From 09c8c8fd569fdeb90e1acfad821a277a78e5dcc9 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Thu, 17 Feb 2011 13:57:38 -0500
Subject: [PATCH 1/2] Fix displaying the stdout/stderr of a library upload when
 the stdout/stderr is None

---
 templates/library/common/ldda_info.mako | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/templates/library/common/ldda_info.mako b/templates/library/common/ldda_info.mako
index 82ac6107f26..57f491eb0c7 100644
--- a/templates/library/common/ldda_info.mako
+++ b/templates/library/common/ldda_info.mako
@@ -117,14 +117,14 @@
         </div>
         %if ldda.creating_job_associations:
             <% job = ldda.creating_job_associations[0].job %>
-            %if job.stdout.strip() != '':
+            %if job.stdout and job.stdout.strip() != '':
                 <div class="form-row">
                     <label>Job Standard Output</label>
                     <pre>${job.stdout}</pre>
                     <div style="clear: both"></div>
                 </div>
             %endif
-            %if job.stderr.strip() != '':
+            %if job.stderr and job.stderr.strip() != '':
                 <div class="form-row">
                     <label>Job Standard Error</label>
                     <pre>${job.stderr}</pre>

From 6cc9dd1159b5f3b158040cae4c61c5f42adc9d90 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Thu, 17 Feb 2011 14:25:56 -0500
Subject: [PATCH 2/2] Set default value for Cuffdiff's minimum alignment count
 parameter to reflect v0.9.3

---
 tools/ngs_rna/cuffdiff_wrapper.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/ngs_rna/cuffdiff_wrapper.xml b/tools/ngs_rna/cuffdiff_wrapper.xml
index 2741deae96c..376d8dbb3b2 100644
--- a/tools/ngs_rna/cuffdiff_wrapper.xml
+++ b/tools/ngs_rna/cuffdiff_wrapper.xml
@@ -90,7 +90,7 @@
 
         <param name="fdr" type="float" value="0.05" label="False Discovery Rate" help="The allowed false discovery rate."/>
         <param name="min_mapqual" type="integer" value="0" label="Min SAM Mapping Quality" help="Instructs Cufflinks to ignore alignments with a SAM mapping quality lower than this number."/>
-        <param name="min_alignment_count" type="integer" value="0" label="Min Alignment Count" help="The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples."/>
+        <param name="min_alignment_count" type="integer" value="1000" label="Min Alignment Count" help="The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples."/>
         <param name="do_normalization" type="select" label="Perform quartile normalization" help="Removes top 25% of genes from FPKM denominator to improve accuracy of differential expression calls for low abundance transcripts.">
             <option value="No">No</option>
             <option value="Yes">Yes</option>