removed hardcoded paths to use software config params instead

jorvis · Jul 27, 2015 · 356b034 · 356b034
1 parent b34afb5
commit 356b034
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/components/ber/ber.config b/components/ber/ber.config
@@ -29,7 +29,7 @@ $;INPUT_DIRECTORY$; =
 ;; the following is only used when iterating over an INPUT_DIRECTORY
 $;INPUT_EXTENSION$; = btab
 ;; subject database used for wu-blastp run
-$;PROTEIN_DB$; = /local/projects/uniref/uniref100.fasta
+$;PROTEIN_DB$; = $;DB_UNIPROT_100$;
 ;; format of subject database
 $;PROTEIN_DB_FORMAT$; = formatdb
 ;; database of nucleotide sequences corresponding to query polypeptides

diff --git a/components/hmmpfam3/hmmpfam3.config b/components/hmmpfam3/hmmpfam3.config
@@ -46,9 +46,9 @@ $;INPUT_DIRECTORY$; =
 ;; the following is only used when iterating over an INPUT_DIRECTORY
 $;INPUT_EXTENSION$; = fsa
 ;;This needs to be formatted for HMMER 3.0. HMMER 2.0 and 3.0 dbs are not compatible
-$;DATABASE_PATH$; = /local/db/repository/igs/hmm/latest/coding_hmm.lib.bin
+$;DATABASE_PATH$; = $;HMM_ALL$;
 ;; MLDBM file  
-$;HMM_INFO_FILE$; =  /local/db/repository/igs/hmm/latest/coding_hmm.lib.db
+$;HMM_INFO_FILE$; = $;HMM_LIB_DB$;
 
 [output]
 $;OUTPUT_TOKEN$; = default