From 00aba34ac05463f2d30348f94762001ffc75bfa9 Mon Sep 17 00:00:00 2001 From: Hui Lan Date: Fri, 7 Oct 2022 14:56:59 +0800 Subject: Change the place used to store downloaded raw RNASeq data. --- Code/configure.py | 3 +-- Code/download_and_map.py | 2 +- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/Code/configure.py b/Code/configure.py index cdccad5..825cedc 100644 --- a/Code/configure.py +++ b/Code/configure.py @@ -12,8 +12,7 @@ RNA_SEQ_INFO_FILE = '../Data/information/rnaseq_info_database.json' # some data DOWNLOADED_SRA_ID_LOG_FILE = '../Data/log/download_log.txt' # a list of downloaded SRA IDs IGNORED_SRA_ID_LOG_FILE = '../Data/log/download_log_small_sized_ids.txt' # store SRA IDs with small file size. MAPPED_RDATA_DIR = '../Data/R/Mapped/public' # mapped RNA-seq (file names ended with _quant.txt) go here -RAW_RDATA_DIR = '../Data/R/Raw' # downloaded files go here - +RAW_RDATA_DIR = '/disk1/Data/R/Raw' # downloaded files go here, was "../Data/R/Raw" (now almost full). # From update_network.py # Don'T change the following paths and names diff --git a/Code/download_and_map.py b/Code/download_and_map.py index aeeb3b3..568032c 100644 --- a/Code/download_and_map.py +++ b/Code/download_and_map.py @@ -340,7 +340,7 @@ if not os.path.exists(RNA_SEQ_INFO_FILE): sys.exit() # If there is no enough disk space for storing the downloaded sequencing data, then stop -available_G = 4 * os.statvfs('/home').f_bavail / (1024*1024) # compute available space (in G). Each block has 4k bytes, work for Linux/UNIX systems only +available_G = 4 * os.statvfs(RAW_RDATA_DIR).f_bavail / (1024*1024) # compute available space (in G). Each block has 4k bytes, work for Linux/UNIX systems only if available_G < 2 * DAILY_MAP_NUMBER: print('[download_and_map.py] home directory does not have enough space (only %d G available) ' % (available_G)) write_network_log_file('[download_and_map.py] home directory does not have enough space (only %d G available).' % (available_G), UPDATE_NETWORK_LOG_FILE) -- cgit v1.2.1