Containerized version of chip-seq analysis
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This is containerized version of chipseq, where all processes are wrapped in containers. This version contains identical packages to non-containerized version, except for the meme-chip, where we use meme-5.5.4.
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requested review from @s232407
assigned to @s231284
106 106 107 107 # Name sort bam to make BEDPE 108 108 nmsrt_bam_filename = bam_basename + ".nmsrt.bam" 109 # Allocate memory for each thread used during samtools sort. 110 # Determine the available memory on the host system (kB). 111 avail_sys_mem = int(subprocess.check_output("grep MemTotal /proc/meminfo | grep -o '[0-9]*'", shell=True).decode("utf-8").strip()) 112 # Divide the total by the number of processors and apply a scaling factor (0.85) to not use all memory. 113 mem_per_thread = math.floor((avail_sys_mem ) * 0.7) 114 # DEBUGGING changed this line in version 2 of the diff
168 175 if err: 169 176 logger.error("sampe error: %s", err) 170 177 178 # Allocate memory for each thread used during samtools sort. 179 # Determine the available memory on the host system (kB). 180 avail_sys_mem = int(subprocess.check_output("grep MemTotal /proc/meminfo | grep -o '[0-9]*'", shell=True).decode("utf-8").strip()) 181 # Divide the total by the number of processors and apply a scaling factor (0.85) to not use all memory. 182 mem_per_thread = math.floor((avail_sys_mem // cpu_count()) * 0.85) 183 # DEBUGGING 184 mem_per_thread = mem_per_thread * 4 changed this line in version 2 of the diff
15 15 import subprocess 16 16 from multiprocessing import Pool 17 17 import pandas as pd 18 import utils 18 import utils2 as utils changed this line in version 2 of the diff
1 FROM continuumio/miniconda3:24.3.0-0 2 3 LABEL IMAGE="chipseq-analysis-motifSearch" \ 4 IMAGE_VERSION="1.0.0" \ 5 AUTHORS="Felix Perez,Peng Lian" \ 6 EMAIL="biohpc-help@utsouthwestern.edu" 7 8 WORKDIR /motif-search/ 9 10 # Environment variables for the campus proxy. 11 ENV http_proxy="http://proxy.swmed.edu:3128" \ 12 https_proxy="http://proxy.swmed.edu:3128" 13 added 1 commit
- 45521260 - Removed debugging code and fixed memory_per_thread assignment