diff --git a/ondemand.osc.edu/apps/dashboard/projects/BLAST/.ondemand/manifest.yml b/ondemand.osc.edu/apps/dashboard/projects/BLAST/.ondemand/manifest.yml new file mode 100644 index 0000000..7a2d9cd --- /dev/null +++ b/ondemand.osc.edu/apps/dashboard/projects/BLAST/.ondemand/manifest.yml @@ -0,0 +1,5 @@ +--- +id: mrnpex50 +name: BLAST template +description: This is a template for a project using BLAST software. +icon: fas://syringe diff --git a/ondemand.osc.edu/apps/dashboard/projects/BLAST/.ondemand/scripts/uq2zwimz/form.yml b/ondemand.osc.edu/apps/dashboard/projects/BLAST/.ondemand/scripts/uq2zwimz/form.yml new file mode 100644 index 0000000..e4e95eb --- /dev/null +++ b/ondemand.osc.edu/apps/dashboard/projects/BLAST/.ondemand/scripts/uq2zwimz/form.yml @@ -0,0 +1,51 @@ +--- +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 diff --git a/ondemand.osc.edu/apps/dashboard/projects/BLAST/100.fasta b/ondemand.osc.edu/apps/dashboard/projects/BLAST/100.fasta new file mode 100644 index 0000000..704835f --- /dev/null +++ b/ondemand.osc.edu/apps/dashboard/projects/BLAST/100.fasta @@ -0,0 +1,5 @@ +>P01013 GENE X PROTEIN (OVALBUMIN-RELATED) +QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTREMPFHVTKQESKPVQMMCMNNSFNVATLPAE +KMKILELPFASGDLSMLVLLPDEVSDLERIEKTINFEKLTEWTNPNTMEKRRVKVYLPQMKIEEKYNLTS +VLMALGMTDLFIPSANLTGISSAESLKISQAVHGAFMELSEDGIEMAGSTGVIEDIKHSPESEQFRADHP +FLFLIKHNPTNTIVYFGRYWSP diff --git a/ondemand.osc.edu/apps/dashboard/projects/BLAST/blast.sh b/ondemand.osc.edu/apps/dashboard/projects/BLAST/blast.sh new file mode 100644 index 0000000..83d2d76 --- /dev/null +++ b/ondemand.osc.edu/apps/dashboard/projects/BLAST/blast.sh @@ -0,0 +1,30 @@ +#!/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