From 726a662c2c2fe3e366005f188b4c2fa41bb3f0dc Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Wed, 15 Jan 2020 11:31:51 -0600 Subject: Change encoding for scripts in repeatmasker (#14358) This PR converts ISO-8859 encoding to UTF-8 encoding for three scripts in repeatmasker. - the main RepeatMasker script - SimpleBatcher.pm - wublastToCrossmatch.pl The ISO-8859 encoding prevented the sbang replacement of long paths when spack uses python3. --- .../repos/builtin/packages/repeatmasker/package.py | 2 + .../repos/builtin/packages/repeatmasker/utf8.patch | 198 +++++++++++++++++++++ 2 files changed, 200 insertions(+) create mode 100644 var/spack/repos/builtin/packages/repeatmasker/utf8.patch (limited to 'var') diff --git a/var/spack/repos/builtin/packages/repeatmasker/package.py b/var/spack/repos/builtin/packages/repeatmasker/package.py index c9b7d52875..15aa062b35 100644 --- a/var/spack/repos/builtin/packages/repeatmasker/package.py +++ b/var/spack/repos/builtin/packages/repeatmasker/package.py @@ -29,6 +29,8 @@ class Repeatmasker(Package): depends_on('phrap-crossmatch-swat', type=('build', 'run'), when='+crossmatch') + patch('utf8.patch') + def url_for_version(self, version): url = 'http://www.repeatmasker.org/RepeatMasker-open-{0}.tar.gz' return url.format(version.dashed) diff --git a/var/spack/repos/builtin/packages/repeatmasker/utf8.patch b/var/spack/repos/builtin/packages/repeatmasker/utf8.patch new file mode 100644 index 0000000000..529b8809d5 --- /dev/null +++ b/var/spack/repos/builtin/packages/repeatmasker/utf8.patch @@ -0,0 +1,198 @@ +diff -ru a/RepeatMasker b/RepeatMasker +--- a/RepeatMasker 2020-01-01 16:16:26.201675025 -0600 ++++ b/RepeatMasker 2020-01-01 16:18:02.059526821 -0600 +@@ -1347,7 +1347,7 @@ + ## + ## Globals Used: None + ## +-##-------------------------------------------------------------------------##· ++##-------------------------------------------------------------------------##· + sub adjustFragmentPositions { + my $batcher = shift; + my $catfile = shift; +@@ -1456,7 +1456,7 @@ + ## to decypher this subroutine. + ## + ## Globals Used: none +-##-------------------------------------------------------------------------##· ++##-------------------------------------------------------------------------##· + sub locateISElements { + my %options = %{ shift() }; + my $batcher = shift; +@@ -2951,7 +2951,7 @@ + ## + ## Globals Used: None + ## Globals Modified: None +-##-------------------------------------------------------------------------##· ++##-------------------------------------------------------------------------##· + sub runLowComplexTests { + my %options = %{ shift() }; # The RepeatMasker option hashtable + my $DIRECTORY = shift; +@@ -3988,7 +3988,7 @@ + ## + ## Globals Used: None + ## Globals Modified: None +-##-------------------------------------------------------------------------##· ++##-------------------------------------------------------------------------##· + sub runSearchStages { + my %options = %{ shift() }; # The RepeatMasker option hashtable + my $DIRECTORY = shift; +@@ -4707,7 +4707,7 @@ + ## Returns + ## + ## Globals Used: None +-##-------------------------------------------------------------------------##· ++##-------------------------------------------------------------------------##· + sub chooseMatrices { + my $GC_frac = shift; + +@@ -4910,7 +4910,7 @@ + ## + ## Globals Used: None + ## +-##-------------------------------------------------------------------------##· ++##-------------------------------------------------------------------------##· + sub preMaskLevelFilter { + my $searchResults = shift; + +@@ -4999,7 +4999,7 @@ + ## + ## Globals Used: None + ## +-##-------------------------------------------------------------------------##· ++##-------------------------------------------------------------------------##· + sub filterResults { + my %options = %{ shift() }; + my $chooseClass = shift; +@@ -5860,7 +5860,7 @@ + ## Returns + ## + ## Globals Used: None +-##-------------------------------------------------------------------------##· ++##-------------------------------------------------------------------------##· + sub calcSimpleRepeatComplexityFromName { + my %num = ( "A", 0, "C", 0, "G", 0, "T", 0 ); + my %log = ( "A", 0, "C", 0, "G", 0, "T", 0 ); +@@ -5902,7 +5902,7 @@ + ## revamped to use a SearchResultCollection. + ## + ## NO Globals Used +-##-------------------------------------------------------------------------##· ++##-------------------------------------------------------------------------##· + sub getSegments { + my $resultsCollection = shift; + +@@ -6661,7 +6661,7 @@ + ## Returns + ## + ## Globals Used: None +-##-------------------------------------------------------------------------##· ++##-------------------------------------------------------------------------##· + sub saveOldFiles { + my $fijl = shift; + my $fileend = shift; +@@ -6708,7 +6708,7 @@ + ## Returns + ## + ## Globals Used: None +-##-------------------------------------------------------------------------##· ++##-------------------------------------------------------------------------##· + sub SkipFile { + my $file = shift; + +@@ -6734,7 +6734,7 @@ + ## about how files are passed to repeatmasker etc.. + ## + ## Globals Used: ARGV[0] +-##-------------------------------------------------------------------------##· ++##-------------------------------------------------------------------------##· + sub createTempDir { + my %options = %{ shift() }; + my $date = shift; +@@ -6792,7 +6792,7 @@ + ## Returns + ## + ## Globals Used: None +-##-------------------------------------------------------------------------##· ++##-------------------------------------------------------------------------##· + ### Interrupt handler used by systemint() ### + sub handler { + my ( $sig ) = @_; +@@ -6808,7 +6808,7 @@ + ## Returns + ## + ## Globals Used: None +-##-------------------------------------------------------------------------##· ++##-------------------------------------------------------------------------##· + ### systemint -- Interruptible system call routine. ### + sub systemint { + my ( $cmd ) = @_; +@@ -6869,7 +6869,7 @@ + ## Expects $options{'dir'} ( if set ) to already exist. + ## + ## Globals Used: None +-##-------------------------------------------------------------------------##· ++##-------------------------------------------------------------------------##· + sub cleanUp { + my %options = %{ shift() }; + my $runnumber = shift; +@@ -6987,7 +6987,7 @@ + ## matching sequences. + ## + ## Globals Used: None +-##-------------------------------------------------------------------------##· ++##-------------------------------------------------------------------------##· + sub createLib { + my $options = %{ shift() }; + my $db = shift; +@@ -7322,7 +7322,7 @@ + ## will create the frozen databases for WUBlast. + ## + ## Globals Used: None +-##-------------------------------------------------------------------------##· ++##-------------------------------------------------------------------------##· + sub processCustomLib { + my $options = %{ shift() }; + my $tempdir = shift; +@@ -7416,7 +7416,7 @@ + ## refined. + ## + ## Globals Used: None +-##-------------------------------------------------------------------------##· ++##-------------------------------------------------------------------------##· + sub buildRefineableHash { + my $db = shift; + +@@ -7447,7 +7447,7 @@ + ## Returns + ## + ## Globals Used: None +-##-------------------------------------------------------------------------##· ++##-------------------------------------------------------------------------##· + sub initLibraries { + my %options = %{ shift() }; + my $rmLibDir = shift; +diff -ru a/SimpleBatcher.pm b/SimpleBatcher.pm +--- a/SimpleBatcher.pm 2020-01-01 16:16:26.203675022 -0600 ++++ b/SimpleBatcher.pm 2020-01-01 16:17:24.464585016 -0600 +@@ -559,7 +559,7 @@ + ## } + ## }; + ## +-##------------------------------------------------------------------------##· ++##------------------------------------------------------------------------##· + sub _packBatches { + my $this = shift; + my $seqDBObj = shift; +diff -ru a/util/wublastToCrossmatch.pl b/util/wublastToCrossmatch.pl +--- a/util/wublastToCrossmatch.pl 2020-01-01 16:16:26.202675024 -0600 ++++ b/util/wublastToCrossmatch.pl 2020-01-01 16:17:38.181563793 -0600 +@@ -244,7 +244,7 @@ + + =cut + +-##-------------------------------------------------------------------------##· ++##-------------------------------------------------------------------------##· + sub publicMethod { + my %parameters = @_; + -- cgit v1.2.3-60-g2f50