From d92d0c055b87c2e85df7d6326ad1a3146cd2ece4 Mon Sep 17 00:00:00 2001 From: Colin Date: Wed, 20 Feb 2019 19:43:22 -0500 Subject: [PATCH] Revert "Remove hardcoded bioperl" This reverts commit b98c454c2a3dd3a36fe1247b9a45ca7a6827d23b. --- Makefile.PL | 2 +- setup.sh | 5 +++++ 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/Makefile.PL b/Makefile.PL index e0df04e220..fa810f223e 100644 --- a/Makefile.PL +++ b/Makefile.PL @@ -51,7 +51,6 @@ my %WriteMakefileArgs = ( "NAME" => "JBrowse", "PREREQ_PM" => { "Bio::Annotation::SimpleValue" => 0, - "Bio::DB::SeqFeature" => 0, "Bio::FeatureIO" => 0, "Bio::GFF3::LowLevel" => "1.8", "Bio::GFF3::LowLevel::Parser" => "1.8", @@ -59,6 +58,7 @@ my %WriteMakefileArgs = ( "Bio::OntologyIO" => 0, "Bio::Root::Version" => "1.006000", "Bio::SeqFeature::Annotated" => 0, + "Bio::SeqFeature::Lite" => 0, #< for Bio::DB::BAM "Carp" => 0, "Cwd" => 0, "DBI" => 0, diff --git a/setup.sh b/setup.sh index 90d90be15d..85dc6829b7 100755 --- a/setup.sh +++ b/setup.sh @@ -130,6 +130,11 @@ if ! ( perl -MExtUtils::MakeMaker -e 1 >/dev/null 2>&1); then log_echo "WARNING: Your Perl installation does not seem to include a complete set of core modules. Attempting to cope with this, but if installation fails please make sure that at least ExtUtils::MakeMaker is installed. For most users, the best way to do this is to use your system's package manager: apt, yum, fink, homebrew, or similar."; fi; ( set -x; + bin/cpanm -v --notest -l extlib/ Bio::Perl@1.7.2 < /dev/null; + bin/cpanm -v --notest -l extlib/ Bio::Perl@1.7.2 < /dev/null; + set -e + bin/cpanm -v --notest -l extlib/ Bio::Perl@1.7.2 < /dev/null; + set -x; bin/cpanm -v --notest -l extlib/ --installdeps . < /dev/null; bin/cpanm -v --notest -l extlib/ --installdeps . < /dev/null; set -e;