# HG changeset patch
# User chrisw
# Date 1550091105 18000
# Node ID 849ab444b4f1d25fb98b95d6b16a7de68c7bda78
# Parent  35ed7314038dafaa560f8b65c1eeb59f31e229b5
Uploaded

diff -r 35ed7314038d -r 849ab444b4f1 Snakefile
--- a/Snakefile	Wed Feb 13 15:43:07 2019 -0500
+++ b/Snakefile	Wed Feb 13 15:51:45 2019 -0500
@@ -14,6 +14,9 @@
          'all.exon_bw_count.zst', 'unique.exon_bw_count.zst',
          'manifest']
 
+import os
+config['output']=os.path.abspath(config['output'])
+
 import subprocess
 def run_command(cmd_args):
     cmd_args = ' '.join(cmd_args)
@@ -26,7 +29,6 @@
 
 import re
 FASTQ_PATT=re.compile(r'([^_\.]+)(_(\d+))?\.((fastq)|fq)(\.gz)?$')
-import os
 def prep_for_galaxy_run():
     try:
         os.mkdir(config['temp'])
@@ -37,7 +39,7 @@
     run_acc = 'sample'
     if m is not None:
         run_acc = m.group(1)
-    study_acc = run_acc
+    study_acc = 'study'
     if 'study' in config:
         study_acc = config['study']
     genome = 'hg38'
diff -r 35ed7314038d -r 849ab444b4f1 monorail.xml
--- a/monorail.xml	Wed Feb 13 15:43:07 2019 -0500
+++ b/monorail.xml	Wed Feb 13 15:51:45 2019 -0500
@@ -19,7 +19,7 @@
                             inputs="$singlePaired.input1,$singlePaired.input2"
                         #end if
                     #end if
-                    output="./"
+                    output="."
                     temp="./tmp"
                     ref="$refGenomeSource.GTFconditional.genomeDir.fields.path"
                     genome="ath10"