# HG changeset patch
# User yating-l
# Date 1489592169 14400
# Node ID 5580dbf2a31c5653362de92391fe28ac7449148a
# Parent  e025fa070c8d113935b1e608e7c5375c3a90e69c
planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit e81fecac281f299db00cfc88a068e056b031ae9d-dirty

diff -r e025fa070c8d -r 5580dbf2a31c jbrowse_hub.py
--- a/jbrowse_hub.py	Wed Mar 15 10:54:24 2017 -0400
+++ b/jbrowse_hub.py	Wed Mar 15 11:36:09 2017 -0400
@@ -44,8 +44,6 @@
 
     # BAM format
     parser.add_argument('--bam', action='append', help='BAM format from HISAT')
-    # put bam index file at the same directory with bam file
-    parser.add_argument('--bai', action='append', help='BAM index format from HISAT') 
 
     # BIGWIG format
     parser.add_argument('--bigwig', action='append', help='BIGWIG format to show rnaseq coverage')
@@ -73,7 +71,6 @@
     chrom_size = utils.getChromSizes(reference, tool_directory)
     all_tracks = trackObject.trackObject(chrom_size.name, genome, extra_files_path) #store converted files in the array: all_tracks.tracks
     array_inputs_bam = args.bam
-    array_inputs_bai = args.bai
     array_inputs_bed_simple_repeats = args.bedSimpleRepeats
     array_inputs_bed_splice_junctions = args.bedSpliceJunctions
     array_inputs_bigwig = args.bigwig
diff -r e025fa070c8d -r 5580dbf2a31c trackObject.py
--- a/trackObject.py	Wed Mar 15 10:54:24 2017 -0400
+++ b/trackObject.py	Wed Mar 15 11:36:09 2017 -0400
@@ -30,16 +30,21 @@
         Convert gff3, BED, blastxml and gtf files into gff3 files 
         and store converted files in folder 'raw'
         '''
+        
         fileName = os.path.basename(dataFile)
         des_path = os.path.join(self.raw_folder, fileName)
         track = {}
         if dataType == 'gff3_mrna' or dataType == 'gff3_transcript' or dataType == 'fasta' or dataType == 'bam' or dataType == 'bigwig' or dataType == 'bai':
             if dataType == 'bam':
+                # JBrowse will raise error: not a BAM file if the filename hasn't .bam extension
+                fileName = os.path.basename(dataFile) + '.bam'
+                des_path = os.path.join(self.raw_folder, fileName)
                 bam_index = utils.createBamIndex(dataFile)
                 indexname = os.path.basename(bam_index)
                 des_path_for_index = os.path.join(self.raw_folder, indexname)
                 shutil.copyfile(bam_index, des_path_for_index)  
                 track['index'] = indexname
+
             try:
                 shutil.copyfile(dataFile, des_path)
             except shutil.Error as err1: