Merge pull request #1 from stjude/docker_rework

Docker rework

Dockerfile

@@ -0,0 +1,52 @@
+FROM alpine:latest
+# build from Alpine for much smaller final image
+
+# Set working dir as /RNApeg
+WORKDIR /RNApeg
+
+# Tell the OS that this is a non-interactive frontend only for build
+ARG DEBIAN_FRONTEND=noninteractive
+
+#
+#  Alpine-based install:
+#
+RUN apk add --no-cache openjdk8-jre
+# don't need full JDK, just runtime
+RUN apk add --no-cache curl
+RUN apk add --no-cache make
+RUN apk add --no-cache gcc
+RUN apk add --no-cache perl
+RUN apk add --no-cache perl-utils
+# for "cpan" command-line utility
+RUN apk add --no-cache perl-dev
+RUN apk add --no-cache musl-dev
+# these two for headers required to build perl DBI module
+RUN apk add --no-cache perl-doc
+# required for perl "use diagnostics", used by SampleName.pm
+RUN apk add --no-cache db-dev
+RUN apk add --no-cache expat-dev
+
+# Install perl modules
+RUN cpan App:cpanminus
+RUN cpanm --no-wget Data::Compare && chown -R root:root /root/.cpanm
+RUN cpanm --no-wget DB_File XML::Parser::PerlSAX XML::Twig XML::DOM
+RUN cpanm --no-wget Bio::Tools::CodonTable
+RUN cpanm --no-wget DBI
+RUN cpanm --no-wget Set::IntSpan
+
+# Put code into place
+COPY src/main/scripts /RNApeg/src/bin
+COPY src/main/java /RNApeg/src/javalib
+COPY src/main/perllib /RNApeg/src/perllib
+COPY dependencies/bin /RNApeg/src/bin
+COPY dependencies/lib/java /RNApeg/src/javalib
+COPY dependencies/lib/perl /RNApeg/src/perllib
+COPY src/main/docker/RNApeg.sh /RNApeg/src/bin
+
+# Change environment variables
+ENV PATH="/RNApeg/src/bin:${PATH}"
+ENV PERL5LIB="/RNApeg/src/perllib:${PERL5LIB}"
+ENV CLASSPATH=/RNApeg/src/javalib/*
+
+ENTRYPOINT ["/RNApeg/src/bin/RNApeg.sh"]
+CMD ["-h"]

src/main/scripts/aberrant_splicing_summary.pl

@@ -1,4 +1,4 @@
-#!/bin/env perl
+#!/usr/bin/env perl
 # simple reporting of strongest evidence of aberrant splicing by gene
 #
 # TO DO:

src/main/scripts/junction2bed.pl

@@ -1,4 +1,4 @@
-#!/bin/env perl
+#!/usr/bin/env perl
 # convert tab-delimited annotated junction file to .bed format
 # (w/various optional filters)
 #

src/main/scripts/junction2gencode.pl

@@ -1,4 +1,4 @@
-#!/bin/env perl
+#!/usr/bin/env perl
 # annotate junction files re: "primary" ENSEMBL transcripts
 # MNE 2/2015
 #

src/main/scripts/junction_excerpt.pl

@@ -1,4 +1,4 @@
-#!/bin/env perl
+#!/usr/bin/env perl
 # create
 
 use strict;

src/main/scripts/junction_extraction_wrapper.pl

@@ -347,15 +347,15 @@ sub perl_test {
 
 
   my @cmds;
-  push @cmds, "/bin/env perl -v";
-  push @cmds, '/bin/env perl -e \'print "perl binary=$^X\n"\'';
+  push @cmds, "/usr/bin/env perl -v";
+  push @cmds, '/usr/bin/env perl -e \'print "perl binary=$^X\n"\'';
 
   foreach my $script (qw(
 			  bam_junction.pl
 			  floating_junction_fix.pl
 			  junction2gene.pl
 		       )) {
-    push @cmds, sprintf '/bin/env perl -cw `which %s`', $script;
+    push @cmds, sprintf '/usr/bin/env perl -cw `which %s`', $script;
   }
 
   foreach my $cmd (@cmds) {

src/main/scripts/junction_filter.pl

@@ -1,4 +1,4 @@
-#!/bin/env perl
+#!/usr/bin/env perl
 # remove novel junctions present in other junction files
 
 use strict;

src/main/scripts/junction_gene_extract.pl

@@ -1,4 +1,4 @@
-#!/bin/env perl
+#!/usr/bin/env perl
 # extract results for individual genes from rnapeg output,
 # in tab-delimited and .bed format
 # MNE 7/2014

src/main/scripts/known_downgrade.pl

@@ -1,4 +1,4 @@
-#!/bin/env perl
+#!/usr/bin/env perl
 # downgrade "known" junctions to "novel" if evidence is exclusive to
 # a database we don't want to use for aberrant classification (e.g. AceView)
 # Do this AFTER standard annotation/correction:

src/main/scripts/novel_exon_junction_finder.pl

@@ -1,4 +1,4 @@
-#!/bin/env perl
+#!/usr/bin/env perl
 # in corrected junction counts, find:
 # - novel skips of known exons
 # - novel exons (1 end bounding known exon)

src/main/scripts/report_excerpt.pl

@@ -1,4 +1,4 @@
-#!/bin/env perl
+#!/usr/bin/env perl
 
 use strict;
 use warnings;