diff --git a/shell/buildRODs.sh b/shell/buildRODs.sh
deleted file mode 100755
index 76584826c..000000000
--- a/shell/buildRODs.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-java -Xmx40000m -cp ../java/dist/AnalysisTK.jar org.broadinstitute.sting.atk.PrepareROD REF_FILE_ARG=/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta ROD_FILE=/seq/references/dbsnp/downloads/snp129_hg18.txt OUT=`echo $1/snp129_hg18.txt.rod` ROD_TYPE=dbSNP ROD_NAME=dbSNP
-
diff --git a/shell/calcCallerMD5s.csh b/shell/calcCallerMD5s.csh
deleted file mode 100755
index c1b2eed21..000000000
--- a/shell/calcCallerMD5s.csh
+++ /dev/null
@@ -1,9 +0,0 @@
-#!/bin/tcsh
-
-foreach model (ONE_STATE THREE_STATE EMPIRICAL)
-java -Xmx4096m -jar ~/dev/GenomeAnalysisTK/trunk/dist/GenomeAnalysisTK.jar -l INFO -L 1:10,000,000-11,000,000 -R /broad/1KG/reference/human_b36_both.fasta -T SingleSampleGenotyper -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout ./$model.geli.calls -lod 5 -m $model
-end
-wc -l *.geli.calls
-md5sum *.geli.calls
-
-
diff --git a/shell/makeResources.sh b/shell/makeResources.sh
deleted file mode 100755
index 2337f4858..000000000
--- a/shell/makeResources.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-cd dist/packages/GATKResources
-tar cvhzf gatk_resources_062309.tgz resources
diff --git a/shell/readStatsDiff.sh b/shell/readStatsDiff.sh
deleted file mode 100755
index 87b97984c..000000000
--- a/shell/readStatsDiff.sh
+++ /dev/null
@@ -1,66 +0,0 @@
-#!/usr/bin/csh
-# ##############################################################################
-# this file can be used to diff the flagstat values for a whole genome,
-# along with sub-diffs for each chromosome.  This may be helpful if you're 
-# debugging a specific reads problem, and you want to know the differences
-# between the output of the GATK and samtools
-# ##############################################################################
-
-if ($#argv != 3) then
-    echo "usage readStatsDiff <bamfile.bam> <referenceSequence.fasta> <outputFile>"; exit 1
-endif
-
-if (! -f $1) then
-    echo bam file $2 does not seem to exist; exit 1
-endif
-if (! -f $2) then
-    echo reference file $2 does not seem to exist; exit 1
-endif
-if ( -e $3) then
-    echo output file $3 already exists!; exit 1
-endif
-
-
-# set the bam and the reference index
-set bam = $1
-set seq = $2
-set out = $3
-
-# diff the whole chromosome
-java -ea -Xmx4096m \
--Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=n,address=8015 \
--jar dist/GenomeAnalysisTK.jar \
--S SILENT \
--T FlagStatRead \
--I $bam \
--R $seq \
--oe 1.out 
-samtools flagstat $bam > 2.out
-echo "\n" >> $out
-echo results for whole bam file >> $out
-echo "\n" >> $out
-diff 1.out 2.out >> $out
-rm 1.out
-rm 2.out
-
-
-
-foreach chromosome (chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX)
-java -ea -Xmx4096m \
--Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=n,address=8015 \
--jar dist/GenomeAnalysisTK.jar \
--S SILENT \
--T FlagStatRead \
--I $bam \
--R $seq \
--oe 1.out \
--L $chromosome
-samtools view -h -b $bam $chromosome > temp.bam
-samtools flagstat temp.bam > 2.out
-echo results for $chromosome >> $out
-echo "\n" >> $out
-diff 1.out 2.out >> $out
-rm temp.bam
-rm 1.out
-rm 2.out
-end
diff --git a/shell/syncWithDevOnGSA2.csh b/shell/syncWithDevOnGSA2.csh
index 7048f8212..045ac49b6 100755
--- a/shell/syncWithDevOnGSA2.csh
+++ b/shell/syncWithDevOnGSA2.csh
@@ -1,6 +1,6 @@
 #!/bin/tcsh
 
-setenv HERE java
+setenv HERE "java tribble"
 setenv THERE \~/dev/GenomeAnalysisTKFromLaptop/trunk
 
-rsync -e ssh -aCvz $HERE depristo@gsa2:$THERE
+rsync -e ssh -aCvz $HERE depristo@gsa1:$THERE