About run_salmon_spg_wf_on_biowulf …

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run_salmon_spg_wf_on_biowulf is a command line python script that runs salmon_spg_wf only or both salmon_spg_wf then quant_sf2express_table (with use of flag –generate_exp_tables ).

Command-line Usage to run salmon_spg_wf only

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python run_salmon_spg_wf_on_biowulf.py \
–bill_to org-nci_ccr_so1 \
–invitees mcintoshc, pcf \
–salmon_library project-FXgYz7005FKkPZkbBxbVGXQv:file-FXYq2180v1xq1k4p3g5g99q8 \
–fastq_directory /…/FASTQ \
–with_project A_JUNK_PROJECT \
–name analysis_name

Command-line Usage to run both salmon_spg_wf and quant_sf2express_tables.

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python run_salmon_spg_wf_on_biowulf.py \
–bill_to org-nci_ccr_so1 \
–invitees mcintoshc, pcf \
–salmon_library project-FXgYz7005FKkPZkbBxbVGXQv:file-FXYq2180v1xq1k4p3g5g99q8\
–fastq_directory /…/FASTQ \
–with_project A_JUNK_PROJECT \
–generate_exp_tables \
–name analysis_name 

Output Files

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• Salmon SPG WF output files -see Output Files section with link salmon_spg_wf.
• QuantSF output files -see Output Files section with link quant_sf2express_table.

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• Find out more about GAU’s DNAnexus Pilot Program.
• For NCI Members who want to use DNAnexus or develop you must get an account.

Developed by GAU

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• Peter FitzGerald (email: fitzgepe@mail.nih.gov)
• Carl McIntosh (email: mcintoshc@mail.nih.gov)