printf'HINT: The FASTA and DATABASE items need to be full paths to files.\n'
printf"\\t\\033[1m%s\\033[0m\\t\\t%s\\n""<FASTA>""path to the query FASTA file"
printf"\\t\\033[1m%s\\033[0m\\t%s\\n""<DATABASE>""path to the database file"
...
...
@@ -142,11 +150,8 @@ print_help ()
printf"\\t\\033[1m%s\\033[0m\\t%s\\n""-N,--nodes""number of nodes (1 is the default)"
printf"\\t\\033[1m%s\\033[0m\\t%s\\n""--reservation""reservation to use (none is the default)"
printf"\\t\\033[1m%s\\033[0m\\t%s\\n""--time""time in minutes (300 is the default)"
printf"\\t\\033[1m%s\\033[0m\\t%s\\n""-m,--mem""memory which is required per node (defaults to 115500 M, but should be min. 242500 M for blastn, omit the unit for submitting)"
printf"\\t\\033[1m%s\\033[0m\\t%s\\n""-r,--ramdisk""ramdisk size in units of GiB (default is 40 GiB)"
printf"\\t\\033[1m%s\\033[0m\\t%s\\n""-t,--threads""blast threads (default is 1)"
printf"\\t\\033[1m%s\\033[0m\\t%s\\n""--blastparams""blast parameters (default is -outfmt 6 (for blank tabulated output))"
printf"\\t\\033[1m%s\\033[0m\\t%s\\n""-s,--splitup""No. of FASTA sequences per query file (default is to generate ~5000 files)"
printf"\\t\\033[1m%s\\033[0m\\t%s\\n""--blastdir""output directory (default is composition of input names)"
printf"\\t\\033[1m%s\\033[0m\\t%s\\n""--executable""choose executable (currently only from NCBI-BLAST, default: blastx)"
printf"\\t\\033[1m%s\\033[0m\\t%s\\n""--compress""if set, the output files will be merged and compressed (time consuming!, defaultt: off)"
...
...
@@ -217,6 +222,11 @@ credits()
echo" - faster stage-in for reference data"
echo" - automerge for -outfmt=6"
echo" - -outfmt=6 is now the default"
echo"- v0.5.1 -- 29. Aug. 2019 -- numerous housekeeping fixes"
echo"- v0.5.2 -- 02. Sep. 2019 -- fix:"
echo" - consistent biopython inclusion"
echo" - auto-detection of database size and memory selection"