diff --git a/smoke_test/.gitignore b/smoke_test/.gitignore
index 41fe567351e913c052d8dfdabbd05260fa068435..6b2ed881b6cd7829275f44eaa8c8d2736827e189 100644
--- a/smoke_test/.gitignore
+++ b/smoke_test/.gitignore
@@ -1,2 +1,3 @@
./output_dir/
+output_dir/
diff --git a/smoke_test/batch_app_report b/smoke_test/batch_app_report
new file mode 100755
index 0000000000000000000000000000000000000000..0ca17eb4724a4146ccad15801e4835a0d2d42888
--- /dev/null
+++ b/smoke_test/batch_app_report
@@ -0,0 +1,6 @@
+#!/bin/bash
+inputfile=$1
+for app in $(cat $inputfile); do
+ version=$(ls /usr/local/Modules/modulefiles/$app)
+ mtime=360 ./application_report $app $version
+done
diff --git a/smoke_test/generate_bin_test b/smoke_test/generate_bin_test
index de567fa839cd69d4be707b0578560ec0d72fa69b..3adba5c75e3c95b4d77933de27df622263b82aa1 100755
--- a/smoke_test/generate_bin_test
+++ b/smoke_test/generate_bin_test
@@ -1,10 +1,11 @@
#!/bin/bash
+USAGE_REPORT=${1:-software_usage.txt}
NUM_MODULE=${2:-100}
TESTCASE_DIR='./tests'
-USAGE_REPORT=software_usage.txt
+
if [ ! -f $USAGE_REPORT ]; then
software_usage $USAGE_REPORT
fi
diff --git a/smoke_test/output_dir/anaconda/5.1.0-Python3.6-gcc5 b/smoke_test/output_dir/anaconda/5.1.0-Python3.6-gcc5
deleted file mode 100644
index 8fcfabdcdd11cbe45d8dfd7904f9c173e44634b3..0000000000000000000000000000000000000000
--- a/smoke_test/output_dir/anaconda/5.1.0-Python3.6-gcc5
+++ /dev/null
@@ -1 +0,0 @@
-anaconda Command line client (version 1.6.9)
diff --git a/smoke_test/output_dir/atlas/3.10.2-gcc4 b/smoke_test/output_dir/atlas/3.10.2-gcc4
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/smoke_test/output_dir/atlas/3.10.2-gcc5 b/smoke_test/output_dir/atlas/3.10.2-gcc5
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/smoke_test/output_dir/cuda/7.5 b/smoke_test/output_dir/cuda/7.5
deleted file mode 100644
index 91d5b8d810df82bf2f83fd2b40e404cf9092b2bb..0000000000000000000000000000000000000000
--- a/smoke_test/output_dir/cuda/7.5
+++ /dev/null
@@ -1,17 +0,0 @@
-nvcc: NVIDIA (R) Cuda compiler driver
-Copyright (c) 2005-2015 NVIDIA Corporation
-Built on Tue_Aug_11_14:27:32_CDT_2015
-Cuda compilation tools, release 7.5, V7.5.17
-deviceQuery Starting...
-
- CUDA Device Query (Runtime API) version (CUDART static linking)
-
-cudaGetDeviceCount returned 35
--> CUDA driver version is insufficient for CUDA runtime version
-Result = FAIL
-CUDA error at bandwidthTest.cu:255 code=35(cudaErrorInsufficientDriver) "cudaSetDevice(currentDevice)"
-[CUDA Bandwidth Test] - Starting...
-Running on...
-
-cudaGetDeviceProperties returned 35
--> CUDA driver version is insufficient for CUDA runtime version
diff --git a/smoke_test/output_dir/fftw/3.3.4-gcc b/smoke_test/output_dir/fftw/3.3.4-gcc
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/smoke_test/output_dir/fftw/3.3.5-gcc b/smoke_test/output_dir/fftw/3.3.5-gcc
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/smoke_test/output_dir/fftw/3.3.5-gcc5 b/smoke_test/output_dir/fftw/3.3.5-gcc5
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/smoke_test/output_dir/fsl/6.0.3 b/smoke_test/output_dir/fsl/6.0.3
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/smoke_test/output_dir/gcc/4.9.3 b/smoke_test/output_dir/gcc/4.9.3
deleted file mode 100644
index 4a88085389346543e4f16d8f6fe8796e32337b06..0000000000000000000000000000000000000000
--- a/smoke_test/output_dir/gcc/4.9.3
+++ /dev/null
@@ -1,5 +0,0 @@
-gcc (GCC) 4.9.3
-Copyright (C) 2015 Free Software Foundation, Inc.
-This is free software; see the source for copying conditions. There is NO
-warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-
diff --git a/smoke_test/output_dir/gcc/5.4.0 b/smoke_test/output_dir/gcc/5.4.0
deleted file mode 100644
index 992dafa3e64f98433a957067deda8630f0084711..0000000000000000000000000000000000000000
--- a/smoke_test/output_dir/gcc/5.4.0
+++ /dev/null
@@ -1,5 +0,0 @@
-gcc (GCC) 5.4.0
-Copyright (C) 2015 Free Software Foundation, Inc.
-This is free software; see the source for copying conditions. There is NO
-warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-
diff --git a/smoke_test/output_dir/gcc/6.1.0 b/smoke_test/output_dir/gcc/6.1.0
deleted file mode 100644
index a8512b91d579516dd23eef684bfac7f77bc4fa5a..0000000000000000000000000000000000000000
--- a/smoke_test/output_dir/gcc/6.1.0
+++ /dev/null
@@ -1,5 +0,0 @@
-gcc (GCC) 6.1.0
-Copyright (C) 2016 Free Software Foundation, Inc.
-This is free software; see the source for copying conditions. There is NO
-warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-
diff --git a/smoke_test/output_dir/gcc/8.1.0 b/smoke_test/output_dir/gcc/8.1.0
deleted file mode 100644
index e36598d113122ff39334a811670ae72df25e4834..0000000000000000000000000000000000000000
--- a/smoke_test/output_dir/gcc/8.1.0
+++ /dev/null
@@ -1,5 +0,0 @@
-gcc (GCC) 8.1.0
-Copyright (C) 2018 Free Software Foundation, Inc.
-This is free software; see the source for copying conditions. There is NO
-warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-
diff --git a/smoke_test/output_dir/geos/3.6 b/smoke_test/output_dir/geos/3.6
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/smoke_test/output_dir/gmp/6.1.2 b/smoke_test/output_dir/gmp/6.1.2
deleted file mode 100644
index 8acc639ace65bd0fa4eff5bfc3e6ea176e7afc3b..0000000000000000000000000000000000000000
--- a/smoke_test/output_dir/gmp/6.1.2
+++ /dev/null
@@ -1 +0,0 @@
-find: ‘/usr/local/gmp/6.1.2/bin’: No such file or directory
diff --git a/smoke_test/output_dir/hdf5/1.10.0-patch1 b/smoke_test/output_dir/hdf5/1.10.0-patch1
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/smoke_test/output_dir/htslib/1.9-gcc5 b/smoke_test/output_dir/htslib/1.9-gcc5
deleted file mode 100644
index c77ee76259cefb3b9b92746e9e1e37c0d5e16675..0000000000000000000000000000000000000000
--- a/smoke_test/output_dir/htslib/1.9-gcc5
+++ /dev/null
@@ -1,6 +0,0 @@
-htsfile (htslib) 1.9-20-ge1650a9
-Copyright (C) 2018 Genome Research Ltd.
-tabix (htslib) 1.9-20-ge1650a9
-Copyright (C) 2018 Genome Research Ltd.
-bgzip (htslib) 1.9-20-ge1650a9
-Copyright (C) 2018 Genome Research Ltd.
diff --git a/smoke_test/output_dir/java/1.8.0_77 b/smoke_test/output_dir/java/1.8.0_77
deleted file mode 100644
index b35c6a061e64f1772cabd5bd2c0bb3bd890ad6b8..0000000000000000000000000000000000000000
--- a/smoke_test/output_dir/java/1.8.0_77
+++ /dev/null
@@ -1,3 +0,0 @@
-Unrecognized option: --version
-Error: Could not create the Java Virtual Machine.
-Error: A fatal exception has occurred. Program will exit.
diff --git a/smoke_test/output_dir/lapack/3.6.1-gcc4 b/smoke_test/output_dir/lapack/3.6.1-gcc4
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/smoke_test/output_dir/lapack/3.6.1-gcc5 b/smoke_test/output_dir/lapack/3.6.1-gcc5
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/smoke_test/output_dir/libjpeg-turbo/1.4.2 b/smoke_test/output_dir/libjpeg-turbo/1.4.2
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/smoke_test/output_dir/libtiff/3.9.7 b/smoke_test/output_dir/libtiff/3.9.7
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/smoke_test/output_dir/mpfr/3.1.5 b/smoke_test/output_dir/mpfr/3.1.5
deleted file mode 100644
index a599d561d08277af1e3dd9f961ecc25edc49bd7a..0000000000000000000000000000000000000000
--- a/smoke_test/output_dir/mpfr/3.1.5
+++ /dev/null
@@ -1 +0,0 @@
-find: ‘/usr/local/mpfr/3.1.5/bin’: No such file or directory
diff --git a/smoke_test/output_dir/openblas/0.2.20 b/smoke_test/output_dir/openblas/0.2.20
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/smoke_test/output_dir/openmpi/1.10.7-mlx b/smoke_test/output_dir/openmpi/1.10.7-mlx
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/smoke_test/output_dir/picard/2.9.2 b/smoke_test/output_dir/picard/2.9.2
deleted file mode 100644
index 0ee2c2a976c6f1a536fb1fc467e555718c1b8240..0000000000000000000000000000000000000000
--- a/smoke_test/output_dir/picard/2.9.2
+++ /dev/null
@@ -1,127 +0,0 @@
-[1m[31mUSAGE: PicardCommandLine [32m<program name>[1m[31m [-h]
-
-[0m[1m[31mAvailable Programs:
-[0m[37m--------------------------------------------------------------------------------------
-[0m[31mAlpha Tools: Tools that are currently UNSUPPORTED until further testing and maturation.[0m
-[32m CollectIndependentReplicateMetrics [36mEstimates the rate of independent replication of reads within a bam.[0m
-[32m CollectWgsMetricsWithNonZeroCoverage [36mCollect metrics about coverage and performance of whole genome sequencing (WGS) experiments. [0m
-[32m UmiAwareMarkDuplicatesWithMateCigar [36mIdentifies duplicate reads using information from read positions and UMIs. [0m
-
-[37m--------------------------------------------------------------------------------------
-[0m[31mFasta: Tools for manipulating FASTA, or related data.[0m
-[32m CreateSequenceDictionary [36mCreates a sequence dictionary for a reference sequence. [0m
-[32m ExtractSequences [36mSubsets intervals from a reference sequence to a new FASTA file.[0m
-[32m NonNFastaSize [36mCounts the number of non-N bases in a fasta file.[0m
-[32m NormalizeFasta [36mNormalizes lines of sequence in a FASTA file to be of the same length.[0m
-
-[37m--------------------------------------------------------------------------------------
-[0m[31mFingerprinting Tools: Tools for manipulating fingerprints, or related data.[0m
-[32m CheckFingerprint [36mComputes a fingerprint from the supplied input (SAM/BAM or VCF) file and compares it to the provided genotypes[0m
-[32m CrosscheckReadGroupFingerprints [36mChecks if all read groups appear to come from the same individual[0m
-
-[37m--------------------------------------------------------------------------------------
-[0m[31mIllumina Tools: Tools for manipulating data specific to Illumina sequencers.[0m
-[32m CheckIlluminaDirectory [36mAsserts the validity for specified Illumina basecalling data. [0m
-[32m CollectIlluminaBasecallingMetrics [36mCollects Illumina Basecalling metrics for a sequencing run. [0m
-[32m CollectIlluminaLaneMetrics [36mCollects Illumina lane metrics for the given BaseCalling analysis directory. [0m
-[32m ExtractIlluminaBarcodes [36mTool determines the barcode for each read in an Illumina lane. [0m
-[32m IlluminaBasecallsToFastq [36mGenerate FASTQ file(s) from Illumina basecall read data. [0m
-[32m IlluminaBasecallsToSam [36mTransforms raw Illumina sequencing data into an unmapped SAM or BAM file.[0m
-[32m MarkIlluminaAdapters [36mReads a SAM or BAM file and rewrites it with new adapter-trimming tags. [0m
-
-[37m--------------------------------------------------------------------------------------
-[0m[31mInterval Tools: Tools for manipulating Picard interval lists.[0m
-[32m BedToIntervalList [36mConverts a BED file to a Picard Interval List. [0m
-[32m IntervalListToBed [36mConverts an Picard IntervalList file to a BED file.[0m
-[32m IntervalListTools [36mManipulates interval lists. [0m
-[32m LiftOverIntervalList [36mLifts over an interval list from one reference build to another. [0m
-[32m ScatterIntervalsByNs [36mWrites an interval list based on splitting a reference by Ns. [0m
-
-[37m--------------------------------------------------------------------------------------
-[0m[31mMetrics: Tools for reporting metrics on various data types.[0m
-[32m CollectAlignmentSummaryMetrics [36m<b>Produces a summary of alignment metrics from a SAM or BAM file.</b> [0m
-[32m CollectBaseDistributionByCycle [36mChart the nucleotide distribution per cycle in a SAM or BAM file[0m
-[32m CollectGcBiasMetrics [36mCollect metrics regarding GC bias. [0m
-[32m CollectHiSeqXPfFailMetrics [36mClassify PF-Failing reads in a HiSeqX Illumina Basecalling directory into various categories.[0m
-[32m CollectHsMetrics [36mCollects hybrid-selection (HS) metrics for a SAM or BAM file. [0m
-[32m CollectInsertSizeMetrics [36mCollect metrics about the insert size distribution of a paired-end library.[0m
-[32m CollectJumpingLibraryMetrics [36mCollect jumping library metrics. [0m
-[32m CollectMultipleMetrics [36mCollect multiple classes of metrics. [0m
-[32m CollectOxoGMetrics [36mCollect metrics to assess oxidative artifacts.[0m
-[32m CollectQualityYieldMetrics [36mCollect metrics about reads that pass quality thresholds and Illumina-specific filters. [0m
-[32m CollectRawWgsMetrics [36mCollect whole genome sequencing-related metrics. [0m
-[32m CollectRnaSeqMetrics [36mProduces RNA alignment metrics for a SAM or BAM file. [0m
-[32m CollectRrbsMetrics [36m<b>Collects metrics from reduced representation bisulfite sequencing (Rrbs) data.</b> [0m
-[32m CollectSequencingArtifactMetrics [36mCollect metrics to quantify single-base sequencing artifacts. [0m
-[32m CollectTargetedPcrMetrics [36mCalculate PCR-related metrics from targeted sequencing data. [0m
-[32m CollectVariantCallingMetrics [36mCollects per-sample and aggregate (spanning all samples) metrics from the provided VCF file[0m
-[32m CollectWgsMetrics [36mCollect metrics about coverage and performance of whole genome sequencing (WGS) experiments.[0m
-[32m CompareMetrics [36mCompare two metrics files.[0m
-[32m ConvertSequencingArtifactToOxoG [36mExtract OxoG metrics from generalized artifacts metrics. [0m
-[32m EstimateLibraryComplexity [36mEstimates the numbers of unique molecules in a sequencing library. [0m
-[32m MeanQualityByCycle [36mCollect mean quality by cycle.[0m
-[32m QualityScoreDistribution [36mChart the distribution of quality scores. [0m
-
-[37m--------------------------------------------------------------------------------------
-[0m[31mMiscellaneous Tools: A set of miscellaneous tools. [0m
-[32m BaitDesigner [36m<b>Designs oligonucleotide baits for hybrid selection reactions.</b> [0m
-[32m FifoBuffer [36mFIFO buffer used to buffer input and output streams with a customizable buffer size [0m
-
-[37m--------------------------------------------------------------------------------------
-[0m[31mSAM/BAM: Tools for manipulating SAM, BAM, or related data.[0m
-[32m AddCommentsToBam [36mAdds comments to the header of a BAM file.[0m
-[32m AddOrReplaceReadGroups [36mReplace read groups in a BAM file.[0m
-[32m BamIndexStats [36mGenerate index statistics from a BAM file[0m
-[32m BamToBfq [36mCreate BFQ files from a BAM file for use by the maq aligner. [0m
-[32m BuildBamIndex [36mGenerates a BAM index ".bai" file. [0m
-[32m CalculateReadGroupChecksum [36mCreates a hash code based on the read groups (RG). [0m
-[32m CheckTerminatorBlock [36mAsserts the provided gzip file's (e.g., BAM) last block is well-formed; RC 100 otherwise[0m
-[32m CleanSam [36mCleans the provided SAM/BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads[0m
-[32m CompareSAMs [36mCompare two input ".sam" or ".bam" files. [0m
-[32m DownsampleSam [36mDownsample a SAM or BAM file. [0m
-[32m FastqToSam [36mConverts a FASTQ file to an unaligned BAM or SAM file. [0m
-[32m FilterSamReads [36mSubset read data from a SAM or BAM file[0m
-[32m FixMateInformation [36mVerify mate-pair information between mates and fix if needed.[0m
-[32m GatherBamFiles [36mConcatenate one or more BAM files as efficiently as possible[0m
-[32m MarkDuplicates [36mIdentifies duplicate reads. [0m
-[32m MarkDuplicatesWithMateCigar [36mIdentifies duplicate reads, accounting for mate CIGAR. [0m
-[32m MergeBamAlignment [36mMerge alignment data from a SAM or BAM with data in an unmapped BAM file. [0m
-[32m MergeSamFiles [36mMerges multiple SAM and/or BAM files into a single file. [0m
-[32m PositionBasedDownsampleSam [36mDownsample a SAM or BAM file to retain a subset of the reads based on the reads location in each tile in the flowcell.[0m
-[32m ReorderSam [36mReorders reads in a SAM or BAM file to match ordering in reference[0m
-[32m ReplaceSamHeader [36mReplaces the SAMFileHeader in a SAM or BAM file. [0m
-[32m RevertOriginalBaseQualitiesAndAddMateCigar [36mReverts the original base qualities and adds the mate cigar tag to read-group BAMs[0m
-[32m RevertSam [36mReverts SAM or BAM files to a previous state. [0m
-[32m SamFormatConverter [36mConvert a BAM file to a SAM file, or a SAM to a BAM[0m
-[32m SamToFastq [36mConverts a SAM or BAM file to FASTQ. [0m
-[32m SetNmAndUqTags [36mDEPRECATED: Use SetNmMdAndUqTags instead.[0m
-[32m SetNmMdAndUqTags [36mFixes the NM, MD, and UQ tags in a SAM file. [0m
-[32m SortSam [36mSorts a SAM or BAM file. [0m
-[32m SplitSamByLibrary [36mSplits a SAM or BAM file into individual files by library[0m
-[32m ValidateSamFile [36mValidates a SAM or BAM file. [0m
-[32m ViewSam [36mPrints a SAM or BAM file to the screen[0m
-
-[37m--------------------------------------------------------------------------------------
-[0m[31mUnit Testing: Unit testing [0m
-[32m SimpleMarkDuplicatesWithMateCigar [36mExamines aligned records in the supplied SAM or BAM file to locate duplicate molecules.[0m
-
-[37m--------------------------------------------------------------------------------------
-[0m[31mVCF/BCF: Tools for manipulating VCF, BCF, or related data.[0m
-[32m FilterVcf [36mHard filters a VCF.[0m
-[32m FindMendelianViolations [36mFinds mendelian violations of all types within a VCF[0m
-[32m FixVcfHeader [36mReplaces or fixes a VCF header.[0m
-[32m GatherVcfs [36mGathers multiple VCF files from a scatter operation into a single VCF file[0m
-[32m GenotypeConcordance [36mEvaluate genotype concordance between callsets.[0m
-[32m LiftoverVcf [36mLifts over a VCF file from one reference build to another. [0m
-[32m MakeSitesOnlyVcf [36mCreates a VCF bereft of genotype information from an input VCF or BCF[0m
-[32m MergeVcfs [36mMerges multiple VCF or BCF files into one VCF file or BCF[0m
-[32m RenameSampleInVcf [36mRenames a sample within a VCF or BCF. [0m
-[32m SortVcf [36mSorts one or more VCF files. [0m
-[32m SplitVcfs [36mSplits SNPs and INDELs into separate files. [0m
-[32m UpdateVcfSequenceDictionary [36mTakes a VCF and a second file that contains a sequence dictionary and updates the VCF with the new sequence dictionary.[0m
-[32m VcfFormatConverter [36mConverts VCF to BCF or BCF to VCF. [0m
-[32m VcfToIntervalList [36mConverts a VCF or BCF file to a Picard Interval List.[0m
-
-[37m--------------------------------------------------------------------------------------
-
-[0m'--version' is not a valid command. See PicardCommandLine -h for more information.
diff --git a/smoke_test/output_dir/python/3.7.3-system b/smoke_test/output_dir/python/3.7.3-system
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/smoke_test/output_dir/report.txt b/smoke_test/output_dir/report.txt
deleted file mode 100644
index 8bebed2a393cc5e44aaa6b0e86c50c0f3a3ae93c..0000000000000000000000000000000000000000
--- a/smoke_test/output_dir/report.txt
+++ /dev/null
@@ -1,12 +0,0 @@
-
-virtualgl 2.5.0 return non-zero exitcode 1 for testcase /home/luhanc/HPCasCode/smoke_test/tests/virtualgl/bashcmd
-tigervnc 1.8.0 return non-zero exitcode 1 for testcase /home/luhanc/HPCasCode/smoke_test/tests/tigervnc/bashcmd
-java 1.8.0_77 return non-zero exitcode 1 for testcase /home/luhanc/HPCasCode/smoke_test/tests/java/bintest
-cuda 7.5 return non-zero exitcode 1 for testcase /home/luhanc/HPCasCode/smoke_test/tests/cuda/bashcmd
-mpfr 3.1.5 return non-zero exitcode 1 for testcase /home/luhanc/HPCasCode/smoke_test/tests/mpfr/bashcmd
-picard 2.9.2 return non-zero exitcode 1 for testcase /home/luhanc/HPCasCode/smoke_test/tests/picard/bintest
-Summary
-Failed: 0
-Success: 40
-minor error: 6, this is often due to executable not having --version option
-Num applications that has no test case: 0
diff --git a/smoke_test/output_dir/samtools/1.9-gcc5 b/smoke_test/output_dir/samtools/1.9-gcc5
deleted file mode 100644
index af4914670ddc2b0d65a26a706895d748f99eff06..0000000000000000000000000000000000000000
--- a/smoke_test/output_dir/samtools/1.9-gcc5
+++ /dev/null
@@ -1,3 +0,0 @@
-samtools 1.9-24-gff68e70
-Using htslib 1.9-20-ge1650a9
-Copyright (C) 2018 Genome Research Ltd.
diff --git a/smoke_test/output_dir/singularity/3.2.1 b/smoke_test/output_dir/singularity/3.2.1
deleted file mode 100644
index 5d79d2f4a92b85b6ef8b01a83fab0197e660cea1..0000000000000000000000000000000000000000
--- a/smoke_test/output_dir/singularity/3.2.1
+++ /dev/null
@@ -1 +0,0 @@
-singularity version 3.2.1
diff --git a/smoke_test/output_dir/tigervnc/1.8.0 b/smoke_test/output_dir/tigervnc/1.8.0
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/smoke_test/output_dir/virtualgl/2.5.0 b/smoke_test/output_dir/virtualgl/2.5.0
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000