User: mainulhossain

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Posts by mainulhossain

<prev • 8 results • page 1 of 1 • next >
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Out Of Disk Space with Picard's FastqtoSam Tools from Galaxy
... Hi, I am trying to use FastqToSam tool from Picard toolshed. But I keep getting the following exception: Fatal error: Exit code 1 () Picked up _JAVA_OPTIONS: -Xmx2048m -Xms256m Exception in thread "main" htsjdk.samtools.util.RuntimeIOException: java.io.IOException: No space left on device at htsjd ...
picard galaxy samtools written 3 months ago by mainulhossain0 • updated 3 months ago by Bjoern Gruening5.0k
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Answer: A: How to create and run a pipeline using BioBlend and Galaxy API?
... I was at last able to pass input parameters as the following: params = { "fastq_R1": {"values":[{"src":"hda", "id":"9ac6c47a8515c831"}]}, "fastq_R2":{"values":[{"src":"hda","id":"6dbc21d257b88b00"}]} } Thanks, ...
written 7 months ago by mainulhossain0
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Answer: A: How to create and run a pipeline using BioBlend and Galaxy API?
... I think I have got it. The format of input parameters is as below: params = { "fastq_R1": {"values":[{"src":"hda", "id":"9ac6c47a8515c831"}]}, "fastq_R2":{"values":[{"src":"hda","id":"6dbc21d257b88b00"}]} } Thanks, ...
written 7 months ago by mainulhossain0
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Comment: C: Inputs for the FASTQ Grooming
... Thank you very much. I was able to pass input parameters to run_tool command. But I still have a problem with run_tool. For some tools, for example FASTQ Groomer, where a single input parameter is enough, the command works. param = {'name': dataset_id} runtool(history_id, tool_id, param) B ...
written 7 months ago by mainulhossain0
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Comment: C: How to create and run a pipeline using BioBlend and Galaxy API?
... Thank you very much. I was able to pass input parameters to run_tool command. But I still have a problem with run_tool. For some tools, for example FASTQ Groomer, where a single input parameter is enough, the command works. param = {'name': dataset_id} runtool(history_id, tool_id, param) B ...
written 7 months ago by mainulhossain0
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Inputs for the FASTQ Grooming
... Hi All, I am a newbie to Galaxy and Bioblend programming and have problem to find out the the name and format of the input parameter which **ToolClient.run_tool** call for a particular tool needs. For example, I am trying to use FASTQ Groomer tool as the following: from bioblend.galaxy impor ...
fastq groomer bioblend written 8 months ago by mainulhossain0 • updated 7 months ago by Jennifer Hillman Jackson24k
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Comment: C: How to create and run a pipeline using BioBlend and Galaxy API?
... Hi Martin, thanks for your reply. I will try as you suggested. ...
written 8 months ago by mainulhossain0
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How to create and run a pipeline using BioBlend and Galaxy API?
... I need to build the following pipeline: 1. Upload an SRA file from a remote FTP server (with anonymous access) 2. Convert SRA to FASTQ file 3. Grooming the FASTQ data 4. Upload reference dataset from another remote FTP server 5. Map data from steps 3 and 4 with BWA 6. Create BAM file from SAM ...
pipeline galaxy api bioblend written 8 months ago by mainulhossain0

Latest awards to mainulhossain

Scholar 3 months ago, created an answer that has been accepted. For A: How to create and run a pipeline using BioBlend and Galaxy API?
Scholar 7 months ago, created an answer that has been accepted. For A: How to create and run a pipeline using BioBlend and Galaxy API?

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