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..8532c11 --- /dev/null +++ b/ondemand.osc.edu/apps/dashboard/projects/BLAST/.ondemand/scripts/uq2zwimz/form.yml @@ -0,0 +1,53 @@ +--- +title: Simple BLAST job +created_at: 1707923522 +form: +- auto_accounts +- auto_scripts +- auto_batch_clusters +attributes: + auto_accounts: + options: + - - PZS1118 + - PZS1118 + - data-option-for-cluster-cardinal: false + - - PZS0715 + - PZS0715 + - data-option-for-cluster-cardinal: false + - - PZS0714 + - PZS0714 + - {} + - - PZS1117 + - PZS1117 + - data-option-for-cluster-ascend: false + data-option-for-cluster-cardinal: false + - - PAS1604 + - PAS1604 + - data-option-for-cluster-ascend: false + data-option-for-cluster-cardinal: false + value: PZS0714 + label: Account + help: '' + required: false + auto_scripts: + options: + - - blast.sh + - "/users/PZS0714/johrstrom/ondemand/data/sys/dashboard/projects/lzdlglik/blast.sh" + directory: "/users/PZS0714/johrstrom/ondemand/data/sys/dashboard/projects/lzdlglik" + value: "/users/PZS0714/johrstrom/ondemand/data/sys/dashboard/projects/lzdlglik/blast.sh" + label: Script + help: '' + required: false + auto_batch_clusters: + options: + - ascend + - cardinal + - owens + - pitzer + value: owens + exclude_options: + - ascend + fixed: true + 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 diff --git a/ondemand.osc.edu/apps/dashboard/projects/QCHEM/.ondemand/manifest.yml b/ondemand.osc.edu/apps/dashboard/projects/QCHEM/.ondemand/manifest.yml new file mode 100644 index 0000000..57d17b9 --- /dev/null +++ b/ondemand.osc.edu/apps/dashboard/projects/QCHEM/.ondemand/manifest.yml @@ -0,0 +1,5 @@ +--- +id: rndy3vti +name: QChem template +description: 'This is an example project using QChem software.' +icon: fas://vial diff --git a/ondemand.osc.edu/apps/dashboard/projects/QCHEM/.ondemand/scripts/7c4d6ilx/form.yml b/ondemand.osc.edu/apps/dashboard/projects/QCHEM/.ondemand/scripts/7c4d6ilx/form.yml new file mode 100644 index 0000000..8d96645 --- /dev/null +++ b/ondemand.osc.edu/apps/dashboard/projects/QCHEM/.ondemand/scripts/7c4d6ilx/form.yml @@ -0,0 +1,55 @@ +--- +title: Simple QChem job +created_at: 1709137595 +form: +- auto_accounts +- auto_scripts +- auto_batch_clusters +attributes: + auto_accounts: + options: + - - PZS1118 + - PZS1118 + - data-option-for-cluster-cardinal: false + - - PZS0715 + - PZS0715 + - data-option-for-cluster-cardinal: false + - - PZS0714 + - PZS0714 + - {} + - - PZS1117 + - PZS1117 + - data-option-for-cluster-ascend: false + data-option-for-cluster-cardinal: false + - - PAS1604 + - PAS1604 + - data-option-for-cluster-ascend: false + data-option-for-cluster-cardinal: false + value: PZS0714 + label: Account + help: '' + required: false + auto_scripts: + options: + - - qchem.sh + - "/users/PZS0714/johrstrom/ondemand/data/sys/dashboard/projects/hahsuaru/qchem.sh" + directory: "/users/PZS0714/johrstrom/ondemand/data/sys/dashboard/projects/hahsuaru" + value: "/users/PZS0714/johrstrom/ondemand/data/sys/dashboard/projects/hahsuaru/qchem.sh" + label: Script + help: '' + required: false + auto_batch_clusters: + options: + - ascend + - cardinal + - owens + - pitzer + value: owens + exclude_options: + - pitzer + - cardinal + - ascend + fixed: true + label: Cluster + help: '' + required: false diff --git a/ondemand.osc.edu/apps/dashboard/projects/QCHEM/qchem.sh b/ondemand.osc.edu/apps/dashboard/projects/QCHEM/qchem.sh new file mode 100644 index 0000000..efb8182 --- /dev/null +++ b/ondemand.osc.edu/apps/dashboard/projects/QCHEM/qchem.sh @@ -0,0 +1,31 @@ +#!/bin/bash + +# +# This is a sample script for running a basic Q-Chem job. +# The only thing you need to modify is 'sample' here +# +export INPUTFILENAME="sample" + +# +# replace 'sample' with the actual name of your input file. +# +module load intel +module load mvapich2 +module load qchem + +# copy input file to $TMPDIR +cp $INPUTFILENAME.inp $TMPDIR +cd $TMPDIR + +# QChem guide at +# http://www.q-chem.com/qchem-website/manual/qchem43_manual/sect-running.html +# +# Not all calculation types can be run in parallel with MPI. +# +# Temporary hack to get multinode jobs running - it is not yet +# known whether multinode qchem requires a global filesystem. +# setenv QCLOCALSCR $TMPDIR +# export QCSCRATCH=$TMPDIR + +qchem -np $SLURM_NTASKS $INPUTFILENAME.inp +ls -al diff --git a/ondemand.osc.edu/apps/dashboard/projects/QCHEM/sample.inp b/ondemand.osc.edu/apps/dashboard/projects/QCHEM/sample.inp new file mode 100644 index 0000000..7a7f2ba --- /dev/null +++ b/ondemand.osc.edu/apps/dashboard/projects/QCHEM/sample.inp @@ -0,0 +1,34 @@ +$comment +ethene +$end + +$molecule +0 1 + C -2.3620772 0.9207308 0.2821606 + C -1.0130626 0.5278664 -0.2865418 + H -2.6220345 1.9481860 -0.0474867 + H -3.1392310 0.2143160 -0.0767561 + H -0.7529560 -0.4993875 0.0434971 + H -0.2358785 1.2345592 0.0718086 +$end + +$rem + BASIS = 6-31G* + EXCHANGE = HF + GUI = 2 + JOB_TYPE = Optimization + PURECART = 2222 +$end + +@@@ + +$molecule +read +$end + +$rem +basis 6-31G* +exchange hf +molden_format true +print_orbitals true +$end