10.1. Command line options for sequescan¶
The arguments for sequescan can be listed by typing:
~/sequedex/bin/sequescan run -h
at the comand line, resulting in the following output:
Command line execution of sequescan run mode: sequescan run [-h] [-q] [-c config_file] -d data_module [-o output_directory] [-s function_set] [-a min_prot_frag_length] [-t thread_num] [-f database_writer_flag] [-l] INFILE Example: sequescan run -d Life2550-4GB.0 -s seed_0911.m1 -f 1 /Users/jsmith/mgData Option descriptions: -h mode help -q quiet option - less messages to console or progress window -c user-defined configuration file (overrides system configuation file) -d name of data module -o user-defined directory for data output (default is directory where input is located) -s name of function set -a minimum protein fragment length (overrides configuration file; default is 15) -t maximum number of threads in threadpool (default = 1) -f database writer flag (arguments: 0 = no, 1 = yes); analysis_writer_list in config determines type of database (currently fasta/fastq file) -l required if INFILE contains list of fasta/fastq files; if argument is "none", the list contains absolute paths; otherwise argument is base directory and paths in list are relative to base directory; when paths are relative to base directory and the -o option is set, output will inlcude relative paths INFILE may be a fasta/fastq file, a directory with fasta/fastq files, or a file containing a list of fasta/fastq files. However, only fasta or fastq files or their gzipped (.gz) versions with an extension in the config file parameter fa_ext_list will be processed. Parameters: INFILE is the input file in FASTA format. Complete paths, relatives paths, and symlinks may be used here.
10.2. Environmental variables¶
The environment variables can be seen by typing:
Global Configuration Variables: SEQUEDEX_USERDIR (user directory location) set to "/home/localhost/username/.sqdx/" from default. SEQUEDEX_LOGLEVEL (debug|info|warning|error) set to "info" from default. SEQUEDEX_LOGFILE_DIR (location of launcher log file) set to "/home/localhost/username/.sqdx/" from default. SEQUEDEX_SEES_STDOUT (if False, pop up windows) set to "True" from default. SEQUEDEX_HOME (top-level installation directory) set to "/home/localhost/username/sequedex/" from location of launcher binary. SEQUEDEX_ETC (location of system config files) set to "/home/localhost/username/sequedex/etc/" from default. SEQUEDEX_LIB (location of library files) set to "/home/localhost/username/sequedex/lib/" from default. SEQUEDEX_BIN (location of executable files) set to "/home/localhost/username/sequedex/bin/" from default. SEQUEDEX_DATA (location of data modules) set to "/home/localhost/username/sequedex/data/" from default. SEQUEDEX_DOC (location of documentation and help files) set to "/home/localhost/username/sequedex/doc/" from default. SEQUEDEX_CONTRIB (location of contributed files and data) set to "/home/localhost/username/sequedex/contrib/" from default. SEQUEDEX_JAVA (absolute path to java executable) set to "/usr/bin/java" from output of "which java". SEQUEDEX_CHECK_JAVA_VERSION (if True, check java version) set to "True" from default. SEQUEDEX_REQUIRE_JAVA_VERSION (java version must be above this) set to "7" from default. SEQUEDEX_PLATFORM_MEMSIZE (amount of system RAM in GB) set to "31" from reported system memory size. SEQUEDEX_PYTHON (absolute path to python executable) set to "/usr/bin/python" from first python in PATH that has scipy. SEQUINATOR_COMMAND (command run upon "Display Output") set to "/home/localhost/username/sequedex/bin/sequinator" from default. SEQUINATOR_BROWSER (path to browser, with arguments) set to "/usr/bin/firefox" from plat-dependent default. SEQUINATOR_SERVER (write and serve files) set to "True" from default. SEQUINATOR_CLIENT (start browser) set to "True" from default. SEQUEDEX_HAS_INTERNET (has web access for update) set to "True" from default. SEQUINATOR_DATA (location of data library) set to "/home/localhost/username/sequedex/data/sequinator/" from default. SEQUINATOR_SEARCH_PATH (path searched for output) set to "/home/localhost/username/:/home/localhost/username/sequedex/data/sequinator/" from default. SEQUINATOR_HOST (IP address for sequinator to use) set to "127.0.0.1" from default. SEQUINATOR_PORT (IP port for sequinator to use) set to "52707" from default. SEQUINATOR_MAX_BROWSER_TABS (max tabs for sequinator to open) set to "10" from default. SEQUINATOR_TITLE (format string for sequinator titles) set to "%(filename)s" from default. SEQUEDEX_LAUNCHER_VERSION (sequedex-launcher version number) set to "1.0.10" from internal version number. SEQUEDEX_LAUNCHER_DEFAULT_COMMAND (default command) set to "sequescan" from default. SEQUEDEX_WWW (URL for updates and sequinator) set to "http://sequedex.lanl.gov" from default. http_proxy (system http proxy setting) set to "None" from default. ARCHY_ETC (location of Archaeoptryx config file) set to "/home/localhost/username/sequedex/etc/archy/" from default. ARCHY_DEFAULT_TREE (default tree for archy) set to "/home/localhost/username/sequedex/data/trees/Life2550/tree.phyloxml" from default. SEQUESCAN_ETC (location of sequescan conf files) set to "/home/localhost/username/sequedex/etc/sequescan" from default. SEQUESCAN_HEAPSIZE_MB (java heapsize in MB for sequescan) set to "30000" from user config file. SEQUESCAN_JAVA_ARGS (full java arguments to sequescan) set to "-Xms1000m -Xmx30000m" from platform-dependent default. Data Module Configuration Variables: Module virus1252: minimumMemSize: 4 moduleName: virus1252 installDate: Sat Jun 21 08:30:56 2014 filename: virus1252.1.jar version: 1 nextMemSize: 1000 Module Life2550: minimumMemSize: 16 moduleName: Life2550 installDate: Sat Jun 21 08:30:55 2014 filename: Life2550-16GB.0.jar version: 0 nextMemSize: 32 Use the sequedex-config command for setting these variables.
To check a specific environmental variable, add the variable as an argument to sequedex-config:
and to change a particular variable, provide both the variable name and a new value:
sequedex-config SEQUESCAN_HEAPSIZE 3000
10.3. Configuration options¶
The configuration options for sequescan can be seen by typing: