Add project templates (#249)

Add BLAST and QChem project templates.

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

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

ondemand.osc.edu/apps/dashboard/projects/BLAST/100.fasta

@@ -0,0 +1,5 @@
+>P01013 GENE X PROTEIN (OVALBUMIN-RELATED)
+QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTREMPFHVTKQESKPVQMMCMNNSFNVATLPAE
+KMKILELPFASGDLSMLVLLPDEVSDLERIEKTINFEKLTEWTNPNTMEKRRVKVYLPQMKIEEKYNLTS
+VLMALGMTDLFIPSANLTGISSAESLKISQAVHGAFMELSEDGIEMAGSTGVIEDIKHSPESEQFRADHP
+FLFLIKHNPTNTIVYFGRYWSP

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

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

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

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 

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