This is an automated email from the git hooks/post-receive script. afif pushed a commit to branch master in repository pbsuite.
commit 913cb02adf111255e229bdf462e4ad95e7865fd0 Author: Afif Elghraoui <[email protected]> Date: Fri Feb 26 23:37:50 2016 -0800 Replace /usr/bin/env python with /usr/bin/python --- debian/patches/fix-shebang-lines.patch | 317 +++++++++++++++++++++++++++++++++ 1 file changed, 317 insertions(+) diff --git a/debian/patches/fix-shebang-lines.patch b/debian/patches/fix-shebang-lines.patch index c3a475d..bd7cda1 100644 --- a/debian/patches/fix-shebang-lines.patch +++ b/debian/patches/fix-shebang-lines.patch @@ -1,3 +1,8 @@ +Description: Fix shebang lines + Fix invalid paths and replace usr/bin/env python with usr/bin/python. +Author: Afif Elghraoui <[email protected]> +Forwarded: no +Last-Update: 2016-02-26 --- pbsuite.orig/pbsuite/utils/quickN50.py +++ pbsuite/pbsuite/utils/quickN50.py @@ -1,4 +1,4 @@ @@ -14,3 +19,315 @@ import sys, os, glob, subprocess, logging from string import Template +--- pbsuite.orig/pbsuite/banana/MakeOverlapTable.py ++++ pbsuite/pbsuite/banana/MakeOverlapTable.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python + + import sys, glob, re, logging, json, os + from optparse import OptionParser +--- pbsuite.orig/pbsuite/banana/MakeReciprocal.py ++++ pbsuite/pbsuite/banana/MakeReciprocal.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python + + import sys, glob, re + from optparse import OptionParser +--- pbsuite.orig/pbsuite/banana/OLCAssembly.py ++++ pbsuite/pbsuite/banana/OLCAssembly.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python + import sys, os, tempfile, logging, subprocess, shutil, re, signal + from optparse import OptionParser + from StringIO import StringIO +--- pbsuite.orig/pbsuite/banana/Polish.py ++++ pbsuite/pbsuite/banana/Polish.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python + import sys, re, random, argparse, textwrap, logging + import operator + from collections import defaultdict, namedtuple +--- pbsuite.orig/pbsuite/honey/ComplexResolver.py ++++ pbsuite/pbsuite/honey/ComplexResolver.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python + import itertools, copy, argparse + from collections import defaultdict, Counter + import intervaltree_bio as bio +--- pbsuite.orig/pbsuite/honey/Force.py ++++ pbsuite/pbsuite/honey/Force.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python + import sys, argparse, re + from collections import defaultdict, namedtuple, Counter + import pysam +--- pbsuite.orig/pbsuite/honey/HSpots.py ++++ pbsuite/pbsuite/honey/HSpots.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python + import gc + import os + import re +--- pbsuite.orig/pbsuite/honey/HSpots.pyx ++++ pbsuite/pbsuite/honey/HSpots.pyx +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python + + import sys, time, re, gc, argparse, logging, bisect, math, copy, shutil, multiprocessing + import pysam, numpy, h5py +--- pbsuite.orig/pbsuite/honey/Honey.py ++++ pbsuite/pbsuite/honey/Honey.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python + + import argparse, sys + from pbsuite.utils.setupLogging import * +--- pbsuite.orig/pbsuite/honey/TGraf.py ++++ pbsuite/pbsuite/honey/TGraf.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python + import sys, bisect, argparse, tarfile, StringIO, os, pwd + import grp, logging, time, copy + from tempfile import NamedTemporaryFile +--- pbsuite.orig/pbsuite/honey/bakH.py ++++ pbsuite/pbsuite/honey/bakH.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python + + import sys, time, re, gc, argparse, logging, bisect, math, copy, shutil, multiprocessing, os, random + import pysam, numpy, h5py +--- pbsuite.orig/pbsuite/honey/bampie.py ++++ pbsuite/pbsuite/honey/bampie.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python + import os, re, argparse, logging, tempfile, sys + from collections import defaultdict + import pysam +--- pbsuite.orig/pbsuite/honey/massivePhrap.py ++++ pbsuite/pbsuite/honey/massivePhrap.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python + import os + import sys + import shutil +--- pbsuite.orig/pbsuite/honey/realign.py ++++ pbsuite/pbsuite/honey/realign.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python + import sys, re, time, logging + from collections import defaultdict + +--- pbsuite.orig/pbsuite/honey/recallSpots.py ++++ pbsuite/pbsuite/honey/recallSpots.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python + + import sys, logging, argparse + import pysam +--- pbsuite.orig/pbsuite/honey/spotH5Merge.py ++++ pbsuite/pbsuite/honey/spotH5Merge.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python + import sys, h5py, argparse + + from pbsuite.utils.setupLogging import * +--- pbsuite.orig/pbsuite/honey/spotH5dump.py ++++ pbsuite/pbsuite/honey/spotH5dump.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python + import sys + import h5py + +--- pbsuite.orig/pbsuite/honey/spotToBed.py ++++ pbsuite/pbsuite/honey/spotToBed.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python + import sys + import argparse + from pbsuite.utils import VCFIO +--- pbsuite.orig/pbsuite/honey/spotToVCF.py ++++ pbsuite/pbsuite/honey/spotToVCF.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python + import sys, os, argparse + from pbsuite.honey.HSpots import SpotResult + from pbsuite.utils import VCFIO +--- pbsuite.orig/pbsuite/jelly/Assembly.py ++++ pbsuite/pbsuite/jelly/Assembly.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python + import os, sys, argparse, logging, json + from tempfile import NamedTemporaryFile + +--- pbsuite.orig/pbsuite/jelly/Collection.py ++++ pbsuite/pbsuite/jelly/Collection.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python + + import sys, json + from glob import glob +--- pbsuite.orig/pbsuite/jelly/Extraction.py ++++ pbsuite/pbsuite/jelly/Extraction.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python + + import sys, glob, os, random + from optparse import OptionParser +--- pbsuite.orig/pbsuite/jelly/Jelly.py ++++ pbsuite/pbsuite/jelly/Jelly.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python + """ + document the protocol + """ +--- pbsuite.orig/pbsuite/jelly/QFix.py ++++ pbsuite/pbsuite/jelly/QFix.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python + + from pbsuite.utils.FileHandlers import FastqFile, M5File + from pbsuite.utils.CommandRunner import exe +--- pbsuite.orig/pbsuite/jelly/Setup.py ++++ pbsuite/pbsuite/jelly/Setup.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python + import sys, re, os, logging, subprocess + from optparse import OptionParser + +--- pbsuite.orig/pbsuite/jelly/Support.py ++++ pbsuite/pbsuite/jelly/Support.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python + import re, os, sys, logging, json, copy + from bisect import bisect_left, bisect_right + from optparse import OptionParser +--- pbsuite.orig/pbsuite/jelly/m4pie.py ++++ pbsuite/pbsuite/jelly/m4pie.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python + import os, re, argparse, logging, tempfile, sys + from collections import defaultdict + +--- pbsuite.orig/pbsuite/utils/BamStat.py ++++ pbsuite/pbsuite/utils/BamStat.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python + import sys, json, re, logging, argparse + + from pysam import Samfile +--- pbsuite.orig/pbsuite/utils/bamToFastq.py ++++ pbsuite/pbsuite/utils/bamToFastq.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python + import pysam, sys, argparse + from pbsuite.utils.FileHandlers import revComp + +--- pbsuite.orig/pbsuite/utils/blasrToBed.py ++++ pbsuite/pbsuite/utils/blasrToBed.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python + import sys + from pbsuite.utils.FileHandlers import M4File, M5File + +--- pbsuite.orig/pbsuite/utils/fakeQuals.py ++++ pbsuite/pbsuite/utils/fakeQuals.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python + import sys + from optparse import OptionParser + from FileHandlers import FastaFile +--- pbsuite.orig/pbsuite/utils/fastqDivide.py ++++ pbsuite/pbsuite/utils/fastqDivide.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python + import sys, argparse + from pbsuite.utils.setupLogging import * + +--- pbsuite.orig/pbsuite/utils/fastqSplit.py ++++ pbsuite/pbsuite/utils/fastqSplit.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python + + import sys + from optparse import OptionParser +--- pbsuite.orig/pbsuite/utils/longCCSCombine.py ++++ pbsuite/pbsuite/utils/longCCSCombine.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python + import sys, argparse + from collections import defaultdict, namedtuple + from pbsuite.utils.FileHandlers import FastqFile +--- pbsuite.orig/pbsuite/utils/mapStats.py ++++ pbsuite/pbsuite/utils/mapStats.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python + + """ + Parse a directory of m4 files and report mapping stats like: +--- pbsuite.orig/pbsuite/utils/mergeFaQu.py ++++ pbsuite/pbsuite/utils/mergeFaQu.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python + import sys + + from pbsuite.utils.FileHandlers import mergeFastaQual +--- pbsuite.orig/pbsuite/utils/readSummary.py ++++ pbsuite/pbsuite/utils/readSummary.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python + + import argparse, json + from pbsuite.jelly.Jelly import JellyProtocol +--- pbsuite.orig/pbsuite/utils/summarizeAssembly.py ++++ pbsuite/pbsuite/utils/summarizeAssembly.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python + import sys, re, math + from optparse import OptionParser + from string import Template +--- pbsuite.orig/pbsuite/utils/vcfTemplates/spotToVCF.py ++++ pbsuite/pbsuite/utils/vcfTemplates/spotToVCF.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python + import sys, os, argparse + from pbsuite.honey.HSpots import SpotResult + from pbsuite.utils import VCFIO -- Alioth's /usr/local/bin/git-commit-notice on 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