From e7adf9392699caa317898391d79d09bbd399f8e8 Mon Sep 17 00:00:00 2001 From: Nathan Dunn Date: Mon, 4 Feb 2019 20:23:14 -0800 Subject: [PATCH] reverting back to a working state --- apollo | 5 +++-- tools/data/add_features_from_gff3_to_annotations.pl | 1 + tools/data/add_transcripts_from_gff3_to_annotations.pl | 1 + 3 files changed, 5 insertions(+), 2 deletions(-) diff --git a/apollo b/apollo index 6f12c1d99d..1523f96931 100755 --- a/apollo +++ b/apollo @@ -207,8 +207,9 @@ function link_jbrowse_tools(){ rm -rf bin ln -s jbrowse/bin bin cd jbrowse - ./bin/cpanm --notest --local-lib=extlib Bio::GFF3::LowLevel::Parser CGI Devel::Size Digest::Crc32 JSON File::Next Hash::Merge Heap::Simple Heap::Simple::Perl Heap::Simple::XS PerlIO::gzip - ./bin/cpanm --notest --local-lib=jbrowse/src/perl5 LWP::UserAgent +# ./bin/cpanm --notest --local-lib=extlib Bio::GFF3::LowLevel::Parser CGI Devel::Size Digest::Crc32 JSON File::Next Hash::Merge Heap::Simple Heap::Simple::Perl Heap::Simple::XS PerlIO::gzip +# ./bin/cpanm --notest --local-lib=jbrowse/src/perl5 LWP::UserAgent + ./bin/cpanm --notest --local-lib=ext-lib Bio::GFF3::LowLevel::Parser CGI Devel::Size Digest::Crc32 JSON File::Next Hash::Merge Heap::Simple Heap::Simple::Perl Heap::Simple::XS PerlIO::gzip cd .. echo "**********************************"; echo "JBrowse Tools installed in './bin'"; diff --git a/tools/data/add_features_from_gff3_to_annotations.pl b/tools/data/add_features_from_gff3_to_annotations.pl index 8787fbd9d9..58fe93242f 100755 --- a/tools/data/add_features_from_gff3_to_annotations.pl +++ b/tools/data/add_features_from_gff3_to_annotations.pl @@ -5,6 +5,7 @@ use FindBin qw($RealBin); use lib "$RealBin/../../jbrowse/src/perl5"; +use JBlibs; use File::Basename; use lib dirname($0); diff --git a/tools/data/add_transcripts_from_gff3_to_annotations.pl b/tools/data/add_transcripts_from_gff3_to_annotations.pl index 6a871f34ea..f28b2533c7 100755 --- a/tools/data/add_transcripts_from_gff3_to_annotations.pl +++ b/tools/data/add_transcripts_from_gff3_to_annotations.pl @@ -5,6 +5,7 @@ use FindBin qw($RealBin); use lib "$RealBin/../../jbrowse/src/perl5"; +use JBlibs; use File::Basename; use lib dirname($0);