v1.8.51

• modified bit-figshare-upload to be able to deal with large files
  • required altering split command and the for loop used for uploading parts

v1.8.50

• added bit-figshare-upload
  • this is just an implementation of the bash script example kindly provided in the figshare docs here, with some modifications so as to not need to modify the script each use, and so that it will work on darwin (mac) distributions also due to some changes and the environment setup with a conda installation
• added in scripts to download NCBI taxonomy and GO databases when they are first needed, rather than during package install
• removed bit-cov-* scripts that were developed for, and are in the CoV-IRT-Micro package
• fixed spacing issues from early scripts (those with 2 spaces instead of 4... gross)

v1.8.47

• robustness improvements to bit-GL-combine-KO-and-tax-tables and bit-GL-combine-contig-tax-tables thanks to report from Rene Miller-Xavier, now they deal with if an input table is empty by removing it from the list of those being combined

v1.8.46

• adding script to pull genome-assembly summarization workflow, bit-get-genome-summarize-wf

v1.8.45

• adding citation info

v1.8.44

• adding bit-parse-fastq-by-headers

v1.8.42

• another attempt to make bit-dl-ncbi-assemblies more robust to instances where the assembly summary tables don't download successfully (i can't pin down why it works sometimes and not others, it doesn't just seem to be time between requests ¯_(ツ)_/¯ )
  • so added a while loop with set number of tries for now

v1.8.41

• changing from ftp to https for downloading ncbi assembly summary tables in bit-dl-ncbi-assemblies, as the ftp way seems to be giving some trouble lately

v1.8.39

• robustness improvement to bit-dl-ncbi-assemblies when wanted file type doesn't exist in ncbi

v1.8.38

• Fixing bit-dl-ncbi-accessions new problem if a target file type doesn't exist. Previously, the download would fail if the built URL was not there. Now it downloads a file telling us it's not there. So put it a check to catch this situation and still be able to tell the user which target accessions failed to download successfully. Thanks to note from @Arkadiy-Garber!