User: biomonika

gravatar for biomonika
biomonika60
Reputation:
60
Status:
New User
Location:
United States
Last seen:
3 months, 3 weeks ago
Joined:
3 years, 3 months ago
Email:
b********@psu.edu

Posts by biomonika

<prev • 6 results • page 1 of 1 • next >
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Naive Variant Caller doesn't output variants wile mpileup does
... I am interested in calling Illumina errors. Therefore, I need to output variants with such a low support as a single read. I am using Naive Variant Caller and most of the time I get VCF file as expected. However, there are peculiar regions for which NVC reports empty VCF file such as this region: 8: ...
nvc samtools mpileup written 3 months ago by biomonika60
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Get notified when Galaxy server stops running
... I am starting my local Galaxy instance with command: sh run.sh --daemon However, this way I don't get notified when Galaxy server stops working for whatever reason. I would like to get email when this happens so that I could start it again. What would you recommend? Thanks. ...
daemon written 2.9 years ago by biomonika60 • updated 2.9 years ago by Bjoern Gruening4.8k
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installation of perl modules from toolshed
... Hello, I am writing custom tool for Galaxy that uses perl scripts. These perl scripts use specific perl modules and therefore I need to make sure that those perl modules are installed. What is the recommended way to install perl modules from tool_dependencies.xml? I have found following code that ...
modules toolshed perl written 3.3 years ago by biomonika60 • updated 2.8 years ago by mateusbellomo10
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difference between $REPOSITORY_INSTALL_DIR and $INSTALL_DIR
... I wrote a tool for Galaxy and now I want to upload it to Toolshed. I am writing tool_dependencies.xml and I would like to know what's the difference between built-it variables $REPOSITORY_INSTALL_DIR and $INSTALL_DIR. Thanks. ...
toolshed tool_dependencies.xml written 3.3 years ago by biomonika60 • updated 3.3 years ago by Jennifer Hillman Jackson23k
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Comment: C: Convert SAM to sorted BAM
... samtools_sort is exactly what I needed, thanks! I was searching in the toolshed under "sam" and "bam", didn't think of this. ...
written 3.3 years ago by biomonika60
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Convert SAM to sorted BAM
... I am looking for a tool to convert SAM to sorted BAM (sorted by the coordinates, such as with samtools sort or picard's SortSam). ...
bam samtools sam sort written 3.3 years ago by biomonika60 • updated 3.3 years ago by Jennifer Hillman Jackson23k

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Popular Question 2.9 years ago, created a question with more than 1,000 views. For Convert SAM to sorted BAM

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