Add singularity cache to every singularity run command in ci

5883960d · Gervaise Henry · 3cf19393 · 5883960d
Commit 5883960d authored 4 years ago by Gervaise Henry
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -2,7 +2,6 @@ before_script:
  - module load python/3.6.4-anaconda
  - pip install --user attrs==20.3.0 pytest==6.2.2 pytest-pythonpath==0.7.3 pytest-cov==2.11.1
  - module load singularity/3.5.3
-  - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/
  - module load nextflow/20.01.0
  - ln -sfn /project/BICF/BICF_Core/shared/gudmap/test_data/* ./test_data/
  - mkdir -p ~/.deriva
@@ -33,8 +32,8 @@ build_badges:
    - chmod +x ./workflow/scripts/get_updated_badge_info.sh
  script:
    - echo "Building badges"
-    - singularity run 'docker://gudmaprbk/gudmap-rbk_base:1.0.0' bash ./workflow/scripts/get_updated_badge_info.sh
-    - singularity run 'docker://gudmaprbk/gudmap-rbk_base:1.0.0' bash ./workflow/scripts/get_updated_rep_count.sh
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/gudmap-rbk_base:1.0.0' bash ./workflow/scripts/get_updated_badge_info.sh
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/gudmap-rbk_base:1.0.0' bash ./workflow/scripts/get_updated_rep_count.sh
  artifacts:
    paths:
      - badges/
@@ -64,8 +63,8 @@ getBag:
    - schedules
  script:
    - ln -sfn `readlink -e ./test_data/auth/credential.json` ~/.deriva/credential.json
-    - singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-download-cli --version > version_deriva.txt
-    - singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-download-cli staging.gudmap.org --catalog 2 ./workflow/conf/Replicate_For_Input_Bag.json . rid=Q-Y5F6
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-download-cli --version > version_deriva.txt
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-download-cli staging.gudmap.org --catalog 2 ./workflow/conf/Replicate_For_Input_Bag.json . rid=Q-Y5F6
    - pytest -m getBag
  artifacts:
    name: "$CI_JOB_NAME"
@@ -83,10 +82,10 @@ getData:
    - merge_requests
    - schedules
  script:
-    - singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' bdbag --version > version_bdbag.txt
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' bdbag --version > version_bdbag.txt
    - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
    - unzip ./test_data/bag/Q-Y5F6_inputBag_xxxxtest.zip
-    - singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' bash ./workflow/scripts/bdbag_fetch.sh Q-Y5F6_inputBag Q-Y5F6
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' bash ./workflow/scripts/bdbag_fetch.sh Q-Y5F6_inputBag Q-Y5F6
    - pytest -m getData
  artifacts:
    name: "$CI_JOB_NAME"
@@ -104,17 +103,17 @@ parseMetadata:
    - merge_requests
    - schedules
  script:
-    - singularity run 'docker://gudmaprbk/python3:1.0.0' python3 --version > version_python.txt
-    - rep=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p repRID)
-    - exp=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p expRID)
-    - study=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p studyRID)
-    - endsRaw=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p endsMeta)
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/python3:1.0.0' python3 --version > version_python.txt
+    - rep=$(export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p repRID)
+    - exp=$(export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p expRID)
+    - study=$(export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p studyRID)
+    - endsRaw=$(export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p endsMeta)
    - endsMeta="uk"
    - endsManual="se"
-    - stranded=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p stranded)
-    - spike=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p spike)
-    - species=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p species)
-    - readLength=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p readLength)
+    - stranded=$(export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p stranded)
+    - spike=$(export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p spike)
+    - species=$(export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p species)
+    - readLength=$(export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p readLength)
    - echo -e "${endsMeta},${endsRaw},${endsManual},${stranded},${spike},${species},${readLength},${exp},${study},${rep}" > design.csv
    - pytest -m parseMetadata
  artifacts:
@@ -133,8 +132,8 @@ fastqc:
    - merge_requests
    - schedules
  script:
-    - singularity run 'docker://gudmaprbk/fastqc0.11.9:1.0.0' fastqc --version > version_fastqc.txt
-    - singularity run 'docker://gudmaprbk/fastqc0.11.9:1.0.0' fastqc ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz -o .
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/fastqc0.11.9:1.0.0' fastqc --version > version_fastqc.txt
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/fastqc0.11.9:1.0.0' fastqc ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz -o .
    - pytest -m fastqc
  artifacts:
    name: "$CI_JOB_NAME"
@@ -154,8 +153,8 @@ seqwho:
  script:
    - wget -O SeqWho.ix https://cloud.biohpc.swmed.edu/index.php/s/eeNWqZz8jqN5zWY/download
    - mkdir -p SeqWho_call_plots/test_data/fastq/small/
-    - singularity run 'docker://gudmaprbk/seqwho0.0.1:1.0.0' seqwho.py -h | grep -o Version.* > version_seqwho.txt
-    - singularity run 'docker://gudmaprbk/seqwho0.0.1:1.0.0' seqwho.py -f test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz -x SeqWho.ix
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/seqwho0.0.1:1.0.0' seqwho.py -h | grep -o Version.* > version_seqwho.txt
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/seqwho0.0.1:1.0.0' seqwho.py -f test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz -x SeqWho.ix
    - pytest -m seqwho
  artifacts:
    name: "$CI_JOB_NAME"
@@ -173,9 +172,9 @@ trimData:
    - merge_requests
    - schedules
  script:
-    - singularity run 'docker://gudmaprbk/trimgalore0.6.5:1.0.0' trim_galore --version > version_trimgalore.txt
-    - singularity run 'docker://gudmaprbk/trimgalore0.6.5:1.0.0' trim_galore --gzip -q 25 --length 35 --basename Q-Y5F6_1M.se ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz
-    - singularity run 'docker://gudmaprbk/trimgalore0.6.5:1.0.0' trim_galore --gzip -q 25 --length 35 --paired --basename Q-Y5F6_1M.pe ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz ./test_data/fastq/small/Q-Y5F6_1M.R2.fastq.gz
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/trimgalore0.6.5:1.0.0' trim_galore --version > version_trimgalore.txt
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/trimgalore0.6.5:1.0.0' trim_galore --gzip -q 25 --length 35 --basename Q-Y5F6_1M.se ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/trimgalore0.6.5:1.0.0' trim_galore --gzip -q 25 --length 35 --paired --basename Q-Y5F6_1M.pe ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz ./test_data/fastq/small/Q-Y5F6_1M.R2.fastq.gz
    - readLengthSE=$(zcat *_trimmed.fq.gz | awk '{if(NR%4==2) print length($1)}' | sort -n | awk '{a[NR]=$0}END{print(NR%2==1)?a[int(NR/2)+1]:(a[NR/2]+a[NR/2+1])/2}')
    - readLengthPE=$(zcat *_1.fq.gz | awk '{if(NR%4==2) print length($1)}' | sort -n | awk '{a[NR]=$0}END{print(NR%2==1)?a[int(NR/2)+1]:(a[NR/2]+a[NR/2+1])/2}')
    - pytest -m trimData
@@ -195,8 +194,8 @@ downsampleData:
    - merge_requests
    - schedules
  script:
-    - singularity run 'docker://gudmaprbk/seqtk1.3:1.0.0' seqtk 2>&1 | grep -o Version.* > version_seqtk.txt&
-    - singularity run 'docker://gudmaprbk/seqtk1.3:1.0.0' seqtk sample -s100 ./test_data/fastq/small/Q-Y5F6_1M.se_trimmed.fq.gz 1000 1> sampled.1.fq
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/seqtk1.3:1.0.0' seqtk 2>&1 | grep -o Version.* > version_seqtk.txt&
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/seqtk1.3:1.0.0' seqtk sample -s100 ./test_data/fastq/small/Q-Y5F6_1M.se_trimmed.fq.gz 1000 1> sampled.1.fq
    - pytest -m downsampleData
  artifacts:
    name: "$CI_JOB_NAME"
@@ -214,13 +213,13 @@ inferMetadata:
    - merge_requests
    - schedules
  script:
-    - singularity run 'docker://gudmaprbk/rseqc4.0.0:1.0.0' infer_experiment.py --version > version_rseqc.txt
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/rseqc4.0.0:1.0.0' infer_experiment.py --version > version_rseqc.txt
    - >
      align=$(echo $(grep "Overall alignment rate" ./test_data/meta/Q-Y5F6_1M.se.alignSummary.txt | cut -f2 -d ':' | cut -f2 -d ' ' | tr -d '%')) &&
      if [[ ${align} == "" ]]; then exit 1; fi
    - >
-      singularity run 'docker://gudmaprbk/rseqc4.0.0:1.0.0' infer_experiment.py -r "/project/BICF/BICF_Core/shared/gudmap/references/new/GRCh38.p13.v36/data/annotation/genome.bed" -i "./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam" 1>> Q-Y5F6_1M.se.inferMetadata.log &&
-      ended=`singularity run 'gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/infer_meta.sh endness Q-Y5F6_1M.se.inferMetadata.log` &&
+      export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/rseqc4.0.0:1.0.0' infer_experiment.py -r "/project/BICF/BICF_Core/shared/gudmap/references/new/GRCh38.p13.v36/data/annotation/genome.bed" -i "./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam" 1>> Q-Y5F6_1M.se.inferMetadata.log &&
+      ended=`export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/infer_meta.sh endness Q-Y5F6_1M.se.inferMetadata.log` &&
      if [[ ${ended} == "" ]]; then exit 1; fi
    - pytest -m inferMetadata
  artifacts:
@@ -239,16 +238,16 @@ alignData:
    - merge_requests
    - schedules
  script:
-    - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' hisat2 --version > version_hisat2.txt
-    - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools --version > version_samtools.txt
-    - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' hisat2 -p 20 --add-chrname --un-gz Q-Y5F6_1M.se.unal.gz -S Q-Y5F6_1M.se.sam -x /project/BICF/BICF_Core/shared/gudmap/references/new/GRCh38.p13.v36/data/hisat2/genome --rna-strandness F -U ./test_data/fastq/small/Q-Y5F6_1M.se_trimmed.fq.gz --summary-file Q-Y5F6_1M.se.alignSummary.txt --new-summary
-    - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools view -1 -@ 20 -F 4 -F 8 -F 256 -o Q-Y5F6_1M.se.bam Q-Y5F6_1M.se.sam
-    - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools sort -@ 20 -O BAM -o Q-Y5F6_1M.se.sorted.bam Q-Y5F6_1M.se.bam
-    - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools index -@ 20 -b Q-Y5F6_1M.se.sorted.bam Q-Y5F6_1M.se.sorted.bam.bai
-    - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' hisat2 -p 20 --add-chrname --un-gz Q-Y5F6_1M.pe.unal.gz -S Q-Y5F6_1M.pe.sam -x /project/BICF/BICF_Core/shared/gudmap/references/new/GRCh38.p13.v36/data/hisat2/genome --rna-strandness FR --no-mixed --no-discordant -1 ./test_data/fastq/small/Q-Y5F6_1M.pe_val_1.fq.gz -2 ./test_data/fastq/small/Q-Y5F6_1M.pe_val_2.fq.gz --summary-file Q-Y5F6_1M.pe.alignSummary.txt --new-summary
-    - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools view -1 -@ 20 -F 4 -F 8 -F 256 -o Q-Y5F6_1M.pe.bam Q-Y5F6_1M.pe.sam
-    - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools sort -@ 20 -O BAM -o Q-Y5F6_1M.pe.sorted.bam Q-Y5F6_1M.pe.bam
-    - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools index -@ 20 -b Q-Y5F6_1M.pe.sorted.bam Q-Y5F6_1M.pe.sorted.bam.bai
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' hisat2 --version > version_hisat2.txt
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools --version > version_samtools.txt
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' hisat2 -p 20 --add-chrname --un-gz Q-Y5F6_1M.se.unal.gz -S Q-Y5F6_1M.se.sam -x /project/BICF/BICF_Core/shared/gudmap/references/new/GRCh38.p13.v36/data/hisat2/genome --rna-strandness F -U ./test_data/fastq/small/Q-Y5F6_1M.se_trimmed.fq.gz --summary-file Q-Y5F6_1M.se.alignSummary.txt --new-summary
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools view -1 -@ 20 -F 4 -F 8 -F 256 -o Q-Y5F6_1M.se.bam Q-Y5F6_1M.se.sam
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools sort -@ 20 -O BAM -o Q-Y5F6_1M.se.sorted.bam Q-Y5F6_1M.se.bam
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools index -@ 20 -b Q-Y5F6_1M.se.sorted.bam Q-Y5F6_1M.se.sorted.bam.bai
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' hisat2 -p 20 --add-chrname --un-gz Q-Y5F6_1M.pe.unal.gz -S Q-Y5F6_1M.pe.sam -x /project/BICF/BICF_Core/shared/gudmap/references/new/GRCh38.p13.v36/data/hisat2/genome --rna-strandness FR --no-mixed --no-discordant -1 ./test_data/fastq/small/Q-Y5F6_1M.pe_val_1.fq.gz -2 ./test_data/fastq/small/Q-Y5F6_1M.pe_val_2.fq.gz --summary-file Q-Y5F6_1M.pe.alignSummary.txt --new-summary
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools view -1 -@ 20 -F 4 -F 8 -F 256 -o Q-Y5F6_1M.pe.bam Q-Y5F6_1M.pe.sam
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools sort -@ 20 -O BAM -o Q-Y5F6_1M.pe.sorted.bam Q-Y5F6_1M.pe.bam
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools index -@ 20 -b Q-Y5F6_1M.pe.sorted.bam Q-Y5F6_1M.pe.sorted.bam.bai
    - pytest -m alignData
  artifacts:
    name: "$CI_JOB_NAME"
@@ -267,15 +266,15 @@ dedupData:
    - merge_requests
    - schedules
  script:
-    - singularity run 'docker://gudmaprbk/picard2.23.9:1.0.0' samtools --version > version_samtools.txt
-    - singularity run 'docker://gudmaprbk/picard2.23.9:1.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates --version 2> version_markdups.txt&
-    - singularity run 'docker://gudmaprbk/picard2.23.9:1.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates I=./test_data/bam/small/Q-Y5F6_1M.se.sorted.bam O=Q-Y5F6_1M.se.deduped.bam M=Q-Y5F6_1M.se.deduped.Metrics.txt REMOVE_DUPLICATES=true
-    - singularity run 'docker://gudmaprbk/picard2.23.9:1.0.0' samtools sort -@ 20 -O BAM -o Q-Y5F6_1M.se.sorted.deduped.bam ./test_data/bam/small/Q-Y5F6_1M.se.deduped.bam
-    - singularity run 'docker://gudmaprbk/picard2.23.9:1.0.0' samtools index -@ 20 -b ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam Q-Y5F6_1M.se.sorted.deduped.bam.bai
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/picard2.23.9:1.0.0' samtools --version > version_samtools.txt
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/picard2.23.9:1.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates --version 2> version_markdups.txt&
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/picard2.23.9:1.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates I=./test_data/bam/small/Q-Y5F6_1M.se.sorted.bam O=Q-Y5F6_1M.se.deduped.bam M=Q-Y5F6_1M.se.deduped.Metrics.txt REMOVE_DUPLICATES=true
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/picard2.23.9:1.0.0' samtools sort -@ 20 -O BAM -o Q-Y5F6_1M.se.sorted.deduped.bam ./test_data/bam/small/Q-Y5F6_1M.se.deduped.bam
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/picard2.23.9:1.0.0' samtools index -@ 20 -b ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam Q-Y5F6_1M.se.sorted.deduped.bam.bai
    - >
      for i in {"chr8","chr4","chrY"}; do
        echo "samtools view -b Q-Y5F6_1M.se.sorted.deduped.bam ${i} > Q-Y5F6_1M.se.sorted.deduped.${i}.bam; samtools index -@ 20 -b Q-Y5F6_1M.se.sorted.deduped.${i}.bam Q-Y5F6_1M.se.sorted.deduped.${i}.bam.bai;";
-      done | singularity run 'docker://gudmaprbk/picard2.23.9:1.0.0' parallel -j 20 -k
+      done | export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/picard2.23.9:1.0.0' parallel -j 20 -k
    - pytest -m dedupData
  artifacts:
    name: "$CI_JOB_NAME"
@@ -296,12 +295,12 @@ countData:
  script:
    - ln -s /project/BICF/BICF_Core/shared/gudmap/references/new/GRCh38.p13.v36/data/metadata/geneID.tsv
    - ln -s /project/BICF/BICF_Core/shared/gudmap/references/new/GRCh38.p13.v36/data/metadata/Entrez.tsv
-    - singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' featureCounts -T 20 -a /project/BICF/BICF_Core/shared/gudmap/references/new/GRCh38.p13.v36/data/annotation/genome.gtf -G /project/BICF/BICF_Core/shared/gudmap/references/new/GRCh38.p13.v36/data/sequence/genome.fna -g 'gene_name' --extraAttributes 'gene_id' -o Q-Y5F6_1M.se_countData -s 1 -R SAM --primary --ignoreDup ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam
-    - singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' Rscript ./workflow/scripts/calculateTPM.R --count ./test_data/counts/small/Q-Y5F6_1M.se_countData
-    - singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' Rscript ./workflow/scripts/convertGeneSymbols.R --repRID Q-Y5F6_1M.se
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' featureCounts -T 20 -a /project/BICF/BICF_Core/shared/gudmap/references/new/GRCh38.p13.v36/data/annotation/genome.gtf -G /project/BICF/BICF_Core/shared/gudmap/references/new/GRCh38.p13.v36/data/sequence/genome.fna -g 'gene_name' --extraAttributes 'gene_id' -o Q-Y5F6_1M.se_countData -s 1 -R SAM --primary --ignoreDup ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' Rscript ./workflow/scripts/calculateTPM.R --count ./test_data/counts/small/Q-Y5F6_1M.se_countData
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' Rscript ./workflow/scripts/convertGeneSymbols.R --repRID Q-Y5F6_1M.se
    - assignedReads=$(grep -m 1 'Assigned' *.summary | grep -oe '\([0-9.]*\)')
-    - singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' featureCounts -v &> version_featurecounts.txt
-    - singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' R --version > version_r.txt
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' featureCounts -v &> version_featurecounts.txt
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' R --version > version_r.txt
    - pytest -m makeFeatureCounts
  artifacts:
    name: "$CI_JOB_NAME"
@@ -320,8 +319,8 @@ makeBigWig:
    - merge_requests
    - schedules
  script:
-    - singularity run 'docker://gudmaprbk/deeptools3.5.0:1.0.0' deeptools --version > version_deeptools.txt
-    - singularity run 'docker://gudmaprbk/deeptools3.5.0:1.0.0' bamCoverage -p 20 -b ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam -o Q-Y5F6_1M.se.bw
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/deeptools3.5.0:1.0.0' deeptools --version > version_deeptools.txt
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/deeptools3.5.0:1.0.0' bamCoverage -p 20 -b ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam -o Q-Y5F6_1M.se.bw
    - pytest -m makeBigWig
  artifacts:
    name: "$CI_JOB_NAME"
@@ -342,7 +341,7 @@ dataQC:
    - >
      for i in {"chr8","chr4","chrY"}; do
        echo "tin.py -i ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.${i}.bam -r /project/BICF/BICF_Core/shared/gudmap/references/new/GRCh38.p13.v36/data/annotation/genome.bed; cat Q-Y5F6_1M.se.sorted.deduped.${i}.tin.xls | tr -s \"\\w\" \"\\t\" | grep -P \"\\t${i}\\t\";"
-      done | singularity run 'docker://gudmaprbk/rseqc4.0.0:1.0.0' parallel -j 20 -k >> Q-Y5F6_1M.se.sorted.deduped.tin.xls
+      done | export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/rseqc4.0.0:1.0.0' parallel -j 20 -k >> Q-Y5F6_1M.se.sorted.deduped.tin.xls
    - pytest -m dataQC

 uploadInputBag:
@@ -359,12 +358,12 @@ uploadInputBag:
    - >
      md5=$(md5sum ./test.txt | awk '{ print $1 }') &&
      size=$(wc -c < ./test.txt) &&
-      exist=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Input_Bag/File_MD5=${md5}) &&
+      exist=$(export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Input_Bag/File_MD5=${md5}) &&
      if [ "${exist}" == "[]" ]; then
        cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
        cookie=${cookie:11:-1} &&
-        loc=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-hatrac-cli --host staging.gudmap.org put ./test.txt /hatrac/resources/rnaseq/pipeline/input_bag/TEST/test.txt --parents) &&
-        rid=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' python3 ./workflow/scripts/upload_input_bag.py -f test.txt -l ${loc} -s ${md5} -b ${size} -n 'This is a test input bag' -o staging.gudmap.org -c ${cookie}) &&
+        loc=$(export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-hatrac-cli --host staging.gudmap.org put ./test.txt /hatrac/resources/rnaseq/pipeline/input_bag/TEST/test.txt --parents) &&
+        rid=$(export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' python3 ./workflow/scripts/upload_input_bag.py -f test.txt -l ${loc} -s ${md5} -b ${size} -n 'This is a test input bag' -o staging.gudmap.org -c ${cookie}) &&
        echo ${rid} test input bag created
      else
        rid=$(echo ${exist} | grep -o '\"RID\":\".*\",\"RCT') &&
@@ -383,16 +382,16 @@ uploadExecutionRun:
  script:
    - ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json
    - >
-      exist=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Execution_Run/Replicate=17-BTFJ) &&
+      exist=$(export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Execution_Run/Replicate=17-BTFJ) &&
      cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
      cookie=${cookie:11:-1} &&
      if [ "${exist}" == "[]" ]; then
-        rid=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' python3 ./workflow/scripts/upload_execution_run.py -r 17-BTFJ -w 17-BV2Y -g 17-BV90 -i 17-BTFT -s Success -d 'This is a test execution run' -o staging.gudmap.org -c ${cookie} -u F) &&
+        rid=$(export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' python3 ./workflow/scripts/upload_execution_run.py -r 17-BTFJ -w 17-BV2Y -g 17-BV90 -i 17-BTFT -s Success -d 'This is a test execution run' -o staging.gudmap.org -c ${cookie} -u F) &&
        echo ${rid} test execution run created
      else
        rid=$(echo ${exist} | grep -o '\"RID\":\".*\",\"RCT') &&
        rid=${rid:7:-6} &&
-        rid=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' python3 ./workflow/scripts/upload_execution_run.py -r 17-BTFJ -w 17-BV2Y -g 17-BV90 -i 17-BTFT -s Success -d 'This is a test execution run' -o staging.gudmap.org -c ${cookie} -u ${rid}) &&
+        rid=$(export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' python3 ./workflow/scripts/upload_execution_run.py -r 17-BTFJ -w 17-BV2Y -g 17-BV90 -i 17-BTFT -s Success -d 'This is a test execution run' -o staging.gudmap.org -c ${cookie} -u ${rid}) &&
        echo ${rid} test execution run already exists
      fi

@@ -407,17 +406,17 @@ uploadQC:
  script:
    - ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json
    - >
-      exist=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:mRNA_QC/Replicate=17-BTFJ) &&
+      exist=$(export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:mRNA_QC/Replicate=17-BTFJ) &&
      cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
      cookie=${cookie:11:-1} &&
      if [ "${exist}" != "[]" ]; then
        rids=$(echo ${exist} | grep -o '\"RID\":\".\{7\}' | sed 's/^.\{7\}//') &&
        for rid in ${rids}; do
-          singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' python3 ./workflow/scripts/delete_entry.py -r ${rid} -t mRNA_QC -o staging.gudmap.org -c ${cookie}
+          export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' python3 ./workflow/scripts/delete_entry.py -r ${rid} -t mRNA_QC -o staging.gudmap.org -c ${cookie}
        done
        echo all old mRNA QC RIDs deleted
      fi
-        rid=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' python3 ./workflow/scripts/upload_qc.py -r 17-BTFJ -e 17-BVDJ -p "Single End" -s forward -l 35 -w 5 -f 1 -t 1 -n "This is a test mRNA QC" -o staging.gudmap.org -c ${cookie} -u F)
+        rid=$(export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' python3 ./workflow/scripts/upload_qc.py -r 17-BTFJ -e 17-BVDJ -p "Single End" -s forward -l 35 -w 5 -f 1 -t 1 -n "This is a test mRNA QC" -o staging.gudmap.org -c ${cookie} -u F)
        echo ${rid} test mRNA QC created

 uploadProcessedFile:
@@ -434,20 +433,20 @@ uploadProcessedFile:
    - mkdir -p ./deriva/Seq/pipeline/17-BTFE/17-BVDJ/
    - mv 17-BTFJ_test.csv ./deriva/Seq/pipeline/17-BTFE/17-BVDJ/17-BTFJ_test.csv
    - >
-      exist=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Processed_File/Replicate=17-BTFJ) &&
+      exist=$(export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Processed_File/Replicate=17-BTFJ) &&
      cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
      cookie=${cookie:11:-1} &&
      if [ "${exist}" != "[]" ]; then
        rids=$(echo ${exist} | grep -o '\"RID\":\".\{7\}' | sed 's/^.\{7\}//') &&
        for rid in ${rids}; do
-          singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' python3 ./workflow/scripts/delete_entry.py -r ${rid} -t Processed_File -o staging.gudmap.org -c ${cookie}
+          export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' python3 ./workflow/scripts/delete_entry.py -r ${rid} -t Processed_File -o staging.gudmap.org -c ${cookie}
        done
        echo all old processed file RIDs deleted
      fi
-      singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-upload-cli --catalog 2 --token ${cookie:9} staging.gudmap.org ./deriva
+      export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-upload-cli --catalog 2 --token ${cookie:9} staging.gudmap.org ./deriva
      echo test processed file uploaded
    - mkdir test
-    - singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' bdbag test --archiver zip
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' bdbag test --archiver zip
    - echo test output bag created
    - pytest -m outputBag

@@ -465,12 +464,12 @@ uploadOutputBag:
    - >
      md5=$(md5sum ./test.txt | awk '{ print $1 }') &&
      size=$(wc -c < ./test.txt) &&
-      exist=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Output_Bag/File_MD5=${md5}) &&
+      exist=$(export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Output_Bag/File_MD5=${md5}) &&
      if [ "${exist}" == "[]" ]; then
        cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
        cookie=${cookie:11:-1} &&
-        loc=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-hatrac-cli --host staging.gudmap.org put ./test.txt /hatrac/resources/rnaseq/pipeline/output_bag/TEST/test.txt --parents) &&
-        rid=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' python3 ./workflow/scripts/upload_output_bag.py -e 17-BVDJ -f test.txt -l ${loc} -s ${md5} -b ${size} -n 'This is a test output bag' -o staging.gudmap.org -c ${cookie}) &&
+        loc=$(export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-hatrac-cli --host staging.gudmap.org put ./test.txt /hatrac/resources/rnaseq/pipeline/output_bag/TEST/test.txt --parents) &&
+        rid=$(export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' python3 ./workflow/scripts/upload_output_bag.py -e 17-BVDJ -f test.txt -l ${loc} -s ${md5} -b ${size} -n 'This is a test output bag' -o staging.gudmap.org -c ${cookie}) &&
        echo ${rid} test output bag created
      else
        rid=$(echo ${exist} | grep -o '\"RID\":\".*\",\"RCT') &&
@@ -488,7 +487,7 @@ generateVersions:
    - merge_requests
    - schedules
  script:
-    - singularity run 'docker://gudmaprbk/multiqc1.9:1.0.0' multiqc --version > version_multiqc.txt
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/multiqc1.9:1.0.0' multiqc --version > version_multiqc.txt
    - python ./workflow/scripts/generate_versions.py -o software_versions
    - python ./workflow/scripts/generate_references.py -r ./docs/references.md -o software_references
  artifacts:
@@ -546,7 +545,7 @@ human_dev:
    - loc=$(dirname ${refURL})
    - if [ "${loc}" = "/hatrac/*" ]; then echo "reference not present in hatrac"; exit 1; fi
    - filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)')
-    - test=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls ${loc}/)
+    - test=$(export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls ${loc}/)
    - test=$(echo ${test} | grep -o ${filename})
    - if [ "${test}" == "" ]; then echo "reference file not present"; exit 1; fi

@@ -572,7 +571,7 @@ mouse_dev:
    - loc=$(dirname ${refURL})
    - if [ "${loc}" = "/hatrac/*" ]; then echo "reference not present in hatrac"; exit 1; fi
    - filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)')
-    - test=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls ${loc}/)
+    - test=$(export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls ${loc}/)
    - test=$(echo ${test} | grep -o ${filename})
    - if [ "${test}" == "" ]; then echo "reference file not present"; exit 1; fi

@@ -598,7 +597,7 @@ human_staging:
    - loc=$(dirname ${refURL})
    - if [ "${loc}" = "/hatrac/*" ]; then echo "reference not present in hatrac"; exit 1; fi
    - filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)')
-    - test=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls ${loc}/)
+    - test=$(export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls ${loc}/)
    - test=$(echo ${test} | grep -o ${filename})
    - if [ "${test}" == "" ]; then echo "reference file not present"; exit 1; fi

@@ -625,7 +624,7 @@ mouse_staging:
    - loc=$(dirname ${refURL})
    - if [ "${loc}" = "/hatrac/*" ]; then echo "reference not present in hatrac"; exit 1; fi
    - filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)')
-    - test=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls ${loc}/)
+    - test=$(export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls ${loc}/)
    - test=$(echo ${test} | grep -o ${filename})
    - if [ "${test}" == "" ]; then echo "reference file not present"; exit 1; fi

@@ -651,7 +650,7 @@ human_prod:
    - loc=$(dirname ${refURL})
    - if [ "${loc}" = "/hatrac/*" ]; then echo "reference not present in hatrac"; exit 1; fi
    - filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)')
-    - test=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls ${loc}/)
+    - test=$(export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls ${loc}/)
    - test=$(echo ${test} | grep -o ${filename})
    - if [ "${test}" == "" ]; then echo "reference file not present"; exit 1; fi

@@ -678,7 +677,7 @@ mouse_prod:
    - loc=$(dirname ${refURL})
    - if [ "${loc}" = "/hatrac/*" ]; then echo "reference not present in hatrac"; exit 1; fi
    - filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)')
-    - test=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls ${loc}/)
+    - test=$(export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls ${loc}/)
    - test=$(echo ${test} | grep -o ${filename})
    - if [ "${test}" == "" ]; then echo "reference file not present"; exit 1; fi