Changed GALAXY_DATA_INDEX_DIR from an environment variable to a config entry.

tools/data_source/encode_import.py

@@ -16,7 +16,7 @@ def stop_err( msg ):
 def main():
     uids = sys.argv[1].split(",")
     out_file1 = sys.argv[2]
-    file_name = "%s/encode_datasets.loc" % os.environ.get( 'GALAXY_DATA_INDEX_DIR' )
+    file_name = "%s/encode_datasets.loc" % sys.argv[3]
     
     #remove NONE from uids
     have_none = True

tools/data_source/encode_import_all_latest_datasets.xml

@@ -1,5 +1,5 @@
 <tool id="encode_import_all_latest_datasets1" name="Combined Datasets">
-  <command interpreter="python">encode_import.py $hg17,$hg16 $output</command>
+  <command interpreter="python">encode_import.py $hg17,$hg16 $output ${GALAXY_DATA_INDEX_DIR}</command>
   <inputs>
     <display>
       <p><div class="toolFormTitle">hg1 (most recent datasets in bold)</div>$hg17</p>

tools/data_source/encode_import_chromatin_and_chromosomes.xml

@@ -1,5 +1,5 @@
 <tool id="encode_import_chromatin_and_chromosomes1" name="Chromatin and Chromosomes">
-  <command interpreter="python">encode_import.py $hg17,$hg16 $output</command>
+  <command interpreter="python">encode_import.py $hg17,$hg16 $output ${GALAXY_DATA_INDEX_DIR}</command>
   <inputs>
     <display>
       <p><div class="toolFormTitle">hg17 (most recent datasets in bold)</div>$hg17</p>

tools/data_source/encode_import_gencode.xml

@@ -1,5 +1,5 @@
 <tool id="encode_import_gencode1" name="Gencode Datasets">
-  <command interpreter="python">encode_import.py $hg17,$hg16 $output</command>
+  <command interpreter="python">encode_import.py $hg17,$hg16 $output ${GALAXY_DATA_INDEX_DIR}</command>
   <inputs>
     <display>
       <p><div class="toolFormTitle">hg17 (most recent datasets in bold)</div>$hg17</p>

tools/data_source/encode_import_genes_and_transcripts.xml

@@ -1,5 +1,5 @@
 <tool id="encode_import_genes_and_transcripts1" name="Genes and Transcripts">
-  <command interpreter="python">encode_import.py $hg17,$hg16 $output</command>
+  <command interpreter="python">encode_import.py $hg17,$hg16 $output ${GALAXY_DATA_INDEX_DIR}</command>
   <inputs>
     <display>
       <p><div class="toolFormTitle">hg17 (most recent datasets in bold)</div>$hg17</p>

tools/data_source/encode_import_multi-species_sequence_analysis.xml

@@ -1,5 +1,5 @@
 <tool id="encode_import_multi-species_sequence_analysis1" name="Multi-species Sequence Analysis">
-  <command interpreter="python">encode_import.py $hg17,$hg16 $output</command>
+  <command interpreter="python">encode_import.py $hg17,$hg16 $output ${GALAXY_DATA_INDEX_DIR}</command>
   <inputs>
     <display>
       <p><div class="toolFormTitle">hg17 (most recent datasets in bold)</div>$hg17</p>

tools/data_source/encode_import_transcription_regulation.xml

@@ -1,5 +1,5 @@
 <tool id="encode_import_transcription_regulation1" name="Transcription Regulation">
-  <command interpreter="python">encode_import.py $hg17,$hg16 $output</command>
+  <command interpreter="python">encode_import.py $hg17,$hg16 $output ${GALAXY_DATA_INDEX_DIR}</command>
   <inputs>
     <display>
       <p><div class="toolFormTitle">hg17 (most recent datasets in bold)</div>$hg17</p>

tools/data_source/microbial_import.py

@@ -24,7 +24,7 @@ while have_none:
 #create dictionary keyed by uid of tuples of (displayName,filePath,build) for all files
 available_files = {}
 try:
-    filename = "%s/microbial_data.loc" % os.environ.get( 'GALAXY_DATA_INDEX_DIR' )
+    filename = sys.argv[9]
     for i, line in enumerate( file( filename ) ):
         if not line or line[0:1] == "#" : continue
         fields = line.split('\t')

tools/data_source/microbial_import.xml

@@ -1,5 +1,5 @@
 <tool id="microbial_import1" name="Get Microbial Data">
-  <command interpreter="python">microbial_import.py $CDS,$tRNA,$rRNA,$sequence,$GeneMark,$GeneMarkHMM,$Glimmer3 $output</command>
+  <command interpreter="python">microbial_import.py $CDS,$tRNA,$rRNA,$sequence,$GeneMark,$GeneMarkHMM,$Glimmer3 $output ${GALAXY_DATA_INDEX_DIR}/microbial_data.loc</command>
   <inputs>
     <page>
       <display>

tools/data_source/microbial_import_code.py

@@ -1,11 +1,11 @@
 
-def load_microbial_data( sep='\t' ):
+def load_microbial_data( GALAXY_INDEX_DATA_DIR, sep='\t' ):
     # FIXME: this function is duplicated in the DynamicOptions class.  It is used here only to
     # set data.name in exec_after_process(). 
     microbe_info= {}
     orgs = {}
     
-    filename = "%s/microbial_data.loc" % os.environ.get( 'GALAXY_DATA_INDEX_DIR' )
+    filename = "%s/microbial_data.loc" % GALAXY_DATA_INDEX_DIR
     for i, line in enumerate( file( filename ) ):
         line = line.rstrip( '\r\n' )
         if line and not line.startswith( '#' ):
@@ -96,7 +96,7 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr
     if not (kingdom or org):
         print "Parameters are not available."
     
-    microbe_info = load_microbial_data()
+    microbe_info = load_microbial_data( param_dict.get( 'GALAXY_INDEX_DATA_DIR' ), sep='\t' )
     new_stdout = ""
     split_stdout = stdout.split("\n")
     basic_name = ""