added sample slurm script and dependency installation

get_dependencies.sh

+#!/bin/bash
+
+module load shared pymol python/3.7.x-anaconda
+module load slurm
+
+. /cm/shared/apps/python/3.7.x-anaconda/etc/profile.d/conda.sh
+conda activate vish_alascan
+
+conda env create -f vish_alascan_spec.yml
\ No newline at end of file

submit_to_slurm.sh

+#!/bin/bash
+#
+#
+# This file is batch script used to run commands on the BioHPC cluster.
+# The script is submitted to the cluster using the SLURM `sbatch` command.
+# Lines starting with # are comments, and will not be run.
+# Lines starting with #SBATCH specify options for the scheduler.
+# Lines that do not start with # or #SBATCH are commands that will run.
+
+# Name for the job that will be visible in the job queue and accounting tools.
+#SBATCH --job-name [JobName]
+
+# Send an email when the job status changes, to the specfied address.
+#SBATCH --mail-type ALL
+#SBATCH --mail-user [email here]
+
+# Name of the SLURM partition that this job should run on.
+#SBATCH -p 32GB      # partition (queue)
+
+#SBATCH --array=1-11:5
+
+# Time limit for the job in the format Days-H:M:S
+# A job that reaches its time limit will be cancelled.
+# Specify an accurate time limit for efficient scheduling so your job runs promptly.
+#SBATCH -t 1-0:0:00
+
+# The standard output and errors from commands will be written to these files.
+# %j in the filename will be replace with the job number when it is submitted.
+#SBATCH -o job_%j_%a.out
+#SBATCH -e job_%j_%a.err
+
+
+
+module load shared pymol python/3.7.x-anaconda
+module load slurm
+
+. /cm/shared/apps/python/3.7.x-anaconda/etc/profile.d/conda.sh
+conda activate vish_alascan
+
+MIN=${SLURM_ARRAY_TASK_ID}
+MAX=$(( ${SLURM_ARRAY_TASK_ID} + 4 ))
+
+~/.conda/envs/vish_alascan/bin/python [RUN executable here] -m $MIN -x $MAX -c16
\ No newline at end of file

vish_alascan_spec.yml

+name: vish_alascan
+channels:
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1=main
+  - autopep8=1.5.7=pyhd3eb1b0_0
+  - biopython=1.78=py38h7b6447c_0
+  - blas=1.0=mkl
+  - ca-certificates=2022.4.26=h06a4308_0
+  - certifi=2022.5.18.1=py38h06a4308_0
+  - cycler=0.10.0=py38_0
+  - dbus=1.13.18=hb2f20db_0
+  - expat=2.4.1=h2531618_2
+  - fontconfig=2.13.1=h6c09931_0
+  - freetype=2.10.4=h5ab3b9f_0
+  - glib=2.68.2=h36276a3_0
+  - gst-plugins-base=1.14.0=h8213a91_2
+  - gstreamer=1.14.0=h28cd5cc_2
+  - icu=58.2=he6710b0_3
+  - intel-openmp=2021.2.0=h06a4308_610
+  - jpeg=9b=h024ee3a_2
+  - kiwisolver=1.3.1=py38h2531618_0
+  - lcms2=2.12=h3be6417_0
+  - ld_impl_linux-64=2.33.1=h53a641e_7
+  - libffi=3.3=he6710b0_2
+  - libgcc-ng=9.1.0=hdf63c60_0
+  - libgfortran-ng=7.3.0=hdf63c60_0
+  - libpng=1.6.37=hbc83047_0
+  - libstdcxx-ng=9.1.0=hdf63c60_0
+  - libtiff=4.2.0=h85742a9_0
+  - libuuid=1.0.3=h1bed415_2
+  - libwebp-base=1.2.0=h27cfd23_0
+  - libxcb=1.14=h7b6447c_0
+  - libxml2=2.9.10=hb55368b_3
+  - lz4-c=1.9.3=h2531618_0
+  - matplotlib=3.3.4=py38h06a4308_0
+  - matplotlib-base=3.3.4=py38h62a2d02_0
+  - mkl=2021.2.0=h06a4308_296
+  - mkl-service=2.3.0=py38h27cfd23_1
+  - mkl_fft=1.3.0=py38h42c9631_2
+  - mkl_random=1.2.1=py38ha9443f7_2
+  - ncurses=6.2=he6710b0_1
+  - numpy=1.20.2=py38h2d18471_0
+  - numpy-base=1.20.2=py38hfae3a4d_0
+  - olefile=0.46=py_0
+  - openssl=1.1.1o=h7f8727e_0
+  - pandas=1.2.4=py38h2531618_0
+  - pcre=8.44=he6710b0_0
+  - pillow=8.2.0=py38he98fc37_0
+  - pip=21.1.1=py38h06a4308_0
+  - pycodestyle=2.8.0=pyhd3eb1b0_0
+  - pyparsing=2.4.7=pyhd3eb1b0_0
+  - pyqt=5.9.2=py38h05f1152_4
+  - python=3.8.10=hdb3f193_7
+  - python-dateutil=2.8.1=pyhd3eb1b0_0
+  - pytz=2021.1=pyhd3eb1b0_0
+  - qt=5.9.7=h5867ecd_1
+  - readline=8.1=h27cfd23_0
+  - scipy=1.6.2=py38had2a1c9_1
+  - seaborn=0.11.1=pyhd3eb1b0_0
+  - setuptools=52.0.0=py38h06a4308_0
+  - sip=4.19.13=py38he6710b0_0
+  - six=1.15.0=py38h06a4308_0
+  - sqlite=3.35.4=hdfb4753_0
+  - tk=8.6.10=hbc83047_0
+  - toml=0.10.2=pyhd3eb1b0_0
+  - tornado=6.1=py38h27cfd23_0
+  - tqdm=4.59.0=pyhd3eb1b0_1
+  - wheel=0.36.2=pyhd3eb1b0_0
+  - xz=5.2.5=h7b6447c_0
+  - zlib=1.2.11=h7b6447c_3
+  - zstd=1.4.9=haebb681_0
+prefix: /home2/s184069/.conda/envs/vish_alascan