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commit 8fd99a7e927cf243b0a56e71307f940de8589421 Author: Kevin Murray <[email protected]> Date: Sat Feb 6 14:11:04 2016 +0100 Add patch to fix path lookups remove unused patch and use python as executor of scripts --- debian/PartitionFinder | 2 +- debian/PartitionFinderProtein | 2 +- .../0001-Add-crunchbangs-and-chmod-x-scripts.patch | 33 --------------- ...-raxml-path-locate-binaries-under-usr-bin.patch | 49 ++++++++++++++++++++++ debian/patches/series | 2 +- 5 files changed, 52 insertions(+), 36 deletions(-) diff --git a/debian/PartitionFinder b/debian/PartitionFinder index 70e072c..0b399a9 100644 --- a/debian/PartitionFinder +++ b/debian/PartitionFinder @@ -1,3 +1,3 @@ #!/bin/sh -e -PYTHONPATH=/USRLIB/partitionfiner /USRLIB/partitionfinder/PartitionFinder.py $@ +PYTHONPATH=/USRLIB/partitionfiner python /USRLIB/partitionfinder/PartitionFinder.py $@ diff --git a/debian/PartitionFinderProtein b/debian/PartitionFinderProtein index 6477627..ade91e9 100644 --- a/debian/PartitionFinderProtein +++ b/debian/PartitionFinderProtein @@ -1,3 +1,3 @@ #!/bin/sh -e -PYTHONPATH=/USRLIB/partitionfiner /USRLIB/partitionfinder/PartitionFinderProtein.py $@ +PYTHONPATH=/USRLIB/partitionfiner python /USRLIB/partitionfinder/PartitionFinderProtein.py $@ diff --git a/debian/patches/0001-Add-crunchbangs-and-chmod-x-scripts.patch b/debian/patches/0001-Add-crunchbangs-and-chmod-x-scripts.patch deleted file mode 100644 index 3246a1f..0000000 --- a/debian/patches/0001-Add-crunchbangs-and-chmod-x-scripts.patch +++ /dev/null @@ -1,33 +0,0 @@ -From: Kevin Murray <[email protected]> -Date: Tue, 10 Nov 2015 20:34:26 +1100 -Subject: Add crunchbangs and chmod +x scripts - ---- - PartitionFinder.py | 1 + - PartitionFinderProtein.py | 1 + - 2 files changed, 2 insertions(+) - mode change 100644 => 100755 PartitionFinder.py - mode change 100644 => 100755 PartitionFinderProtein.py - -diff --git a/PartitionFinder.py b/PartitionFinder.py -old mode 100644 -new mode 100755 -index 6ef5fbc..f83508a ---- a/PartitionFinder.py -+++ b/PartitionFinder.py -@@ -1,3 +1,4 @@ -+#!/usr/bin/python2.7 - # Copyright (C) 2012 Robert Lanfear and Brett Calcott - # - # This program is free software: you can redistribute it and/or modify it under -diff --git a/PartitionFinderProtein.py b/PartitionFinderProtein.py -old mode 100644 -new mode 100755 -index 2c5517d..27fb759 ---- a/PartitionFinderProtein.py -+++ b/PartitionFinderProtein.py -@@ -1,3 +1,4 @@ -+#!/usr/bin/python2.7 - # Copyright (C) 2012 Robert Lanfear and Brett Calcott - # - # This program is free software: you can redistribute it and/or modify it under diff --git a/debian/patches/0001-Fix-raxml-path-locate-binaries-under-usr-bin.patch b/debian/patches/0001-Fix-raxml-path-locate-binaries-under-usr-bin.patch new file mode 100644 index 0000000..8a7de02 --- /dev/null +++ b/debian/patches/0001-Fix-raxml-path-locate-binaries-under-usr-bin.patch @@ -0,0 +1,49 @@ +From: Kevin Murray <[email protected]> +Date: Sat, 6 Feb 2016 14:09:43 +0100 +Subject: Fix raxml path, locate binaries under /usr/bin + +--- + partfinder/raxml.py | 2 +- + partfinder/util.py | 16 ++-------------- + 2 files changed, 3 insertions(+), 15 deletions(-) + +diff --git a/partfinder/raxml.py b/partfinder/raxml.py +index a3edb93..364240e 100644 +--- a/partfinder/raxml.py ++++ b/partfinder/raxml.py +@@ -37,7 +37,7 @@ _dna_letters = "ATCG" + # This is set as the binary name because the previously compiled raxml had a + # bug when calculating site likelihoods, this needs to be changed back to + # "raxml" once a newer version without the bug is compiled. +-_binary_name = 'raxml' ++_binary_name = 'raxmlHPC' + if sys.platform == 'win32': + _binary_name += ".exe" + _raxml_binary = None +diff --git a/partfinder/util.py b/partfinder/util.py +index 834b251..81b3b4c 100644 +--- a/partfinder/util.py ++++ b/partfinder/util.py +@@ -47,20 +47,8 @@ your alignment. Please check and try again. + + def find_program(binary_name): + """Locate the binary ...""" +- pth = os.path.abspath(__file__) +- +- # Split off the name and the directory... +- pth, notused = os.path.split(pth) +- pth, notused = os.path.split(pth) +- pth = os.path.join(pth, "programs", binary_name) +- pth = os.path.normpath(pth) +- +- log.debug("Checking for program %s", binary_name) +- if not os.path.exists(pth) or not os.path.isfile(pth): +- log.error("No such file: '%s'", pth) +- raise PartitionFinderError +- log.debug("Found program %s at '%s'", binary_name, pth) +- return pth ++ # No, this is Debian. We know where the binary is. ++ return os.path.join('/usr/bin', binary_name) + + + def run_program(binary, command): diff --git a/debian/patches/series b/debian/patches/series index 8ad3202..b712fb0 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1 +1 @@ -0001-Add-crunchbangs-and-chmod-x-scripts.patch +0001-Fix-raxml-path-locate-binaries-under-usr-bin.patch -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/partitionfinder.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
