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Add better test samples (resolves #166) #167

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Add better test samples (resolves #166) #167

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25 changes: 14 additions & 11 deletions src/toil_rnaseq/test/test_rnaseq_cgl.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,6 @@
import logging
import os
import posixpath
import shlex
import shutil
import subprocess
Expand All @@ -9,8 +11,6 @@
from urlparse import urlparse
from uuid import uuid4

import os
import posixpath
from bd2k.util.iterables import concat
from boto.s3.connection import S3Connection, Bucket

Expand All @@ -37,10 +37,13 @@ def setUpClass(cls):
logging.basicConfig(level=logging.INFO)

def setUp(self):
self.input_dir = urlparse('s3://cgl-pipeline/rnaseq_cgl/ci')
# S3 bucket link
self.output_dir = urlparse('s3://cgl-driver-projects/test/ci/%s' % uuid4())
self.sample = urlparse(self.input_dir.geturl() + '/chr6_sample.tar.gz')
self.bam_sample = urlparse(self.input_dir.geturl() + '/chr6.test.bam')
# URLs to chr6 sample
self.input_url = urlparse('http://courtyard.gi.ucsc.edu/~jvivian/toil-rnaseq-inputs/')
self.sample = urlparse(os.path.join(self.input_url.geturl(), 'continuous_integration/chr6_paired.tar.gz'))
self.bam_sample = urlparse(self.input_url.geturl() + 'continuous_integration/chr6.test.bam')
# Command setup
self.workdir = tempfile.mkdtemp()
jobStore = os.getenv('TOIL_SCRIPTS_TEST_JOBSTORE', os.path.join(self.workdir, 'jobstore-%s' % uuid4()))
toilOptions = shlex.split(os.environ.get('TOIL_SCRIPTS_TEST_TOIL_OPTIONS', ''))
Expand Down Expand Up @@ -88,14 +91,14 @@ def _generate_config(self):
path = os.path.join(self.workdir, 'config-toil-rnaseq.yaml')
with open(path, 'w') as f:
f.write(textwrap.dedent("""
star-index: {input_dir}/starIndex_chr6.tar.gz
kallisto-index: s3://cgl-pipeline/rnaseq_cgl/kallisto_hg38.idx
rsem-ref: {input_dir}/rsem_ref_chr6.tar.gz
hera-index: s3://cgl-pipeline/rnaseq_cgl/hera-index.tar.gz
star-index: {input_url}/continuous_integration/starIndex_chr6.tar.gz
rsem-ref: {input_url}/continuous_integration/rsem_ref_chr6.tar.gz
kallisto-index: {input_url}/kallisto_hg38.idx
hera-index: {input_url}/hera-index.tar.gz
output-dir: {output_dir}
max-sample-size: 2G
fastqc: true
cutadapt:
cutadapt: true
ssec:
gdc-token:
wiggle:
Expand All @@ -105,7 +108,7 @@ def _generate_config(self):
bamqc: true
ci-test: true
"""[1:]).format(output_dir=self.output_dir.geturl(),
input_dir=self.input_dir.geturl()))
input_url=self.input_url.geturl()))
return path

def _generate_manifest(self, num_samples=1, bam=False):
Expand Down