<p>Somebody helped me with this one through other channels, but I wanted to make it publicly available:</p>
<p>Make a tarball of the STAR index. The option <code>--strip-components=1</code> strips the first level of the path from the untarred items; thus, the expected tarball was made with something like</p>
<pre><code>tar -cvf ${star_index} the_star_index_directory/
</code></pre>
<p>Then point Cromwell/WDL to the tarball, e.g. on S3. The GTEx container will unwrap the tarball on the fly during execution.</p>

CC BY-SA 4.0
2020-09-14T02:41:15.123Z
2020-09-14T02:41:15.123Z
Kevin L. Keys
<p>I'm trying to run the WDL tasks from the <a href="https://github.com/broadinstitute/gtex-pipeline" rel="nofollow noreferrer">GTEx RNA-Seq pipeline</a> with Cromwell using AWS Batch as a backend.</p>
<p>I store the STAR alignment index on an Elastic Block Store since my Cromwell server instance lacks sufficient disk space. The EBS Block is mounted to my Cromwell server at <code>/data</code>. The STAR index is located at <code>/data/genomic-references/rnaseq/star_index_oh50</code>.</p>
<p>Try as I might, I cannot get Cromwell to run the STAR task correctly.</p>
<p>My JSON inputs file:</p>
<pre><code> {
   &quot;rnaseq_pipeline_fastq_workflow.prefix&quot;: &quot;s3://mybucket/test/CL100148068&quot;,
   &quot;rnaseq_pipeline_fastq_workflow.star.fastq1&quot;: &quot;s3://anotherbucket/genotypedata/sample1.fq.gz&quot;,
   &quot;rnaseq_pipeline_fastq_workflow.star.star_index&quot;: &quot;/data/genomic-references/rnaseq/star_index_oh50/&quot;,
   &quot;rnaseq_pipeline_fastq_workflow.star.memory&quot;: &quot;32&quot;,
   &quot;rnaseq_pipeline_fastq_workflow.star.num_threads&quot;: &quot;4&quot;,
   &quot;rnaseq_pipeline_fastq_workflow.star.disk_space&quot;: &quot;200&quot;,
   &quot;rnaseq_pipeline_fastq_workflow.star.num_preempt&quot;: &quot;0&quot; 
 }
</code></pre>
<p>Error message:</p>
<pre><code>tar: /data/genomic-references/rnaseq/star_index_oh50/: Cannot open: No such file or directory
</code></pre>
<p>Note that <code>/data/genomic-references/rnaseq/star_index_oh50/</code> does exist and is readable.</p>
<p>The relevant command in the GTEx container is <a href="https://github.com/broadinstitute/gtex-pipeline/blob/b53b734a9b096caed237952b34cbce88b38485bd/rnaseq/star.wdl#L69" rel="nofollow noreferrer">here</a>:</p>
<pre><code>tar -xvvf ${star_index} -C star_index --strip-components=1
</code></pre>
<p>If the files are stored locally, then why does <code>tar</code> fail to wrap the directory?</p>

<rna-seq><genomics><wdl><gtex><aws>
Pointing Cromwell to local EBS mounted storage on AWS Batch
# Pointing Cromwell to local EBS mounted storage on AWS Batch

(Asked by: username_0 on 2020-09-11)

I'm trying to run the WDL tasks from the GTEx RNA-Seq pipeline with Cromwell using AWS Batch as a backend.
I store the STAR alignment index on an Elastic Block Store since my Cromwell server instance lacks sufficient disk space. The EBS Block is mounted to my Cromwell server at /data. The STAR index is located at /data/genomic-references/rnaseq/star_index_oh50.
Try as I might, I cannot get Cromwell to run the STAR task correctly.
My JSON inputs file:
 {
   "rnaseq_pipeline_fastq_workflow.prefix": "s3://mybucket/test/CL100148068",
   "rnaseq_pipeline_fastq_workflow.star.fastq1": "s3://anotherbucket/genotypedata/sample1.fq.gz",
   "rnaseq_pipeline_fastq_workflow.star.star_index": "/data/genomic-references/rnaseq/star_index_oh50/",
   "rnaseq_pipeline_fastq_workflow.star.memory": "32",
   "rnaseq_pipeline_fastq_workflow.star.num_threads": "4",
   "rnaseq_pipeline_fastq_workflow.star.disk_space": "200",
   "rnaseq_pipeline_fastq_workflow.star.num_preempt": "0" 
 }

Error message:
tar: /data/genomic-references/rnaseq/star_index_oh50/: Cannot open: No such file or directory

Note that /data/genomic-references/rnaseq/star_index_oh50/ does exist and is readable.
The relevant command in the GTEx container is here:
tar -xvvf ${star_index} -C star_index --strip-components=1

If the files are stored locally, then why does tar fail to wrap the directory?

**Tags:** rna-seq, genomics, wdl, gtex, aws

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## 1 answers

### Answer by username_0 on 2020-09-14. Score: 1 | Accepted answer

Somebody helped me with this one through other channels, but I wanted to make it publicly available:
Make a tarball of the STAR index. The option --strip-components=1 strips the first level of the path from the untarred items; thus, the expected tarball was made with something like
tar -cvf ${star_index} the_star_index_directory/

Then point Cromwell/WDL to the tarball, e.g. on S3. The GTEx container will unwrap the tarball on the fly during execution.


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