Fixes and updates for v1.0.6

mikessh · Dec 1, 2015 · c2b19d7 · c2b19d7
1 parent 1b24cac
commit c2b19d7
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Showing 5 changed files with 9 additions and 9 deletions.
diff --git a/aging/metadata.small.txt b/aging/metadata.small.txt
@@ -2,5 +2,5 @@
 ../samples/A2-i140.txt.gz A2-i140 F 73
 ../samples/A4-i189.txt.gz A4-i189 M 25
 ../samples/A4-i190.txt.gz A4-i190 M 25
-../samples/A3-i150.txt.gz A3-i150 F 87
-../samples/A3-i151.txt.gz A3-i151 F 87
+../samples/A3-i150.txt.gz A3-i150 F 87
+../samples/A3-i151.txt.gz A3-i151 F 87
diff --git a/aging/run.sh b/aging/run.sh
@@ -1,13 +1,13 @@
 # point vdjtools executable
-VDJTOOLS="java -Xmx20G -jar ../vdjtools-1.0-SNAPSHOT.jar"
+VDJTOOLS="java -Xmx20G -jar ../vdjtools.jar"
 
 # demonstrate basic analysis
 $VDJTOOLS CalcBasicStats -m metadata.txt out/0
 $VDJTOOLS CalcSpectratype -m metadata.txt out/1
 $VDJTOOLS CalcSegmentUsage -m metadata.txt -p -f age -n out/2
 $VDJTOOLS PlotFancySpectratype ../samples/A4-i125.txt.gz out/3
 $VDJTOOLS PlotSpectratypeV ../samples/A4-i125.txt.gz out/4
-$VDJTOOLS PlotFancyVJUsage .../samples/A4-i125.txt.gz out/5
+$VDJTOOLS PlotFancyVJUsage ../samples/A4-i125.txt.gz out/5
 
 # demonstrate diversity estimates
 $VDJTOOLS PlotQuantileStats ../samples/A4-i125.txt.gz out/6
@@ -19,8 +19,8 @@ $VDJTOOLS OverlapPair -p ../samples/A4-i189.txt.gz ../samples/A4-i190.txt.gz out
 $VDJTOOLS CalcPairwiseDistances -m metadata.small.txt out/10
 $VDJTOOLS ClusterSamples -p -f age -n -l sample.id out/10 out/10.age
 
-# demonstrate database annotation
-$VDJTOOLS ScanDatabase -m metadata.txt -f --filter "__origin__=~/EBV/" out/11
+# demonstrate database annotation. Only v1.0.4 and earlier
+#$VDJTOOLS ScanDatabase -m metadata.txt -f --filter "__origin__=~/EBV/" out/11
 
 # demonstrate sample operations and filtering
 $VDJTOOLS Decontaminate -m metadata.txt -c out/dec/

diff --git a/hsct/run.sh b/hsct/run.sh
@@ -1,5 +1,5 @@
 # point to vdjtools executable
-VDJTOOLS="java -Xmx8G -jar ../vdjtools-1.0-SNAPSHOT.jar"
+VDJTOOLS="java -Xmx8G -jar ../vdjtools.jar"
 
 # perform basic analysis
 $VDJTOOLS CalcBasicStats -m metadata.txt out/0

diff --git a/ms/run.sh b/ms/run.sh
@@ -1,5 +1,5 @@
 # point the vdjtools executable
-VDJTOOLS="java -Xmx20G -jar ../vdjtools-1.0-SNAPSHOT.jar"
+VDJTOOLS="java -Xmx20G -jar ../vdjtools.jar"
 
 # shows higher clonality for MS samples
 $VDJTOOLS RarefactionPlot -m metadata.txt -l sample_id -f state diversity/

diff --git a/twins/run.sh b/twins/run.sh
@@ -8,6 +8,6 @@ do
  groovy Convert.groovy $f;
 done
 # compute similarity measures
-java -Xmx40G -jar ../vdjtools-1.0-SNAPSHOT.jar CalcPairwiseDistances -m metadata.txt -p .
+java -Xmx40G -jar ../vdjtools.jar CalcPairwiseDistances -m metadata.txt -p .
 # benchmark
 Rscript analyze.R