changeset 4:1a5ea7128b6a draft

Uploaded

--- a/README	Mon May 06 12:55:44 2013 -0400
+++ b/README	Tue May 14 04:52:22 2013 -0400
@@ -1,8 +1,10 @@
 Dependencies
 ============
 
- * ngsroi R package (shipped with tar.gz)
- * Python Cheetah package.
+ * ngsroi R package (shipped as tar.gz, in R subfolder)
+ * R packages: getopt
+ * samtools binary (apparently for SAM upload)
+ * Python packages: Cheetah, matplotlib
  * ngs_roi binaries:
 
    svn co http://svn.seqan.de/seqan/trunk seqan-trunk

--- a/bam2roi.xml	Mon May 06 12:55:44 2013 -0400
+++ b/bam2roi.xml	Tue May 14 04:52:22 2013 -0400
@@ -56,4 +56,12 @@
       Tool Help
     -->
     <help>No help yet.</help>
+
+    <!--
+      Dependencies
+    -->
+    <requirements>
+        <requirement type="binary">bam2roi</requirement>
+        <requirement type="python-module">Cheetah</requirement>
+    </requirements>
 </tool>

--- a/roi_details.xml	Mon May 06 12:55:44 2013 -0400
+++ b/roi_details.xml	Tue May 14 04:52:22 2013 -0400
@@ -62,4 +62,12 @@
       Tool Help
     -->
     <help>No help yet.</help>
+
+    <!--
+      Dependencies
+    -->
+    <requirements>
+        <requirement type="python-module">Cheetah</requirement>
+        <requirement type="python-module">matplotlib</requirement>
+    </requirements>
 </tool>

--- a/roi_feature_projection.xml	Mon May 06 12:55:44 2013 -0400
+++ b/roi_feature_projection.xml	Tue May 14 04:52:22 2013 -0400
@@ -10,7 +10,7 @@
     #if $roi_intersect_in_features # ln -s ${roi_intersect_in_features} ${roi_intersect_in_features}.${roi_intersect_in_features.ext}; #end if
 
     <!-- Call the feature projection on the links -->
-    roi_intersect $roi_intersect_strand_specific
+    roi_feature_projection $roi_intersect_strand_specific
     --in-roi ${roi_intersect_in_roi}.${roi_intersect_in_roi.ext}
     --in-features ${roi_intersect_in_features}.${roi_intersect_in_features.ext}
     --out-roi ${roi_intersect_out_roi}.roi
@@ -76,4 +76,12 @@
       Tool Help
     -->
     <help>No help yet.</help>
+
+    <!--
+      Dependencies
+    -->
+    <requirements>
+        <requirement type="python-module">Cheetah</requirement>
+        <requirement type="binary">roi_feature_projection</requirement>
+    </requirements>
 </tool>

--- a/roi_plot_thumbnails.xml	Mon May 06 12:55:44 2013 -0400
+++ b/roi_plot_thumbnails.xml	Tue May 14 04:52:22 2013 -0400
@@ -75,4 +75,12 @@
   <help>
     You don't need help!
   </help>
+
+    <!--
+      Dependencies
+    -->
+    <requirements>
+        <requirement type="python-module">Cheetah</requirement>
+        <requirement type="binary">roi_plot_thumbnails</requirement>
+    </requirements>
 </tool>

--- a/roi_report.xml	Mon May 06 12:55:44 2013 -0400
+++ b/roi_report.xml	Tue May 14 04:52:22 2013 -0400
@@ -33,4 +33,11 @@
       Tool Help
     -->
     <help>No help yet.</help>
+    <!--
+      Dependencies
+    -->
+    <requirements>
+        <requirement type="python-module">Cheetah</requirement>
+        <requirement type="python-module">matplotlib</requirement>
+    </requirements>
 </tool>

--- a/roi_table.py	Mon May 06 12:55:44 2013 -0400
+++ b/roi_table.py	Tue May 14 04:52:22 2013 -0400
@@ -153,10 +153,11 @@
 
     def createHtml(self, file_name, keys, records):
         print >>sys.stderr, 'Writing %s' % self.args.out_file
-        vals = {'table': RoiTable(self.args, keys, records, self).render()}
+        vals = {'table': RoiTable(self.args, keys, records, self).render(),
+                'args': self.args}
         t = Cheetah.Template.Template(PAGE_TPL, searchList=vals)
         with open(self.args.out_file, 'wb') as f:
-            f.write(str(t))        
+            f.write(str(t))
 
 
 def main():

--- a/roi_table.xml	Mon May 06 12:55:44 2013 -0400
+++ b/roi_table.xml	Tue May 14 04:52:22 2013 -0400
@@ -71,4 +71,12 @@
       Tool Help
     -->
     <help>No help yet.</help>
+
+    <!--
+      Dependencies
+    -->
+    <requirements>
+        <requirement type="python-module">Cheetah</requirement>
+        <requirement type="binary">roi_plot_thumbnails</requirement>
+    </requirements>
 </tool>