3
@@ -975,8 +1028,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52
#alignment = join_collinear(alignment)
alignment = filter_by_coverage(alignment, 0.7)
alignment = join_collinear(alignment)
---- a/scripts/install-sibelia.py
-+++ b/scripts/install-sibelia.py
+Index: ragout/scripts/install-sibelia.py
+===================================================================
+--- ragout.orig/scripts/install-sibelia.py
++++ ragout/scripts/install-sibelia.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
@@ -999,8 +1054,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52
except ImportError:
from urllib.request import urlretrieve
---- a/scripts/run-tests.py
-+++ b/scripts/run-tests.py
+Index: ragout/scripts/run-tests.py
+===================================================================
+--- ragout.orig/scripts/run-tests.py
++++ ragout/scripts/run-tests.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.7
+#!/usr/bin/python3
@@ -1025,8 +1082,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52
print("\n********Running test:", name, "********\n")
run_test(params)
---- a/scripts/simulate-rearrangements.py
-+++ b/scripts/simulate-rearrangements.py
+Index: ragout/scripts/simulate-rearrangements.py
+===================================================================
+--- ragout.orig/scripts/simulate-rearrangements.py
++++ ragout/scripts/simulate-rearrangements.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
@@ -1051,8 +1110,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52
unique_seq.remove(contig)
if not unique_seq:
---- a/scripts/utils/common.py
-+++ b/scripts/utils/common.py
+Index: ragout/scripts/utils/common.py
+===================================================================
+--- ragout.orig/scripts/utils/common.py
++++ ragout/scripts/utils/common.py
@@ -89,7 +89,7 @@ def filter_by_coverage(alignment, thresh
by_name[name] = list(filter(len_filter, by_name[name]))
@@ -1071,8 +1132,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52
for e in alignment:
if prev_start is not None and e.ref.start > prev_start:
contig_pos += 1
---- a/scripts/utils/lastz_parser.py
-+++ b/scripts/utils/lastz_parser.py
+Index: ragout/scripts/utils/lastz_parser.py
+===================================================================
+--- ragout.orig/scripts/utils/lastz_parser.py
++++ ragout/scripts/utils/lastz_parser.py
@@ -68,8 +68,8 @@ def filter_intersecting(alignments):
if not (row_2.start <= row_1.end <= row_2.end):
to_filter.add(row_2)
@@ -1084,8 +1147,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52
return [a for a in alignments if a.ref not in to_filter and
a.qry not in to_filter]
---- a/scripts/verify-minimap.py
-+++ b/scripts/verify-minimap.py
+Index: ragout/scripts/verify-minimap.py
+===================================================================
+--- ragout.orig/scripts/verify-minimap.py
++++ ragout/scripts/verify-minimap.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.7
+#!/usr/bin/python3
@@ -1119,8 +1184,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52
if not miss_ord and prev_strand and cur_strand:
if not agreement_strands(prev_strand, cur_strand, increasing):
breaks.append(contig.name)
---- a/scripts/verify-order.py
-+++ b/scripts/verify-order.py
+Index: ragout/scripts/verify-order.py
+===================================================================
+--- ragout.orig/scripts/verify-order.py
++++ ragout/scripts/verify-order.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.7
+#!/usr/bin/python3
@@ -1146,8 +1213,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52
if not miss_ord and prev_strand and cur_strand:
if not agreement_strands(prev_strand, cur_strand, increasing):
breaks.append(contig.name)
---- a/setup.py
-+++ b/setup.py
+Index: ragout/setup.py
+===================================================================
+--- ragout.orig/setup.py
++++ ragout/setup.py
@@ -2,14 +2,14 @@
#This file is a part of Ragout program.
#Released under the BSD license (see LICENSE file)
@@ -1168,3 +1237,35 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52
from distutils.core import setup
from distutils.command.build import build as DistutilsBuild
+Index: ragout/bin/ragout
+===================================================================
+--- ragout.orig/bin/ragout
++++ ragout/bin/ragout
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python2.7
++#!/usr/bin/python3
+
+ #(c) 2013-2014 by Authors
+ #This file is a part of Ragout program.
+@@ -12,21 +12,6 @@ and invokes Ragout
+ import os
+ import sys
+
+-BIN_DIR = "bin"
+-
+-#Check Python version
+-if sys.version_info[:2] != (2, 7):
+- print("Error: Ragout requires Python version 2.7 ({0}.{1} detected)."
+- .format(sys.version_info[0], sys.version_info[1]))
+- sys.exit(-1)
+-
+-#Setting executable paths
+-ragout_root = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
+-sys.path.insert(0, ragout_root)
+-
+-bin_absolute = os.path.join(ragout_root, BIN_DIR)
+-os.environ["PATH"] = bin_absolute + os.pathsep + os.environ["PATH"]
+-
+ #Ragout entry point
+ from ragout.main import main
+ sys.exit(main())
=====================================
debian/patches/adjustSetupParsingBinaries.patch
=====================================
@@ -0,0 +1,12 @@
+Index: ragout/setup.py
+===================================================================
+--- ragout.orig/setup.py
++++ ragout/setup.py
+@@ -39,6 +39,6 @@ setup(name='ragout',
+ 'ragout/phylogeny', 'ragout/scaffolder', 'ragout/shared',
+ 'ragout/synteny_backend', 'ragout/newick'],
+ package_data={'ragout': ['LICENSE']},
+- scripts = ['bin/ragout-maf2synteny', 'bin/ragout-overlap', 'bin/ragout'],
++ #scripts = ['bin/ragout-maf2synteny', 'bin/ragout-overlap', 'bin/ragout'],
+ cmdclass={'build': MakeBuild}
+ )
=====================================
debian/patches/series
=====================================
@@ -1 +1,2 @@
2to3.patch
+adjustSetupParsingBinaries.patch
=====================================
debian/ragout.install
=====================================
@@ -1 +1,2 @@
usr
+bin/ragout* usr/bin
=====================================
debian/rules
=====================================
@@ -13,3 +13,9 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all
override_dh_install:
dh_install
find debian -name LICENSE -delete
+
+override_dh_auto_clean:
+ dh_auto_clean
+ rm -f bin/ragout-maf2synteny bin/ragout-overlap
+ rm -rf .pybuild
+ find . -name "*.o" -delete
View it on GitLab: https://salsa.debian.org/med-team/ragout/commit/c8991daa17bb287539836c822f77dfe48368fe61
--
View it on GitLab: https://salsa.debian.org/med-team/ragout/commit/c8991daa17bb287539836c822f77dfe48368fe61
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20200104/2d066a4a/attachment-0001.html>
More information about the debian-med-commit
mailing list