Future-proof ncbi URLs to include the nlm subdomain

data/workflow/createtaxdb.sh

@@ -59,7 +59,7 @@ if { [ "${DBMODE}" = "1" ] && notExists "${TAXDBNAME}_taxonomy"; } || { [ "${DBM
         # Download NCBI taxon information
         if notExists "${TMP_PATH}/ncbi_download.complete"; then
             echo "Download taxdump.tar.gz"
-            downloadFile "https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz" "${TMP_PATH}/taxdump.tar.gz"
+            downloadFile "https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz" "${TMP_PATH}/taxdump.tar.gz"
             tar -C "${TMP_PATH}" -xzf "${TMP_PATH}/taxdump.tar.gz" names.dmp nodes.dmp merged.dmp delnodes.dmp
             touch "${TMP_PATH}/ncbi_download.complete"
             rm -f "${TMP_PATH}/taxdump.tar.gz"

data/workflow/databases.sh

@@ -118,9 +118,9 @@ case "${SELECTION}" in
         if notExists "${TMP_PATH}/nr.gz"; then
             date "+%s" > "${TMP_PATH}/version"
             downloadFile "https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz" "${TMP_PATH}/nr.gz"
-            downloadFile "https://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz" "${TMP_PATH}/prot.accession2taxid.gz"
+            downloadFile "https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz" "${TMP_PATH}/prot.accession2taxid.gz"
             gunzip "${TMP_PATH}/prot.accession2taxid.gz"
-            downloadFile "https://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/pdb.accession2taxid.gz" "${TMP_PATH}/pdb.accession2taxid.gz"
+            downloadFile "https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/pdb.accession2taxid.gz" "${TMP_PATH}/pdb.accession2taxid.gz"
             gunzip "${TMP_PATH}/pdb.accession2taxid.gz"
         fi
         push_back "${TMP_PATH}/nr.gz"
@@ -212,8 +212,8 @@ case "${SELECTION}" in
     ;;
     "CDD")
         if notExists "${TMP_PATH}/msa.msa.gz"; then
-            downloadFile "https://ftp.ncbi.nih.gov/pub/mmdb/cdd/cdd.info" "${TMP_PATH}/version"
-            downloadFile "https://ftp.ncbi.nih.gov/pub/mmdb/cdd/fasta.tar.gz" "${TMP_PATH}/msa.tar.gz"
+            downloadFile "https://ftp.ncbi.nlm.nih.gov/pub/mmdb/cdd/cdd.info" "${TMP_PATH}/version"
+            downloadFile "https://ftp.ncbi.nlm.nih.gov/pub/mmdb/cdd/fasta.tar.gz" "${TMP_PATH}/msa.tar.gz"
         fi
         INPUT_TYPE="FASTA_MSA"
         SED_FIX_LOOKUP='s|\.FASTA||g'

src/commons/Parameters.cpp

@@ -283,7 +283,7 @@ Parameters::Parameters():
         // taxonomyreport
         PARAM_REPORT_MODE(PARAM_REPORT_MODE_ID, "--report-mode", "Report mode", "Taxonomy report mode 0: Kraken 1: Krona", typeid(int), (void *) &reportMode, "^[0-1]{1}$"),
         // createtaxdb
-        PARAM_NCBI_TAX_DUMP(PARAM_NCBI_TAX_DUMP_ID, "--ncbi-tax-dump", "NCBI tax dump directory", "NCBI tax dump directory. The tax dump can be downloaded here \"ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz\"", typeid(std::string), (void *) &ncbiTaxDump, ""),
+        PARAM_NCBI_TAX_DUMP(PARAM_NCBI_TAX_DUMP_ID, "--ncbi-tax-dump", "NCBI tax dump directory", "NCBI tax dump directory. The tax dump can be downloaded here \"ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz\"", typeid(std::string), (void *) &ncbiTaxDump, ""),
         PARAM_TAX_MAPPING_FILE(PARAM_TAX_MAPPING_FILE_ID, "--tax-mapping-file", "Taxonomy mapping file", "File to map sequence identifier to taxonomical identifier", typeid(std::string), (void *) &taxMappingFile, ""),
         PARAM_TAX_MAPPING_MODE(PARAM_TAX_MAPPING_MODE_ID, "--tax-mapping-mode", "Taxonomy mapping mode", "Map taxonomy based on sequence database 0: .lookup file 1: .source file", typeid(int), (void *) &taxMappingMode, "^[0-1]{1}$"),
         PARAM_TAX_DB_MODE(PARAM_TAX_DB_MODE_ID, "--tax-db-mode", "Taxonomy db mode", "Create taxonomy database as: 0: .dmp flat files (human readable) 1: binary dump (faster readin)", typeid(int), (void *) &taxDbMode, "^[0-1]{1}$"),