From 4186a549deba1e41181fd1ed22169478c23e362c Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Thu, 10 Sep 2009 17:31:05 -0400
Subject: [PATCH 1/2] POSIXize/Bournize updateucsc.sh.sample

---
 cron/updateucsc.sh.sample | 26 ++++++++++++++++++++++----
 1 file changed, 22 insertions(+), 4 deletions(-)

diff --git a/cron/updateucsc.sh.sample b/cron/updateucsc.sh.sample
index 6e7e2fc0f7f..4ebaf825821 100644
--- a/cron/updateucsc.sh.sample
+++ b/cron/updateucsc.sh.sample
@@ -6,7 +6,8 @@
 
 # Edit this line to refer to galaxy's path:
 GALAXY=/galaxy/path
-export PYTHONPATH=${GALAXY}/lib
+PYTHONPATH=${GALAXY}/lib
+export PYTHONPATH
 
 # setup directories
 echo "Creating required directories."
@@ -32,7 +33,11 @@ echo "Updating builds.txt"
 python ${GALAXY}/cron/parse_builds.py > ${GALAXY}/tool-data/shared/ucsc/new/builds.txt
 if [ $? -eq 0 ]
 then
-    cp -uf ${GALAXY}/tool-data/shared/ucsc/new/builds.txt ${GALAXY}/tool-data/shared/ucsc/builds.txt
+    diff ${GALAXY}/tool-data/shared/ucsc/new/builds.txt ${GALAXY}/tool-data/shared/ucsc/builds.txt > /dev/null 2>&1
+    if [ $? -ne 0 ]
+    then
+        cp -f ${GALAXY}/tool-data/shared/ucsc/new/builds.txt ${GALAXY}/tool-data/shared/ucsc/builds.txt
+    fi
 else
     echo "Failed to update builds.txt" >&2
 fi
@@ -42,7 +47,11 @@ echo "Updating ucsc_build_sites.txt"
 python ${GALAXY}/cron/parse_builds_3_sites.py > ${GALAXY}/tool-data/shared/ucsc/new/ucsc_build_sites.txt
 if [ $? -eq 0 ]
 then
-    cp -uf ${GALAXY}/tool-data/shared/ucsc/new/ucsc_build_sites.txt ${GALAXY}/tool-data/shared/ucsc/ucsc_build_sites.txt
+    diff ${GALAXY}/tool-data/shared/ucsc/new/ucsc_build_sites.txt ${GALAXY}/tool-data/shared/ucsc/ucsc_build_sites.txt > /dev/null 2>&1
+    if [ $? -ne 0 ]
+    then
+        cp -f ${GALAXY}/tool-data/shared/ucsc/new/ucsc_build_sites.txt ${GALAXY}/tool-data/shared/ucsc/ucsc_build_sites.txt
+    fi
 else
     echo "Failed to update builds.txt" >&2
 fi
@@ -52,7 +61,16 @@ echo "Building chromInfo tables."
 python ${GALAXY}/cron/build_chrom_db.py ${GALAXY}/tool-data/shared/ucsc/chrom/new/ ${GALAXY}/tool-data/shared/ucsc/builds.txt
 if [ $? -eq 0 ]
 then
-    cp -uf ${GALAXY}/tool-data/shared/ucsc/chrom/new/*.len ${GALAXY}/tool-data/shared/ucsc/chrom/
+    for src in ${GALAXY}/tool-data/shared/ucsc/chrom/new/*.len
+    do
+        dst=${GALAXY}/tool-data/shared/ucsc/chrom/`basename $src`
+        diff $src $dst > /dev/null 2>&1
+        if [ $? -ne 0 ]
+        then
+            echo "cp -f $src $dst"
+            cp -f $src $dst
+        fi
+    done
 else
     echo "Failed to update chromInfo tables." >&2
 fi

From 140b458dbb6b2565c32177425d54ef5566d7edd2 Mon Sep 17 00:00:00 2001
From: Guruprasad Anada <gua110@bx.psu.edu>
Date: Thu, 10 Sep 2009 17:35:21 -0400
Subject: [PATCH 2/2] Bug fix for 'Fetch closest feature' tool.

---
 tools/new_operations/flanking_features.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/new_operations/flanking_features.py b/tools/new_operations/flanking_features.py
index 37d577465a0..2ef0d77f59f 100644
--- a/tools/new_operations/flanking_features.py
+++ b/tools/new_operations/flanking_features.py
@@ -129,7 +129,7 @@ def proximal_region_finder(readers, region, comments=True):
                             map(outfields.append, result_down[-1].other) #The last element of result_down will be the closest element to the given interval
                     elif result_up:
                         map(outfields.append, result_up[res_ind].other)
-                    else:
+                    elif result_down:
                         map(outfields.append, result_down[-1].other) #The last element of result_down will be the closest element to the given interval
                     yield outfields