working slurm scripts for pymol rendering with conda-based install

README.md

 # PyMol_ray_pipeline
 
-Ray-trace a PyMol session on cheaha 
\ No newline at end of file
+Ray-trace a PyMol session on cheaha
+
+WARNING: PyMol licensing issues have not been addressed.
+
+Sample session to render can be found in test_1aon_struct_spectrum.pse
+which comes from the "[Huge Surfaces](https://pymolwiki.org/index.php/Huge_surfaces)" PyMolWiki page
+
+This project provides 2 different ways to run a pymol ray job:
+
+1. bash shell script that can be submitted with sbatch
+2. Snakemake pipeline script (coming soon)
+
+## sbatch usage
+
+By default, it loads the session "test_1aon_struct_spectrum.pse" and creates the image "test_1aon_struct_spectrum.ray.1200x900.300dpi.png", which takes about 90 minutes to run.
+
+```
+module load Anaconda3/5.3.0
+git clone git@gitlab.rc.uab.edu:CCTS-Informatics-Pipelines/pymol_ray_pipeline.git
+cd pymol_ray_pipeline
+sbatch job.80s_ray_1200x900_dpi300.sh
+```
+this should launch a cluster job, which will wait in the queue.
+You should get 2 emails:
+ * when the job comes off the queue and start running
+```
+From: slurm@cheaha.rc.uab.edu [mailto:slurm@cheaha.rc.uab.edu]
+Subject: SLURM Job_id=2107497 Name=pymol_24c_draw_3572x2400 Began, Queued time 01:40:38
+```
+ * when the jobs finishes successfully (COMPLETED, ExitCode 0)
+```
+From: slurm@cheaha.rc.uab.edu [mailto:slurm@cheaha.rc.uab.edu]
+Subject: SLURM Job_id=2107403 Name=pymol_24c_ray_3572x2400 Ended, Run time 01:49:52, COMPLETED, ExitCode 0
+```
+ * or when if it fails (FAILED, ExitCode 1)
+```
+From: slurm@cheaha.rc.uab.edu [mailto:slurm@cheaha.rc.uab.edu]
+Subject: SLURM Job_id=2107403 Name=pymol_24c_ray_3572x2400 Failed, Run time 01:49:52, FAILED, ExitCode 1
+```
+
+
+# Snakemake usage (not complete)
+
+```
+module load snakemakeslurm/4.8.0/1 Anaconda3/5.3.0 dvctools/0.9
+git clone git@gitlab.rc.uab.edu:CCTS-Informatics-Pipelines/pymol_ray_pipeline.git 
+cd pymol_ray_pipeline
+snakemakeslurm test_ray
+
+```
+
+

job.80s_ray_1200x900_dpi300.sh

+#!/bin/bash
+#SBATCH --job-name pymol_ray_24core_1200x900_300dpi
+#SBATCH --ntasks=1                          ##Number of PROCESSES
+# ====== entire hi-mem node ======
+#SBATCH --cpus-per-task=24                   ##Number of CPUs per task
+#SBATCH --mem-per-cpu=10000                  ##Memory specified for each core used (in MB) (no cores, use --mem=)
+##SBATCH --mem-per-cpu=15000                  ##Memory specified for each core used (in MB) (no cores, use --mem=)
+#                                            ##Runtime in D-HH:MM:SS
+#SBATCH --partition=medium -t 2-02:00:00       ## express(2h), short(12h), medium(2d2h), long(6d6h), interactive(2h)
+#--share                                     ## !!!don't share!!!
+#
+##SBATCH --mail-user=BLAZERID@uab.edu
+#SBATCH --mail-type=ALL                     ## BEGIN, END, ERROR, ALL
+#
+#SBATCH --error=logs/%j.%N.err.txt               ##File to which STDERR will be written
+#SBATCH --output=logs/%j.%N.out.txt              ## File to which STDOUT will be written
+
+PSE_FILE="test_1aon_struct_spectrum.pse"
+PNG_FILE=$(basename $PSE_FILE .pse).ray.1200x900.300dpi.png
+
+module purge
+module load shared rc-base
+module load Anaconda3/5.3.0
+
+. /share/apps/rc/software/Anaconda3/5.3.0/etc/profile.d/conda.sh
+
+# this assumes you have created a pymol2 conda environment previously via :
+if [ ! -e ~/.conda/envs/pymol2 ]; then
+    # install pymol2, if necessary (only first time run, for each users)
+    echo "# INSTALLING pymol into ~/$USER/.conda/envs/pymol2 using Anaconda"
+    conda create --name pymol2 -c schrodinger pymol
+fi
+conda activate pymol2
+
+date;
+pymol -c -d "load $PSE_FILE; set antialias, 2; ray 1200,900; png $PNG_FILE, width=4in, height=3in, dpi=300; quit;"
+date
+

job.80s_ray_192x192_dpi96.sh

+#!/bin/bash
+#
+# fast running test script
+#
+#
+#SBATCH --job-name pymol_ray_8core_192x192_96dpi
+#SBATCH --ntasks=1                          ##Number of PROCESSES
+# ====== entire hi-mem node ======
+#SBATCH --cpus-per-task=8                   ##Number of CPUs per task
+#SBATCH --mem-per-cpu=1000                  ##Memory specified for each core used (in MB) (no cores, use --mem=)
+##SBATCH --mem-per-cpu=15000                  ##Memory specified for each core used (in MB) (no cores, use --mem=)
+#                                            ##Runtime in D-HH:MM:SS
+#SBATCH --partition=medium -t 2-02:00:00       ## express(2h), short(12h), medium(2d2h), long(6d6h), interactive(2h)
+#--share                                     ## !!!don't share!!!
+#
+##SBATCH --mail-user=BLAZERID@uab.edu
+#SBATCH --mail-type=ALL                     ## BEGIN, END, ERROR, ALL
+#
+#SBATCH --error=logs/%j.%N.err.txt               ##File to which STDERR will be written
+#SBATCH --output=logs/%j.%N.out.txt              ## File to which STDOUT will be written
+
+PSE_FILE="test_1aon_struct_spectrum.pse"
+PNG_FILE=$(basename $SESS_FILE .pse).ray.192x192.96dpi.png
+
+module purge
+module load shared rc-base
+module load Anaconda3/5.3.0
+
+. /share/apps/rc/software/Anaconda3/5.3.0/etc/profile.d/conda.sh
+
+# this assumes you have created a pymol2 conda environment previously via :
+if [ ! -e ~/.conda/envs/pymol2 ]; then
+    # install pymol2, if necessary (only first time run, for each users)
+    echo "# INSTALLING pymol into ~/$USER/.conda/envs/pymol2 using Anaconda"
+    conda create --name pymol2 -c schrodinger pymol
+fi
+conda activate pymol2
+
+date;
+pymol -c -d "set max_threads, $SLURM_JOB_CPUS_PER_NODE; load $PSE_FILE; set antialias, 2; ray 192,192; png $PNG_FILE, width=2in, height=2in, dpi=96; quit;"
+date
+

logs/README.md

+Place-holder README so that the logs/ directory always exists