Grooming Error when linking bam files instead of copying into galaxy
The uploaded files need grooming, so change your Copy data into Galaxy? selection to be Copy files into Galaxy instead of Link to files without copying into Galaxy so grooming can be performed. Thoughts? Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny@illumina.com<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com>
On Nov 16, 2011, at 4:12 PM, Chorny, Ilya wrote:
The uploaded files need grooming, so change your Copy data into Galaxy? selection to be Copy files into Galaxy instead of Link to files without copying into Galaxy so grooming can be performed.
BAMs in Galaxy must be sorted. Since the "link to…" option can't modify the source file, the BAM can't be "uploaded" unless it's sorted prior to uploading. --nate
Thoughts?
Thanks,
Ilya
Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny@illumina.com Website: www.illumina.com
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... which brings us back to a past suggestion from one of my colleagues (you can implement his patch in your instance): http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-September/006827.html Cheers, Roman On 2011-11-17 16:19, Nate Coraor wrote:
On Nov 16, 2011, at 4:12 PM, Chorny, Ilya wrote:
The uploaded files need grooming, so change your Copy data into Galaxy? selection to be Copy files into Galaxy instead of Link to files without copying into Galaxy so grooming can be performed.
BAMs in Galaxy must be sorted. Since the "link to…" option can't modify the source file, the BAM can't be "uploaded" unless it's sorted prior to uploading.
--nate
Thoughts?
Thanks,
Ilya
Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny@illumina.com Website: www.illumina.com
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (3)
-
Chorny, Ilya -
Nate Coraor -
Roman Valls