Added option for setting e-value

Added parameter --evalue for setting e-value to RPS-BLAST

Added xlsxwriter as dependency

Now it installs xlxwriter when installing reCOGnizer

Fix on blast version

blast was recently updated to 2.11, but it doesn't work. Now, its version in reCOGnizer is fixed to 2.10.1

Deals with multiple categories

Some COGs and KOGs have several letters/functional categories attributed. Those were not properly handled.

• now, reCOGnizer reads both cog-20.def and kog by adding more rows to account for these multiple categories

Also improved sheet names in reCOGnizer_results, only adds number if multiple sheets will be needed (over 1M proteins)

Improvements on krona plotting

Fixed a bug in krona plot generation.

Now outputs krona plot of COG categories for KOG database.

Minor fix on downloading resources

Minor fix on downloading resources: tar command requires shell to interpret wildcards
Fix on krona installation: build.sh script was not calling install.pl

All databases from CDD are now usable

Added support for all databases for which there are HMMs in CDD:

• COG
• KOG
• NCBIfam
• Pfam
• Protein Clusters
• Smart
• TIGRFAM
• CDD itself

Results obained for each database differ, with all databases getting the base CDD description. Besides that:

• NCBIfam, Protein Clusters, Pfam and TIGRFAM get taxonomic, domain name and ec number information
• COG keeps getting the COG categories and corresponding EC numbers and KOs
• KOG gets the COG categories
• Smart gets domain name information

Minor fix for integration in pipelines

Krona now automatically runs the symlinks script, so now reCOGnizer calls it through the symlink, instead of the literal executable name, which was broken when integrated into environment such as in MOSCA

Several fixes on cog2ko

• Fixed broken bash commands in cog2ko
• Fixed the directories for storing the relational tables
• Fixed the merging of dataframes

Now compatible with MacOS!

• MacOS requires the use of gnu-tar instead of tar to use --wildcards
• wget is now added as dependency
• cog2ko default folder changed to the same as all others