From b8598a888ed9b7302df16baaeb6e473252519d8a Mon Sep 17 00:00:00 2001 From: Chad Laing Date: Thu, 29 Jun 2017 13:46:12 -0600 Subject: [PATCH 1/5] Update .gitignore --- .gitignore | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.gitignore b/.gitignore index 5ec6a48..1cfff3b 100755 --- a/.gitignore +++ b/.gitignore @@ -32,3 +32,6 @@ blib/ /MYMETA.yml /MANIFEST !/MANIFEST +/t/_Inline/ +/t/sha1/ +/t/t/plasmids/ From cfc661deb943860110b3db21f911f70c93b783a7 Mon Sep 17 00:00:00 2001 From: Chad Laing Date: Thu, 29 Jun 2017 14:26:38 -0600 Subject: [PATCH 2/5] Move location of panseq to /bin --- lib/panseq.pl | 33 --------------------------------- 1 file changed, 33 deletions(-) delete mode 100755 lib/panseq.pl diff --git a/lib/panseq.pl b/lib/panseq.pl deleted file mode 100755 index 401298d..0000000 --- a/lib/panseq.pl +++ /dev/null @@ -1,33 +0,0 @@ -#!/usr/bin/env perl - -use strict; -use warnings; -use FindBin; -use lib "$FindBin::Bin"; -use Modules::Setup::Panseq; -use Modules::Setup::Settings; -use Log::Log4perl qw/:easy/; - -#need to get the settings up-front to allow log-file output -my $settings = Modules::Setup::Settings->new($ARGV[0]); -print "Settings file: $ARGV[0]\n"; - -#MUMmmer defaults its messages to STDERR -#we want them logged -#closing STDERR and associating it with Log4perl is done below -close STDERR; -tie *STDERR, "Tie::Log4perl"; - -my $panseq = Modules::Setup::Panseq->new($settings); -Log::Log4perl->init("$FindBin::Bin/log4p.conf"); - -$panseq->run(); - - -#HOOKS for log4p.conf -sub panseq_master_log_file{ - return ($settings->baseDirectory . 'Master.log'); -} - - - From 761c4128fab53c4a27aeeb9961c8caa9e4f7f027 Mon Sep 17 00:00:00 2001 From: Chad Laing Date: Thu, 29 Jun 2017 14:28:03 -0600 Subject: [PATCH 3/5] Update tests to new structure --- t/output.t | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/t/output.t b/t/output.t index a076fab..ad72b0f 100644 --- a/t/output.t +++ b/t/output.t @@ -365,7 +365,7 @@ sub _removeRun{ sub _runPanseq{ my $t=shift; - my $systemLine="perl $SCRIPT_LOCATION/../lib/panseq.pl $SCRIPT_LOCATION/$t.batch"; + my $systemLine="perl $SCRIPT_LOCATION/../bin/panseq $SCRIPT_LOCATION/$t.batch"; print "Systemline: $systemLine\n"; system($systemLine); } From b96d1a131d09bb7ff16c2d4571ba8abc746c7741 Mon Sep 17 00:00:00 2001 From: Chad Laing Date: Thu, 29 Jun 2017 14:28:30 -0600 Subject: [PATCH 4/5] Update tests to new structure --- bin/panseq | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 bin/panseq diff --git a/bin/panseq b/bin/panseq new file mode 100644 index 0000000..96bf371 --- /dev/null +++ b/bin/panseq @@ -0,0 +1,33 @@ +#!/usr/bin/env perl + +use strict; +use warnings; +use FindBin; +use lib "$FindBin::Bin/../lib/"; +use Modules::Setup::Panseq; +use Modules::Setup::Settings; +use Log::Log4perl qw/:easy/; + +#need to get the settings up-front to allow log-file output +my $settings = Modules::Setup::Settings->new($ARGV[0]); +print "Settings file: $ARGV[0]\n"; + +#MUMmmer defaults its messages to STDERR +#we want them logged +#closing STDERR and associating it with Log4perl is done below +close STDERR; +tie *STDERR, "Tie::Log4perl"; + +my $panseq = Modules::Setup::Panseq->new($settings); +Log::Log4perl->init("$FindBin::Bin/../lib/log4p.conf"); + +$panseq->run(); + + +#HOOKS for log4p.conf +sub panseq_master_log_file{ + return ($settings->baseDirectory . 'Master.log'); +} + + + From 39fd923b6e9a561abfa3d49cd9bf7021cfbf1fd7 Mon Sep 17 00:00:00 2001 From: James Hopkin Date: Tue, 4 Jul 2017 17:31:12 -0600 Subject: [PATCH 5/5] ADD: conda recipe --- conda_recipe/build.sh | 26 ++++++++++++++++++++++++++ conda_recipe/meta.yaml | 28 ++++++++++++++++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 conda_recipe/build.sh create mode 100644 conda_recipe/meta.yaml diff --git a/conda_recipe/build.sh b/conda_recipe/build.sh new file mode 100644 index 0000000..1859758 --- /dev/null +++ b/conda_recipe/build.sh @@ -0,0 +1,26 @@ +#!/bin/bash +# If it has Build.PL use that, otherwise use Makefile.PL +if [ -f Build.PL ]; then + perl Build.PL + sed -i.bak -e '1 s|^.*$|#!/usr/bin/env perl|' Build + ./Build installdeps + # Make sure this goes in site + ./Build install --installdirs site +elif [ -f Makefile.PL ]; then + # Make sure this goes in site + perl Makefile.PL INSTALLDIRS=site + make + make install +else + echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.' + exit 1 +fi + +export PERL5LIB="/opt/conda/lib/perl5/site_perl/5.22.0" +export PERL5LIB="/opt/conda/lib/perl5/site_perl/5.22.0/Modules" +export PERL5LIB="/opt/conda/lib/perl5/site_perl/5.22.0/x86_64-linux-thread-multi:$PERL5LIB" +# Add more build steps here, if they are necessary. + +# See +# http://docs.continuum.io/conda/build.html +# for a list of environment variables that are set during the build process. diff --git a/conda_recipe/meta.yaml b/conda_recipe/meta.yaml new file mode 100644 index 0000000..5bfcc7f --- /dev/null +++ b/conda_recipe/meta.yaml @@ -0,0 +1,28 @@ +package: + name: panseq + version: "3.1.1" + +source: + git_url: https://github.com/chadlaing/Panseq.git + +requirements: + build: + - libgcc + - perl-threaded + - perl-module-build + run: + - libgcc + - mummer + - muscle + - perl-threaded + - perl-module-build + - blast + - perl-archive-zip + - perl-bioperl + - perl-tie-log4perl + + +about: + home: https://github.com/chadlaing/Panseq + license: GNU GENERAL PUBLIC LICENSE +