15133: Delete crunch_scripts, start clearing out API server

[arvados.git] / crunch_scripts / rtg-snp

diff --git a/crunch_scripts/rtg-snp b/crunch_scripts/rtg-snp
deleted file mode 100755 (executable)
index 1d8a605..0000000
--- a/crunch_scripts/rtg-snp
+++ /dev/null
@@ -1,34 +0,0 @@
-#!/usr/bin/env python
-# Copyright (C) The Arvados Authors. All rights reserved.
-#
-# SPDX-License-Identifier: Apache-2.0
-
-import arvados
-import os
-import re
-import sys
-import pyrtg
-
-this_job = arvados.current_job()
-this_task = arvados.current_task()
-ref_dir = arvados.util.collection_extract(
-    collection = this_job['script_parameters']['reference'],
-    path = 'reference',
-    decompress = False)
-input_dir = arvados.util.collection_extract(
-    collection = this_job['script_parameters']['input'],
-    path = 'input')
-bam_files = map(lambda f: os.path.join(input_dir, f),
-                filter(lambda f: re.search(r'^(.*/)?alignments.bam$', f),
-                       arvados.util.listdir_recursive(input_dir)))
-out_dir = os.path.join(arvados.current_task().tmpdir, 'out')
-arvados.util.run_command(['rm', '-rf', out_dir], stderr=sys.stderr)
-
-# call sequence variants
-pyrtg.run_rtg('snp', out_dir,
-              ['-t', ref_dir] + bam_files)
-
-# store output
-out = arvados.CollectionWriter()
-out.write_directory_tree(out_dir, max_manifest_depth=0)
-this_task.set_output(out.finish())