WIP Supernova cloud pipeline scripts to convert

bin/run-mkoutput

@@ -0,0 +1,24 @@
+#!/bin/bash
+
+set -e
+
+assembly_id="${1}"
+if [ -z "${assembly_id}" ]; then
+	echo "USAGE: $0 ASSEMBLY_ID"
+	exit 1
+fi
+
+assembly_dir="/mnt/disks/linked-reads-pilot/assembly/${assembly_id}";
+if [ ! -d "${assembly_dir}" ]; then
+	echo "No assembly directory! ${assembly_dir}"
+	exit 1
+fi
+
+mkoutput_dir="${assembly_dir}/mkoutput";
+mkdir -p "${mkoutput_dir}"
+cd "${mkoutput_dir}"
+
+source /opt/supernova-2.0.0/sourceme.bash
+for style in raw megabubbles pseudohap2; do
+	exec "supernova mkoutput --asmdir=$assembly_dir/outs/assembly --outprefix=${assembly_id}.${style} --style=${style}"
+done

bin/run-supernova

@@ -0,0 +1,48 @@
+#!/bin/bash
+
+set -e
+
+sample="${1}"
+if [ -z "${sample}" ]; then
+    echo "No sample given!"
+    exit 1
+fi
+
+echo "GCloud Auth"
+gcloud auth activate-service-account --key-file /etc/gcp-auth/WashU-Genome-Inh-Dis-Analysis.service-account-key.json
+
+data_base_path="/mnt/disks/data"
+fastq_path="${data_base_path}/reads/${sample}"
+mkdir -p "${fastq_path}"
+assembly_base_path="${data_base_path}/assembly"
+mkdir -p "${assembly_base_path}"
+
+echo "Sample: ${sample}"
+echo "Rsyncing fastqs from the object store..."
+cd "${fastq_path}"
+gsutil ls gs://mgi-rg-linked-reads-ccdg-pilot/reads/H53J3DSXX/${sample}/
+gsutil -m rsync -r gs://mgi-rg-linked-reads-ccdg-pilot/reads/H53J3DSXX/${sample}/ .
+echo "Rsyncing fastqs from the object store...OK"
+
+echo "Running supernova..."
+cd "${assbemly_base_path}"
+source /opt/supernova-2.0.1/sourceme.bash
+supernova run --id="${sample}" --fastqs="${fastq_path}" --uiport=63108 --nodebugmem --localcores=50 --localmem=320
+echo "Running supernova...OK"
+
+echo "Running mkoutput..."
+assembly_path="${assembly_base_path}/${sample}"
+mkoutput_path="${assembly_path}/mkoutput";
+mkdir -p "${mkoutput_path}"
+cd "${mkoutput_dir}"
+for style in raw megabubbles pseudohap2; do
+	exec supernova mkoutput --asmdir="${assembly_path}/outs/assembly" --outprefix="${sample}.${style}" --style="${style}"
+done
+echo "Running mkoutput...OK"
+
+echo "Rsyncing assembly to object store..."
+cd "${assembly_base_path}"
+echo gsutil -m rsync -r "${sample}" "gs://mgi-rg-linked-reads-ccdg-pilot/assembly/${sample}"
+echo "Rsyncing assembly to object store...OK"
+
+echo "Done!"

lib/Tenx/Assembly/Command/Mkoutput.pm

@@ -0,0 +1,39 @@
+package Tenx::Assembly::Command::Mkoutput;
+
+use strict;
+use warnings 'FATAL';
+
+class Tenx::Assembly::Command::Mkoutput {
+    is => 'Command::V2',
+    has_input => {
+        assembly => {
+            is => 'Tenx::Assembly',
+            doc => 'The assembly to run mkoutput on.',
+        },
+        styles => {
+            is => 'Text',
+            is_many => 1,
+            valid_values => [qw/ raw megabubbles pseudohap2 /],
+            default_value => 'raw,megabubbles,pseudohap2',
+            doc => 'The style of mkutput to run.',
+        },
+    },
+};
+
+sub shortcut {
+    die "shortcut is not implemented"
+}
+
+sub execute {
+    my ($self) = @_;
+
+    #mkdir $self->assembly->mkoutput_path;
+
+    for my $style ( $self->styles ) {
+        $self->status_message("Style: $style");
+    }
+
+    1;
+}
+
+1;