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ondemand.osc.edu/apps/dashboard/projects/BLAST/.ondemand/manifest.yml
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| --- | ||
| id: mrnpex50 | ||
| name: BLAST template | ||
| description: This is a template for a project using BLAST software. | ||
| icon: fas://syringe |
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ondemand.osc.edu/apps/dashboard/projects/BLAST/.ondemand/scripts/uq2zwimz/form.yml
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| --- | ||
| title: Simple BLAST job | ||
| created_at: 1707923522 | ||
| form: | ||
| - auto_accounts | ||
| - auto_scripts | ||
| - auto_batch_clusters | ||
| attributes: | ||
| auto_accounts: | ||
| options: | ||
| - - PZS1118 | ||
| - PZS1118 | ||
| - {} | ||
| - - PZS0715 | ||
| - PZS0715 | ||
| - {} | ||
| - - PZS0714 | ||
| - PZS0714 | ||
| - {} | ||
| - - PZS1117 | ||
| - PZS1117 | ||
| - data-option-for-cluster-ascend: false | ||
| - - PAS1604 | ||
| - PAS1604 | ||
| - data-option-for-cluster-ascend: false | ||
| value: PZS1118 | ||
| label: Account | ||
| help: '' | ||
| required: false | ||
| auto_scripts: | ||
| options: | ||
| - - blast.sh | ||
| - "/users/PZS0714/johrstrom/ondemand/data/sys/dashboard/projects/mrnpex50/blast.sh" | ||
| - - hello_world.sh | ||
| - "/users/PZS0714/johrstrom/ondemand/data/sys/dashboard/projects/mrnpex50/hello_world.sh" | ||
| directory: "/users/PZS0714/johrstrom/ondemand/data/sys/dashboard/projects/mrnpex50" | ||
| value: "/users/PZS0714/johrstrom/ondemand/data/sys/dashboard/projects/mrnpex50/blast.sh" | ||
| label: Script | ||
| help: '' | ||
| required: false | ||
| auto_batch_clusters: | ||
| options: | ||
| - ascend | ||
| - owens | ||
| - pitzer | ||
| value: owens | ||
| exclude_options: | ||
| - ascend | ||
| label: Cluster | ||
| help: '' | ||
| required: false |
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| >P01013 GENE X PROTEIN (OVALBUMIN-RELATED) | ||
| QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTREMPFHVTKQESKPVQMMCMNNSFNVATLPAE | ||
| KMKILELPFASGDLSMLVLLPDEVSDLERIEKTINFEKLTEWTNPNTMEKRRVKVYLPQMKIEEKYNLTS | ||
| VLMALGMTDLFIPSANLTGISSAESLKISQAVHGAFMELSEDGIEMAGSTGVIEDIKHSPESEQFRADHP | ||
| FLFLIKHNPTNTIVYFGRYWSP |
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| #!/bin/bash | ||
| #SBATCH -J ondemand/sys/projects/basic_blast | ||
|
|
||
| # A Basic BLAST Job | ||
| # https://www.osc.edu/resources/available_software/software_list/blast | ||
|
|
||
| # | ||
| # The following lines set up the Blast environment | ||
| # | ||
| module load blast | ||
| module load blast-database | ||
| set -x | ||
|
|
||
| # | ||
| # Move to the directory where the job was submitted | ||
| # | ||
| cd $SLURM_SUBMIT_DIR | ||
| mkdir $SLURM_JOBID | ||
| cp 100.fasta $TMPDIR | ||
| cd $TMPDIR | ||
|
|
||
| # | ||
| # Run Blast | ||
| # | ||
| /usr/bin/time tblastn -db nt -query 100.fasta -out test.out | ||
|
|
||
| # | ||
| # Now, copy data (or move) back once the simulation has completed | ||
| # | ||
| cp test.out $SLURM_SUBMIT_DIR/$SLURM_JOBID |