Bin directory

.gitignore

@@ -32,3 +32,6 @@ blib/
 /MYMETA.yml
 /MANIFEST
 !/MANIFEST
+/t/_Inline/
+/t/sha1/
+/t/t/plasmids/

lib/panseq.pl → bin/panseq

@@ -3,7 +3,7 @@
 use strict;
 use warnings; 
 use FindBin;
-use lib "$FindBin::Bin";
+use lib "$FindBin::Bin/../lib/";
 use Modules::Setup::Panseq;
 use Modules::Setup::Settings;
 use Log::Log4perl qw/:easy/;
@@ -19,7 +19,7 @@
 tie *STDERR, "Tie::Log4perl";
 
 my $panseq = Modules::Setup::Panseq->new($settings);
-Log::Log4perl->init("$FindBin::Bin/log4p.conf");
+Log::Log4perl->init("$FindBin::Bin/../lib/log4p.conf");
 
 $panseq->run();
 

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.

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
+

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);
 }