Simplified container configuration

src/rsem/rsem_calculate_expression/config.vsh.yaml

@@ -2,7 +2,7 @@ name: "rsem_calculate_expression"
 namespace: "rsem"
 description: | 
   Calculate expression with RSEM.
-keywords: ["Transcriptome", "Index"]
+keywords: [Transcriptome, Index, RSEM]
 links:
   homepage: https://deweylab.github.io/RSEM/
   documentation: https://deweylab.github.io/RSEM/rsem-calculate-expression.html
@@ -42,27 +42,27 @@ argument_groups:
   - name: "--counts_gene"
     type: file
     description: Expression counts on gene level
-    example: $id.genes.results
+    example: genes.results
     direction: output
   - name: "--counts_transcripts"
     type: file
     description: Expression counts on transcript level
-    example: $id.isoforms.results
+    example: isoforms.results
     direction: output
   - name: "--stat"
     type: file
     description: RSEM statistics
-    example: $id.stat
+    example: stat
     direction: output
   - name: "--logs"
     type: file
     description: RSEM logs
-    example: $id.log
+    example: log
     direction: output
   - name: "--bam_star"
     type: file
     description: BAM file generated by STAR (optional)
-    example: $id.STAR.genome.bam
+    example: STAR.genome.bam
     direction: output
   - name: "--bam_genome"
     type: file
@@ -72,7 +72,7 @@ argument_groups:
   - name: "--bam_transcript"
     type: file
     description: Transcript BAM file (optional)
-    example: $id.transcript.bam
+    example: transcript.bam
     direction: output
 
 resources:
@@ -82,7 +82,8 @@ resources:
 test_resources:
   - type: bash_script
     path: test.sh
-  - path: test_data
+  - type: file
+    path: test_data
 
 engines:
   - type: docker
@@ -96,44 +97,25 @@ engines:
         - make 
         - wget 
         - zlib1g-dev 
-        - unzip 
-        - xxd 
-        - perl 
-        - r-base
-        - bowtie2
-        - python3-pip 
-        - git
+        - unzip
     - type: docker
       env: 
         - STAR_VERSION=2.7.11b
         - RSEM_VERSION=1.3.3
-        - TZ=Europe/Brussels
       run: |
-        ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone && \
-        cd /tmp && \
-        wget --no-check-certificate https://github.com/alexdobin/STAR/archive/refs/tags/${STAR_VERSION}.zip && \
-        unzip ${STAR_VERSION}.zip && \
-        cd STAR-${STAR_VERSION}/source && \
-        make STARstatic CXXFLAGS_SIMD=-std=c++11 && \
-        cp STAR /usr/local/bin && \
-        cd /tmp && \
-        wget --no-check-certificate https://github.com/deweylab/RSEM/archive/refs/tags/v${RSEM_VERSION}.zip && \
-        unzip v${RSEM_VERSION}.zip && \
-        cd RSEM-${RSEM_VERSION} && \
-        make && \
-        make install && \
-        rm -rf /tmp/STAR-${STAR_VERSION} /tmp/${STAR_VERSION}.zip && \
-        rm -rf /tmp/RSEM-${RSEM_VERSION} /tmp/v${RSEM_VERSION}.zip && \
-        cd && \
-        apt-get clean && \
-        echo 'export PATH=$PATH:/usr/local/bin' >> /etc/profile && \
-        echo 'export PATH=$PATH:/usr/local/bin' >> ~/.bashrc && \
-        /bin/bash -c "source /etc/profile && source ~/.bashrc && echo $PATH && which STAR"
-
-    - type: docker
-      run: |
-        echo "RSEM: `rsem-calculate-expression --version | sed -e 's/Current version: RSEM v//g'`" > /var/software_versions.txt && \
-        echo "STAR: `STAR --version | sed -e 's/STAR_//g'`" >> /var/software_versions.txt >> /var/software_versions.txt
+          apt-get update && \
+          apt-get clean && \
+          wget --no-check-certificate https://github.com/alexdobin/STAR/archive/refs/tags/2.7.11a.zip && \
+          unzip 2.7.11a.zip && \
+          cp STAR-2.7.11a/bin/Linux_x86_64_static/STAR /usr/local/bin  && \
+          cd && \
+          wget --no-check-certificate https://github.com/deweylab/RSEM/archive/refs/tags/v1.3.3.zip && \
+          unzip v1.3.3.zip && \
+          cd RSEM-1.3.3 && \
+          make && \
+          make install
+          echo "RSEM: `rsem-calculate-expression --version | sed -e 's/Current version: RSEM v//g'`" > /var/software_versions.txt && \
+          echo "STAR: `STAR --version | sed -e 's/STAR_//g'`" >> /var/software_versions.txt >> /var/software_versions.txt
 
 runners:
   - type: executable

src/rsem/rsem_calculate_expression/script.sh

@@ -22,7 +22,7 @@ fi
 
 IFS=";" read -ra input <<< $par_input
 
-INDEX=$(find -L "${meta_resources_dir}/${par_index}/" -name "*.grp" | sed 's/\.grp$//')
+INDEX=$(find -L $meta_resources_dir/$par_index -name "*.grp" | sed 's/\.grp$//')
 
 rsem-calculate-expression \
     $strandedness \

src/rsem/rsem_calculate_expression/test.sh

@@ -2,15 +2,17 @@
 
 echo ">>> Testing $meta_executable"
 
-gunzip "${meta_resources_dir}/test_data/rsem.tar.gz"
-tar -xf "${meta_resources_dir}/test_data/rsem.tar"
+test_dir="${meta_resources_dir}/test_data"
+
+gunzip "${test_dir}/rsem.tar.gz"
+tar -xf "${test_dir}/rsem.tar"
 
 echo ">>> Calculating expression"
 "$meta_executable" \
   --id WT_REP1 \
   --strandedness reverse \
   --paired true \
-  --input "${meta_resources_dir}/test_data/SRR6357070_1.fastq.gz;${meta_resources_dir}/test_data/SRR6357070_2.fastq.gz" \
+  --input "${test_dir}/SRR6357070_1.fastq.gz;${test_dir}/SRR6357070_2.fastq.gz" \
   --index rsem \
   --extra_args "--star --star-output-genome-bam --star-gzipped-read-file --estimate-rspd --seed 1" \
   --counts_gene WT_REP1.genes.results \