Add project templates

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

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
+      - 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

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+>P01013 GENE X PROTEIN (OVALBUMIN-RELATED)
+QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTREMPFHVTKQESKPVQMMCMNNSFNVATLPAE
+KMKILELPFASGDLSMLVLLPDEVSDLERIEKTINFEKLTEWTNPNTMEKRRVKVYLPQMKIEEKYNLTS
+VLMALGMTDLFIPSANLTGISSAESLKISQAVHGAFMELSEDGIEMAGSTGVIEDIKHSPESEQFRADHP
+FLFLIKHNPTNTIVYFGRYWSP

ondemand.osc.edu/apps/dashboard/projects/BLAST/blast.sh

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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

ondemand.osc.edu/apps/dashboard/projects/QCHEM/.ondemand/manifest.yml

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+---
+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

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+---
+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

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+#!/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

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+$comment
+ethene
+$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