Fix standard installation bug with FTP downloads

DerrickWood · Sep 12, 2018 · 77d8dd1a9d827f1acbd31cf11db260337b1b1556 · 77d8dd1
1 parent 81ce38a
commit 77d8dd1a9d827f1acbd31cf11db260337b1b1556
Showing with 11 additions and 6 deletions.

+11 −6 scripts/standard_installation.sh
diff --git a/scripts/standard_installation.sh b/scripts/standard_installation.sh
@@ -21,13 +21,18 @@ if [ -z "$KRAKEN2_MASK_LC" ]; then
   masking_flag="--no-mask"
 fi
 
-kraken2-build --db $KRAKEN2_DB_NAME --download-taxonomy --skip-maps $masking_flag $protein_flag
-kraken2-build --db $KRAKEN2_DB_NAME --download-library archaea $masking_flag $protein_flag
-kraken2-build --db $KRAKEN2_DB_NAME --download-library bacteria $masking_flag $protein_flag
-kraken2-build --db $KRAKEN2_DB_NAME --download-library viral $masking_flag $protein_flag
-kraken2-build --db $KRAKEN2_DB_NAME --download-library human --no-mask $protein_flag
+ftp_flag=""
+if [ -n "$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-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
+kraken2-build --db $KRAKEN2_DB_NAME --download-library human --no-mask $protein_flag $ftp_flag
 if [ -z "$KRAKEN2_PROTEIN_DB" ]; then
-  kraken2-build --db $KRAKEN2_DB_NAME --download-library UniVec_Core $masking_flag
+  kraken2-build --db $KRAKEN2_DB_NAME --download-library UniVec_Core $masking_flag $ftp_flag
 fi
 kraken2-build --db $KRAKEN2_DB_NAME --build --threads $KRAKEN2_THREAD_CT \
               --minimizer-len $KRAKEN2_MINIMIZER_LEN \