Remove --skip-maps from standard install to allow plasmid addition

DerrickWood · Nov 9, 2020 · 4284a9d · 4284a9d
1 parent 9b286c5
commit 4284a9d
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,8 @@
 
 ### Fixed
 - Compilation error with GCC 10, omission of cstdint header
+- Removed --skip-maps from standard install due to addition of plasmids,
+  which require acc/taxid maps
 
 ## [2.1.0] - 2020-10-13
 

diff --git a/scripts/standard_installation.sh b/scripts/standard_installation.sh
@@ -26,7 +26,7 @@ if [ -n "$KRAKEN2_USE_FTP" ]; then
   ftp_flag="--use-ftp"
 fi
 
-kraken2-build --db $KRAKEN2_DB_NAME --download-taxonomy --skip-maps $masking_flag $protein_flag $ftp_flag
+kraken2-build --db $KRAKEN2_DB_NAME --download-taxonomy $masking_flag $protein_flag $ftp_flag
 kraken2-build --db $KRAKEN2_DB_NAME --download-library archaea $masking_flag $protein_flag $ftp_flag
 kraken2-build --db $KRAKEN2_DB_NAME --download-library bacteria $masking_flag $protein_flag $ftp_flag
 kraken2-build --db $KRAKEN2_DB_NAME --download-library viral $masking_flag $protein_flag $ftp_flag